npm - @sjcrh/proteinpaint-client - Versions diffs - 2.76.0 → 2.76.1 - Mend

@sjcrh/proteinpaint-client 2.76.0 → 2.76.1

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package/dist/{block.legend-d3f61ef7.js → block.legend-d2b7f1cb.js} RENAMED Viewed

	@@ -1 +1 @@
1	- import{Z as t,B as e,ap as s,aP as o,aQ as a,aR as n,ar as r,at as i,as as l,ak as c,z as f,a9 as d,p,ac as u,b6 as m,b7 as h,aN as g,q as b,b8 as y,j as x,b9 as k,ba as v,a7 as w,aG as _,bb as j,a8 as M,af as A,aM as z,aL as N,r as P,aW as S,d as C,aF as F,I as R,ah as I,W as B,ag as q,ad as D,O as L,aJ as E,bc as U,bd as G,be as V,bf as O,ae as T,M as H}from"./app-b369b169.js";import{v as X,a as Y}from"./vcf-5cc55588.js";import{p as J}from"./partition-db811f6b.js";import{d as Q}from"./arc-3d6751aa.js";import{b as W}from"./axis-747c801e.js";import{s as Z}from"./legacy-d3-polyfill-bdb2d792.js";const K="__";function $(f){const{mlst:d,tk:p,block:u}=f;if(!d\|\|d.length==0)return;let m;if(f.pane){const e=t({x:f.x,y:f.y});e.header.html(tt(d));m=e.body}else{m=f.holder}if(!m){console.error("no holder provided for showing table");return}const h=new Map;for(const t of d){if(!h.has(t.dt)){h.set(t.dt,[])}h.get(t.dt).push(t)}delete p.__singlevariant_table;for(const[t,f]of h){const d=m.append("div").style("margin","10px");if(h.size>1){d.append("p").text(e[t]).style("color","#858585")}switch(t){case c:et(f,d,p,u);break;case l:case i:ct(f,d,p,u);break;case r:dt(f,d,p,u.genome);break;case n:case a:ut(f,d,p,u.genome);break;case o:pt(f,d,p,u.genome);break;case s:d.append("p").text("cnv not supported yet");break;default:d.append("p").text("unknown dt: "+t)}}Ft(d,m,p,u)}function tt(t){if(t.length==1){const e=t[0];const d=f[e.class];if(e.dt==c){return'<span style="font-weight:bold;color:'+d.color+'">'+(e.mname?e.mname:e.pos?e.chr+":"+(e.pos+1):"")+'</span> <span style="font-size:80%">'+d.label+"</span>"}if(e.dt==l\|\|e.dt==i){const t=[];for(let s=0;s<e.pairlst.length;s++){if(s==0)t.push(e.pairlst[s].a.name?e.pairlst[s].a.name:e.pairlst[s].a.chr);t.push(e.pairlst[s].b.name?e.pairlst[s].b.name:e.pairlst[s].b.chr)}return t.join(" - ")+'  <span style="font-size:80%">'+d.label+"</span>"}if(e.dt==n\|\|e.dt==a\|\|e.dt==r\|\|e.dt==o\|\|e.dt==s){return'<span style="font-size:80%">'+d.label+"</span>"}return"unknown dt "+e.dt}const d=new Set;for(const e of t){d.add(e.dt)}if(d.size==1){const s=[...d][0];return t.length+" "+e[s]}return t.length+" mutations"}function et(e,s,o,a){if(o.ds&&o.ds.id2vcf){if(e.length==1){const t=o.ds.id2vcf[e[0].vcfid];if(!t){s.append("p").text("No vcf config file (id: "+e[0].vcfid+")");return}at(e[0],t,s,o,a);return}for(const n of e){const e=o.ds.id2vcf[n.vcfid];if(!e){s.append("p").text("No vcf config file (id: "+n.vcfid+")");continue}const r=s.append("div").attr("class","sja_menuoption").on("click",(s=>{const r=t({x:s.clientX+100,y:Math.max(100,s.clientY-100)});at(n,e,r.body,o,a)}));if(n.mname){r.append("span").html(n.mname+'\t<span style="font-size:80%;color:#858585">'+f[n.class].label+"</span>")}else if(n.csq){r.append("span").html(n.csq[0]._mname+'\t<span style="font-size:80%;color:#858585">'+n.csq[0].Consequence+"</span>")}r.append("span").html("  "+n.chr+":"+(n.pos+1)+' <span style="font-size:70%">REF</span> '+n.ref+' <span style="font-size:70%">ALT</span> '+n.alt)}return}const n=a.genome.hasSNP;const r={chr:null,bprange:[],holder:null,says:null};const i={set:new Map,butholder:null};for(const t of e){if(n&&t.chr&&t.pos){r.chr=t.chr;let e=true;for(const s of r.bprange){if(s.start<=t.pos&&s.stop>=t.pos){e=false;break}}if(e){r.bprange.push({start:t.pos,stop:t.pos+1})}}}if(!o.snvindelattr){mt(o,e)}if(a.variantPageCall_snv){i.butholder=s.append("div").style("margin","10px")}if(e.length==1){const t=e[0];r.alleleLst=[t.ref,t.alt];if(a.variantPageCall_snv){if(t.chr!=undefined&&t.pos!=undefined&&t.ref!=undefined&&t.alt!=undefined){i.set.set(t.chr+K+t.pos+K+t.ref+K+t.alt,{mname:t.mname,class:t.class})}}const l=[];for(const e of o.snvindelattr){if(e.lst){const s=[];for(const o of e.lst){if(o.ismaf){const e=o.get(t);s.push({k:o.label,v:e?Number.isFinite(e.f)?'<span style="color:'+o.fill+'">'+(e.f100).toFixed(0)+"% ("+e.v1+"/"+e.v2+")</span>":"n/a":""})}else{s.push({k:o.label,v:o.get(t)})}}if(s.length){l.push({k:e.label,kvlst:s})}}else if(e.ismaf){const s=e.get(t);l.push({k:e.label,v:s?Number.isFinite(s.f)?'<span style="color:'+e.fill+'">'+(s.f100).toFixed(0)+"% ("+s.v1+"/"+s.v2+")</span>":"n/a":""})}else{let s=e.get(t);if(e.hover){const o=e.hover(t);if(o){s+=' <span style="color:#aaa;font-size:80%">'+o+"</span>"}}l.push({k:e.label,v:s})}}const c=d(s,l);if(n){const t=c.append("tr");t.append("td").attr("colspan",2).style("color","#9e9e9e").text("dbSNP");r.says=t.append("td").text("loading...")}const f=s.append("div").style("margin-top","10px");if(o.eplst){for(const t of o.eplst){lt(t,f,e)}}if(o.ds&&o.ds.snvindel_legend){f.append("button").text("Legend").on("click",(()=>{if(t.style("display")=="none"){p(t)}else{u(t)}}));const t=f.append("div").style("display","none").style("margin","10px").style("width","400px").html(o.ds.snvindel_legend)}}else{if(a.variantPageCall_snv){for(const t of e){if(t.chr!=undefined&&t.pos!=undefined&&t.ref!=undefined&&t.alt!=undefined){i.set.set(t.chr+K+t.pos+K+t.ref+K+t.alt,{mname:t.mname,class:t.class})}}}const t=s.append("table").style("border-spacing","3px").style("border-collapse","separate").style("margin","0px 7px 7px 0px").style("font-size","90%").style("color","black").style("background-color","white");st(e,t,o.snvindelattr,o);const l=s.append("div").style("margin","10px 5px");let c,f,d;l.append("button").text("Table columns").on("click",(function(){if(c.style("display")=="block"){this.style.color="black";u(c)}else{this.style.color="red";p(c)}}));if(n&&r.bprange.length){r.button=l.append("button").text("loading...").on("click",(function(){if(f.style("display")=="block"){this.style.color="black";u(f)}else{this.style.color="red";p(f)}}))}if(o.eplst){for(const t of o.eplst){lt(t,l,e)}}if(o.ds&&o.ds.snvindel_legend){l.append("button").text("Legend").on("click",(function(){if(d.style("display")=="block"){this.style.color="black";u(d)}else{this.style.color="red";p(d)}}))}c=s.append("div").style("margin","10px").style("display","none");for(const s of o.snvindelattr){const a=Math.random();const n=c.append("input").attr("type","checkbox").attr("id",a);if(!s.hide)n.attr("checked",true);n.on("change",(()=>{s.hide=!n.node().checked;st(e,t,o.snvindelattr,o)}));c.append("label").attr("for",a).text(s.label);c.append("br")}if(n){f=s.append("div").style("margin","10px").style("display","none");r.holder=f;r.says=f}if(o.ds&&o.ds.snvindel_legend){d=s.append("div").style("display","none").style("width","300px").html(o.ds.snvindel_legend)}}if(n&&r.bprange.length){m(r.chr,r.bprange,a.genome,r.alleleLst).then((t=>{if(!t\|\|t.length==0)throw{message:"no SNP"};r.says.text("");if(r.button){r.button.text(t.length+" SNP"+(t.length>1?"s":""))}for(const e of t){const t=r.says.append("div");h(e,t)}})).catch((t=>{r.says.text(t.message);if(r.button){r.button.attr("disabled",true)}if(t.stack)console.log(t.stack)}))}if(a.variantPageCall_snv){const t=[];for(const[e,s]of i.set){const o=e.split(K);t.push({chr:o[0],position:Number.parseInt(o[1])+1,refallele:o[2],altallele:o[3],class:s.class,aachange:s.mname})}if(t.length==1){const e=t[0];e.container=i.butholder;a.variantPageCall_snv(e)}else if(t.length>1){i.butholder.append("div").classed("sja_variantpagesnv",true).text("Variant Page").on("click",(e=>{const s=o.tktip.clear().showunder(e.target).d.append("table");for(const e of t){const t=s.append("tr");t.append("td").text(e.aachange);t.append("td").text(f[e.class].label).style("font-size",".7em").style("color",f[e.class].color);t.append("td").text(e.chr+":"+e.position+" "+e.refallele+">"+e.altallele).attr("font-size",".7em");e.container=t.append("td");a.variantPageCall_snv(e)}}))}}}function st(t,e,s,o,a){e.selectAll("").remove();let n=null;for(const t of s){if(t.lst){for(const e of t.lst){if(e.sort)n=e}}else if(t.sort)n=t}if(n){t.sort(((t,e)=>{const s=n.get(t);const o=n.get(e);if(n.ismaf){if(s==undefined){if(o==undefined)return 0;return 1}else{if(o==undefined)return-1;return n.descend?o.f-s.f:s.f-o.f}}if(s==undefined\|\|s===""){if(o==undefined\|\|o==="")return 0;return 1}if(o==undefined\|\|o==="")return-1;if(typeof s=="string"){if(s<o)return n.descend?1:-1;if(s>o)return n.descend?-1:1}if(typeof s=="number")return n.descend?o-s:s-o;return 0}))}const r=e.append("tr");const i=e.append("tr");r.append("td").attr("rowspan",2);for(const n of s){if(n.hide)continue;if(n.lst){r.append("td").attr("colspan",n.lst.length).style("color","#aaa").style("border-bottom","solid 1px #ccc").style("text-align","center").html(n.label);for(const r of n.lst){i.append("td").attr("class","sja_clbtext").html(r.label+(r.sort?r.descend?" ▼":" ▲":"")).on("click",(()=>{if(r.sort){r.descend=!r.descend}for(const t of s){if(t.lst){for(const e of t.lst)e.sort=false}else{t.sort=false}}r.sort=true;st(t,e,s,o,a)}))}}else{r.append("td").attr("rowspan",2).attr("class","sja_clbtext").html(n.label+(n.sort?n.descend?" ▼":" ▲":"")).on("click",(()=>{if(n.sort){n.descend=!n.descend}for(const t of s){if(t.lst){for(const e of t.lst)e.sort=false}else{t.sort=false}}n.sort=true;st(t,e,s,o,a)}))}}const l=t.length>1e3?900:t.length;for(let n=0;n<l;n++){const r=t[n];const i=e.append("tr").attr("class","sja_tr");if(a){i.on("click",(()=>a(r)))}if(o.eplst){i.on("mouseover",((t,e)=>{for(const t of o.eplst)t.may_hl([r],true)})).on("mouseout",((t,e)=>{for(const t of o.eplst)t.may_hl([r],false)}))}i.append("td").style("font-size",".8em").text(n+1);for(const t of s){if(t.hide)continue;if(t.lst){for(const e of t.lst){const t=i.append("td");if(e.ismaf){const s=e.get(r);if(s&&typeof s=="object"){if(s.v2==0){t.text("0/0");t.attr("aria-label","No coverage")}else{g(t,s,e)}}}else{t.html(e.get(r))}}}else{const e=i.append("td");if(t.hover){const s=t.hover(r);if(s!=undefined){e.attr("aria-label",s)}}if(t.tablecellwidth){e.style("width",t.tablecellwidth).style("word-break","break-all")}if(t.ismaf){const s=t.get(r);if(s){if(s.v2==0){e.text("0/0");e.attr("aria-label","No coverage")}else{g(e,s,t)}}}else{e.html(t.get(r))}}}}}function ot(t){return'<span style="font-size:70%;color:#858585">'+t+"</span>"}function at(t,e,s,o,a){if(!e){s.append("p").text("vcfobj config object missing");return}const n=s.append("div").style("margin-top","10px");n.append("span").text(t.type).style("padding-right","10px");n.append("span").text(t.chr+":"+(t.pos+1)).style("padding-right","10px");if(t.dt==c){n.append("span").style("padding-right","10px").html(ot("REF")+" "+t.ref+" "+ot("ALT")+" "+t.alt);if(a.variantPageCall_snv){const e={chr:t.chr,position:t.pos+1,refallele:t.ref,altallele:t.alt,container:n.append("span").style("padding-left","20px")};a.variantPageCall_snv(e)}if(o.button4variant){zt(n,t,o.button4variant)}if(o.url4variant){At(n,t,o.url4variant)}}if(e.info&&e.info.CSQ&&e.info.CSQ.csqheader&&t.csq){vt(t.csq,n,o,e.info.CSQ.csqheader)}if(e.info&&e.info.ANN&&e.info.ANN.annheader&&t.ann){wt(t.ann,n,o,e.info.ANN.annheader)}if(o.variant2img){_t(t,n,s.append("div"),o)}const r=s.append("div");if(Pt(t,o,r)){r.style("margin-top","10px")}else if(t.sampledata){const e=r.append("div");Promise.resolve().then((()=>{if(t.sampledata.length==0&&o.ds.vcfcohorttrack){e.text("Loading ...");return Mt(t,o,a).then((e=>{if(!e){return}t.sampledata=e.sampledata;return}))}return})).then((()=>{e.remove();if(t.sampledata.length==0){return}if(t.sampledata.length==1){St(t,o,r);return}if(Nt(t,o,r)){r.style("margin-top","10px")}else if(jt(t,o,r)){r.style("margin-top","10px")}else if(Pt(t,o,r)){r.style("margin-top","10px")}else{kt(t,n,o)}})).catch((t=>{e.text(t)}))}if(e.infopipejoin){const o=[];if(t.altinfo){for(const s of e.infopipejoin){const e=t.altinfo[s.key];if(e){if(Array.isArray(e)){o.push(e)}else{o.push(e.split(/[,\|]/))}}else{o.push([])}}}if(o.length){const t=s.append("div");for(let s=0;s<o[0].length;s++){const a=[];for(let t=0;t<e.infopipejoin.length;t++){const n=e.infopipejoin[t];a.push({k:n.label,v:n.values?n.values[o[t][s]]:o[t][s]})}d(t,a).style("display","inline-block").style("border","solid 1px black").style("margin","20px")}}}nt(t,s,o);rt(t,s,o);const i={};const l={};if(o.vcfinfofilter){for(const t of o.vcfinfofilter.lst){if(t.categories){if(t.altalleleinfo){i[t.altalleleinfo.key]=t.categories}else if(t.locusinfo){l[t.locusinfo.key]=t.categories}}}}{const o=[];for(const s in t.altinfo){const a=Array.isArray(t.altinfo[s])?t.altinfo[s]:[t.altinfo[s]];let n;if(i[s]){n=a.map((t=>{const e=i[s][t];if(e){return'<span style="padding:1px 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i=n[0].split(a.col_separator);for(let t=0;t<a.fields.length;t++){if(a.fields[t].hide)continue;r.push({k:a.fields[t].name,v:it(a,i,t)})}d(e,r)}}function rt(t,e,s){if(!s.info2table)return;for(const o in s.info2table){const a=s.info2table[o];const n=t.info[o];if(!n)continue;if(a.separate_tables){const t=JSON.parse(JSON.stringify(a.separate_tables));t.forEach((t=>t.rows=[]));for(const e of n){const s=e.split(a.col_separator);const o=new Map;for(let t=0;t<a.fields.length;t++){o.set(a.fields[t].name,s[t])}for(const e of t){if(e.groupers.reduce(((t,e)=>o.get(e.field)==e.value?t:false),true)){e.rows.push(o)}}}for(const s of t){if(s.rows.length==0)continue;e.append("h3").html(s.headhtml);const t=e.append("table").style("border-spacing","2px").style("border-collapse","separate").style("font-size","90%");const o=t.append("tr");for(const t of a.fields){if(t.hide)continue;o.append("td").text(t.name)}for(const e of s.rows){const s=t.append("tr").attr("class","sja_tr");const o=a.fields.map((t=>e.get(t.name)));for(let t=0;t<a.fields.length;t++){if(a.fields[t].hide)continue;const e=s.append("td");e.html(it(a,o,t))}}}continue}const r=e.append("table").style("border-spacing","2px").style("border-collapse","separate").style("font-size","90%");const i=r.append("tr");for(const t of a.fields){if(t.hide)continue;i.append("td").text(t.name)}for(const t of n){const e=r.append("tr").attr("class","sja_tr");const s=t.split(a.col_separator);for(let t=0;t<a.fields.length;t++){if(a.fields[t].hide)continue;const o=e.append("td");o.html(it(a,s,t))}}}}function it(t,e,s){const o=t.fields[s];if(o.hide)return;let a=e[s];if(a==undefined)return;if(o.eval){a=(0,eval)('"'+a+'"')}if(o.isurl)return"<a href="+a+" target=_blank>"+a+"</a>";if(o.appendUrl){if(o.separator){return a.split(o.separator).map((t=>"<a href="+o.appendUrl+t+" target=_blank>"+t+"</a>")).join(", ")}return"<a href="+o.appendUrl+a+" target=_blank>"+a+"</a>"}if(o.insert2url){return"<a 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f,d,p=true;if(c+o>t.aa.x+t.xoff){p=false;d=t.radius+t.rimwidth;f=d+o}else{d=-t.radius-t.rimwidth-o;f=d-c}e.pica.g.append("rect").attr("x",f-2).attr("y",-2-a-(l?n:n/2)).attr("width",4+c).attr("height",4+a2+n(l?2:1)).attr("fill","white");e.pica.g.append("line").attr("x1",d).attr("x2",d+o).attr("stroke","white").attr("stroke-width",3).attr("shape-rendering","crispEdges");e.pica.g.append("line").attr("x1",d).attr("x2",d+o).attr("stroke",r).attr("shape-rendering","crispEdges");e.pica.g.append("rect").attr("x",f).attr("y",-a-(l?n:n/2)).attr("width",c).attr("height",a2+n(l?2:1)).attr("fill","none").attr("stroke",r).attr("shape-rendering","crispEdges");e.pica.g.append("text").text(t._v).attr("text-anchor",p?"end":"start").attr("font-size",n).attr("font-family",I).attr("x",p?d-a:f+a).attr("y",l?-n/2:0).attr("fill",r).attr("dominant-baseline","central");if(l){e.pica.g.append("text").text(t.mname).attr("text-anchor",p?"end":"start").attr("font-size",n).attr("font-family",I).attr("x",p?d-a:f+a).attr("y",l?n/2:0).attr("fill",r).attr("dominant-baseline","central")}}function Yt(t,e){if(t.textlabel){C(t.textlabel).attr("font-size",t._labfontsize)}e.pica.g.selectAll("").remove()}async function Jt(t,e,s,o){if(t.dt==i\|\|t.dt==l){$({mlst:[t],pane:true,x:e.left-10,y:e.top-10,tk:s,block:o,svgraph:true});return}if(t.occurrence>1){if(await Ut(t.occurrence,[t],t.aa.x+t.xoff,s.numericmode.toplabelheight+s.numericmode.axisheight-t._y,s,o))return}$({mlst:[t],pane:true,x:e.left-10,y:e.top-10,tk:s,block:o})}function Qt(t){const e=[];for(const s of t.data){for(const t of s.mlst){e.push({m:t,w:2(t.radius+t.rimwidth),x:s.x0,y:t._y})}}e.sort(((t,e)=>e.y-t.y));for(let t=0;t<e.length;t++){const s=e[t];let o=false;for(let a=0;a<t;a++){const t=e[a];if(Math.abs(s.x-t.x)<(s.w+t.w)/2-2){o=true;break}}if(!o){s.m.labattop=true}}for(let t=e.length-1;t>=0;t--){const s=e[t];if(s.m.labattop)continue;let o=false;for(let a=e.length-1;a>t;a--){const t=e[a];if(t.m.labatbottom&&Math.abs(t.x-s.x)<(t.w+s.w)/2-2){o=true;break}}if(!o){s.m.labatbottom=true}}}function Wt(t,e){if(t.mlst.length==1){return"M0,0v"+e.stem1+"l"+-t.xoffset+","+e.stem2+"v"+e.stem3}return"M0,0"+"v"+e.stem1+"l"+-t.xoffset+","+e.stem2+"v"+e.stem3+"v-"+e.stem3+"l"+(t.stemw+t.xoffset-1)+",-"+e.stem2+"v-"+e.stem1}function Zt(t,e){t.numericmode;const s=100;let o=0;for(const e of t.data){let t=0;for(const s of e.mlst){t+=2(s.radius+s.rimwidth)}if(e.mlst.length==1){e.width=t}else{e.width=Math.min(s,t);const o=e.mlst[0];const a=e.mlst[e.mlst.length-1];e.fixedgew=o.radius+o.rimwidth+a.radius+a.rimwidth}o+=e.width}if(o<=e.width){let s=0;for(const e of t.data){e.x=s+e.mlst[0].radius+e.mlst[0].rimwidth;s+=e.width;if(e.mlst.length==1){e.stemw=0}else{e.stemw=e.width-e.fixedgew}}Kt(t.data,e.width);for(const e of t.data){e.xoffset=e.x-e.x0;if(e.mlst.length==1){e.mlst[0].xoff=0;e.stemw=0}else{e.stemw=e.width-e.fixedgew;const t=e.stemw/(e.mlst.length-1);for(let s=0;s<e.mlst.length;s++){e.mlst[s].xoff=ts}}}return true}else{for(const e of t.data){e.x=e.x0;e.xoffset=0;for(const t of e.mlst){t.xoff=0}}return false}}function Kt(t,e){for(let s=0;s<t.length;s++){if(t[s].x0<0)continue;if(t[s].x0>e)break;while(1){let o=0,a=0;for(let n=s;n<t.length;n++){const s=t[n];if(s.x0>e){return}o+=Math.abs(s.x-s.x0-s.stemw/2);s.x++;a+=Math.abs(s.x-s.x0-s.stemw/2)}if(t[s].x>t[s].x0-t[s].stemw/2){for(let e=s;e<t.length;e++){t[e].x--}break}const n=t[t.length-1];if(n.x+n.width/2>=e){return}if(a<=o);else{for(let o=s;o<t.length;o++){if(t[o].x0>e){break}t[o].x--}break}}}}const $t="Not annotated";const te=.3;const ee=1;const se=4;const oe=0;const ae=1;async function ne(t,e){try{if(!t)throw"no tk";if(!t.ds)throw"no ds";if(!e.gmmode\|\|e.gmmode==F.genomic){if(e.viewrangeabovelimit(t.viewrangeupperlimit)){t.mlst=[];t.viewrangeupperlimit_above=true;fe(t,e);return}}delete t.viewrangeupperlimit_above;if(t.isvcf){e.tkcloakon(t);Rt(e,t);return}if(e.ds2handle[t.ds.label]){t.__handlesays=e.ds2handle[t.ds.label].handlesays}if(t.ds.bulkdata\|\|t.ds.mlst){return await ie(t,e)}await le(t,e);re(t,e);t.ds.busy=false;e.tkcloakoff(t,{})}catch(s){if(s.stack)console.log(s.stack);t.ds.busy=false;e.tkcloakoff(t,{error:s.message\|\|s});e.setllabel(t);e.block_setheight()}}function re(t,e){if(!t.legacyDsFilter)return;if(!t.legacyDsFilter.key\|\|!t.legacyDsFilter.value)throw"legacyDsFilter is not {key,value}";const s=t.mlst.filter((e=>e[t.legacyDsFilter.key]==t.legacyDsFilter.value));const o={label:t.ds.label+" - "+t.legacyDsFilter.value,bulkdata:{},parentname:t.ds.label,iscustom:true,sampleselectable:t.ds.sampleselectable};o.bulkdata[e.usegm.name.toUpperCase()]=s;e.addchilddsnoload(o);const a=e.block_addtk_template({type:D.ds,ds:o});ne(a,e)}async function ie(t,e){if(e.usegm){if(t.__handlesays){t.__handlesays.style("background-color","#ddd").style("color","black")}let s=[];if(t.ds.bulkdata){const o=t.ds.bulkdata[e.usegm.name.toUpperCase()];if(o){s=[...o]}}if(t.ds.mlst){for(const o of t.ds.mlst){if(o.gene.toUpperCase()==e.usegm.name.toUpperCase()){s.push(o)}}}if(s.length){const o=[];for(const t of s){if(t.isoform&&t.isoform==e.usegm.isoform){o.push(t)}}if(o.length){ce([{lst:o}],e,t)}else{throw"No data from "+t.ds.label+" for "+e.usegm.isoform}}else{throw"No data from "+t.ds.label+" for "+e.usegm.name}if(t.ds.dbexpression&&(!t.eplst\|\|t.eplst.length==0)){const s={jwt:e.jwt,db:t.ds.dbexpression.dbfile,tablename:t.ds.dbexpression.tablename,keyname:t.ds.dbexpression.keyname,key:e.usegm.name};const o=await w("dbdata",{method:"POST",body:JSON.stringify(s)});if(o.error)throw o.error;if(!t.eplst)t.eplst=[];if(t.ds.dbexpression.tidy)t.ds.dbexpression.tidy(o.rows);const a={data:o.rows,expp:t.ds.dbexpression.config,block:e,genome:e.genome,genename:e.usegm.name,dsname:t.ds.label};const n=await import("./ep-d017ec2f.js");t.eplst.push(new n.default(a))}}else{const s=[];const f=new Map;for(const t of e.rglst){if(!f.has(t.chr)){f.set(t.chr,[])}f.get(t.chr).push(t)}const d=[];if(t.ds.bulkdata){for(const e in t.ds.bulkdata){d.push(...t.ds.bulkdata[e])}}if(t.ds.mlst){d.push(...t.ds.mlst)}for(const t of d){switch(t.dt){case c:case r:case o:case n:case a:if(!t.pos){break}if(!t.chr&&!f.has(t.chr)){break}for(const e of f.get(t.chr)){if(t.pos>=e.start&&t.pos<e.stop){s.push(t);break}}break;case l:case i:if(!t.pairlst){break}let e=false;for(const s of t.pairlst){if(s.a.chr&&f.has(s.a.chr)){const t=s.a.position\|\|s.a.pos;if(t){for(const o of f.get(s.a.chr)){if(t>=o.start&&t<o.stop){e=true;break}}}}if(s.b.chr&&f.has(s.b.chr)){const t=s.b.position\|\|s.b.pos;if(t){for(const o of f.get(s.b.chr)){if(t>=o.start&&t<o.stop){e=true;break}}}}}if(e){s.push(t)}break}}if(s.length){ce([{lst:s}],e,t)}}}async function le(t,e){if(t.__handlesays)t.__handlesays.text("Loading...");t.ds.busy=true;e.tkcloakon(t);const s={genome:e.genome.name,dsname:t.ds.label,range:e.tkarg_maygm(t)[0]};if(e.usegm){s.genename=e.usegm.name;s.isoform=e.usegm.isoform}if(t.eplst){s.noexpression=1}if(e.hidedatasetexpression){s.noexpression=1}const o=await w("dsdata",{method:"POST",body:JSON.stringify(s)});if(t.__handlesays){t.__handlesays.text(t.ds.label).style("background-color","#ddd").style("color","black")}if(o.error)throw o.error;ce(o.data,e,t)}function ce(t,e,s){if(s.dsuninitiated){for(let t=0;t<e.tklst.length;t++){if(e.tklst[t].tkid==s.tkid){e.tklst.splice(t,1);break}}delete s.dsuninitiated;let t=-1;for(let s=0;s<e.tklst.length;s++){const o=e.tklst[s];if(o.type==D.usegm&&!o.hidden){t=s;break}}let o=true;if(t==-1){o=true;e.tklst.push(s)}else{let a=false;for(let s=0;s<t;s++){const t=e.tklst[s];if(!t.hidden&&t.type==D.ds){a=true;break}}if(a){o=false;e.tklst.splice(t+1,0,s)}else{o=true;if(t==0){e.tklst.unshift(s)}else{e.tklst.splice(t-1,0,s)}}}if(s.aboveprotein==undefined){s.aboveprotein=o}s.eplst=[]}s.mlst=[];const o=[];for(const a of t){if(a.isgeneexpression){o.push(Me(a,s,e));continue}if(a.vcfid){It(a,s,e);continue}if(a.lst){Ae(a.lst,s,e);Ee(a,s);continue}e.error("unknown data/query type from "+s.ds.label);return}Promise.all(o).then((()=>{if(s.eplst.length>1){for(let t=1;t<s.eplst.length;t++){const e=s.eplst[t];e.pane.pane.style("left",Number.parseInt(s.eplst[0].pane.pane.style("left"))+50t+"px");e.pane.pane.style("top",Number.parseInt(s.eplst[0].pane.pane.style("top"))+50t+"px")}}}));fe(s,e)}function fe(t,e){e.tkcloakoff(t,{});de(t);if(t.vcfinfofilter&&t.vcfinfofilter.setidx4numeric!=undefined){if(!t.numericmode){t.numericmode={axisheight:t.axisheight}}}else{delete t.numericmode}const s=new Set;for(const t in L){if(L[t].hidden){s.add(t)}}Pe(t);if(t.numericmode){Ot(t,e,s)}else{pe(t,e,s)}e.setllabel(t);e.block_setheight();e.tkchangeaffectlegend(t);Ne(t,e);Re(t,e);{const s=Ie(t,e);if(s)console.log("showlegend_sampleattribute: "+s)}}function de(t){if(t.vcfinfofilter&&t.vcfinfofilter.setidx4occurrence!=undefined){const e=t.vcfinfofilter.lst[t.vcfinfofilter.setidx4occurrence];if(!e)throw"mcset not found by setidx4occurrence";for(const s of t.mlst){const[t,o]=Se(e,s);if(t\|\|o==undefined){s.occurrence=1}else{s.occurrence=o[0]}}}else{for(const e of t.mlst){e.occurrence=1}}}function pe(t,e,s){t.leftaxis.selectAll("").remove();if(e.usegm&&e.gmmode!=F.genomic&&e.pannedpx!=undefined&&t.skewer){De(t,e);t.skewer.attr("transform",(t=>"translate("+t.x+","+t.y+")"));ye(t,e)}else{t.glider.selectAll("").remove();qe(t,e,s);const o=new Map;for(const e of t.mlst){if(e.__x==undefined){continue}if(!o.has(e.__x)){o.set(e.__x,[])}o.get(e.__x).push(e)}const a=[];if(e.exonsf>=se){for(const[t,e]of o){a.push({chr:e[0].chr,pos:e[0].pos,mlst:e,x:t,groups:ue(e)})}}else{if(e.usegm&&e.usegm.coding&&e.gmmode!=F.genomic){const t=new Map;for(const[s,a]of o){if(a[0].chr!=e.usegm.chr){continue}let n=undefined;for(const t of a){if(Number.isFinite(t.aapos))n=t.aapos}if(n==undefined){n=_(a[0].pos,e.usegm).aapos}if(n==undefined){console.error("data item cannot map to aaposition");console.log(a[0]);continue}o.delete(s);if(!t.has(n)){t.set(n,[])}let r=true;for(const s of t.get(n)){if(Math.abs(s[0].__x-a[0].__x)<=e.exonsf3){for(const t of a){s.push(t)}r=false;break}}if(r){t.get(n).push(a)}}e.usegm.utr5?e.usegm.utr5.reduce(((t,e)=>t+e[1]-e[0]),0):0;for(const e of t.values()){for(const t of e){let e=null;for(const s of t){if(Number.isFinite(s.rnapos))e=s}if(e==null){console.log("trying to map mlst to codon, but no rnapos found");for(const e of t){console.log(e)}continue}a.push({chr:t[0].chr,pos:e.pos,mlst:t,x:t[0].__x,groups:ue(t)})}}}const t=[];const s=2;for(const[e,a]of o){const o=Math.floor(e/s);if(!t[o]){t[o]=[]}t[o]=[...t[o],...a]}for(const e of t){if(!e)continue;const t=e.reduce(((t,e)=>t+e.__x),0);a.push({isbin:true,chr:e[0].chr,pos:e[0].pos,mlst:e,x:t/e.length,groups:ue(e)})}}a.sort(((t,e)=>t.x-e.x));if(t.data&&e.pannedpx!=undefined&&(!e.usegm\|\|e.gmmode==F.genomic)){const e={};for(const s of t.data){e[s.chr+"."+s.pos]={mode:s.showmode,xoffset:s.xoffset,slabelrotate:s.slabelrotate}}for(const t of a){const s=t.chr+"."+t.pos;if(e[s]){t.showmode=e[s].mode;t.xoffset=e[s].xoffset;t.slabelrotate=e[s].slabelrotate}}}t.data=a;for(const e of t.data){e.occurrence=e.groups.reduce(((t,e)=>t+e.occurrence),0)}me(t,e);t.height_main=t.toppad+t.maxskewerheight+t.stem1+t.stem2+t.stem3+t.bottompad}if(!t.data\|\|t.data.length==0){Le(t,e);return}if(t.hlaachange\|\|t.hlvariants){const s=[];const o=[];if(t.hlaachange){for(const e of t.data){let a=false;for(const s of e.groups){if(t.hlaachange.has(s.mlst[0].mname)){a=true;t.hlaachange.delete(s.mlst[0].mname);break}}if(a){o.push(e)}else{s.push(e)}}if(t.hlaachange.size){if(!e.usegm){e.error("cannot add items from hlaachange: not in gene-mode")}else{ze(t,e)}}delete t.hlaachange}if(t.hlvariants){const e={};for(const s of t.hlvariants){e[s.chr+"."+s.pos+"."+s.ref+"."+s.alt]=1}for(const a of t.data){let t=false;for(const s of a.groups){if(t){break}for(const o of s.mlst){if(e[o.chr+"."+o.pos+"."+o.ref+"."+o.alt]){t=true;break}}}if(t){o.push(a)}else{s.push(a)}}}_e(s,t);xe(o,t,e)}else{ye(t,e)}}function ue(t,e){const s=new Map;for(const e of t){switch(e.dt){case c:if(!s.has(e.dt)){s.set(e.dt,new Map)}if(!s.get(e.dt).has(e.class)){s.get(e.dt).set(e.class,new Map)}const t=e.mname\|\|"";if(!s.get(e.dt).get(e.class).has(t)){s.get(e.dt).get(e.class).set(t,[])}s.get(e.dt).get(e.class).get(t).push(e);break;case l:case i:if(!s.has(e.dt)){s.set(e.dt,new Map)}if(!s.get(e.dt).has(e.class)){s.get(e.dt).set(e.class,{use5:new Map,use3:new Map})}if(e.useNterm){if(!s.get(e.dt).get(e.class).use5.has(e.mname)){s.get(e.dt).get(e.class).use5.set(e.mname,[])}s.get(e.dt).get(e.class).use5.get(e.mname).push(e)}else{if(!s.get(e.dt).get(e.class).use3.has(e.mname)){s.get(e.dt).get(e.class).use3.set(e.mname,[])}s.get(e.dt).get(e.class).use3.get(e.mname).push(e)}break;case r:case o:case n:case a:if(!s.has(e.dt)){s.set(e.dt,[])}s.get(e.dt).push(e);break;default:console.log("unknown datatype: "+e.dt);console.log(e);return}}const f=[];for(const[t,e]of s){switch(t){case c:for(const s of e.values()){for(const e of s.values()){f.push({dt:t,mlst:e})}}break;case l:case i:for(const s of e.values()){for(const e of s.use5.values()){f.push({dt:t,useNterm:true,mlst:e})}for(const e of s.use3.values()){f.push({dt:t,useNterm:false,mlst:e})}}break;case r:case o:case n:case a:f.push({dt:t,mlst:e})}}for(const t of f){let e=0,s=0;for(const o of t.mlst){if(o.isrim1)e++;else if(o.isrim2)s++}t.rim1count=e;t.rim2count=s;t.occurrence=t.mlst.reduce(((t,e)=>t+e.occurrence),0)}f.sort(((t,e)=>e.occurrence-t.occurrence));return f}function me(t,e){delete t.skewer2;const s=e=>{if(t.vcfinfofilter&&t.vcfinfofilter.setidx4mclass!=undefined){const s=t.vcfinfofilter.lst[t.vcfinfofilter.setidx4mclass];const[o,a]=Se(s,e);if(o\|\|a==undefined)return"black";for(const t of a){if(s.categories[t]){return s.categories[t].color}else{return"black"}}}if(f[e.class]){return f[e.class].color}return"black"};const d=[];for(const s of t.data){s.x0=s.x;if(s.xoffset!=undefined){s.x=s.x0+s.xoffset}for(const t of s.groups){t.aa=s;let a=null;if(t.dt==r){a=t.mlst[0].rnaduplength;for(const e of t.mlst){a=Math.max(a,e.rnaduplength)}}else if(t.dt==o){a=t.mlst[0].rnadellength;for(const e of t.mlst){a=Math.max(a,e.rnadellength)}}else{continue}if(!Number.isFinite(a)\|\|a<0){console.log("no rnaspan for stack bar from itd/del");console.log(t.mlst);continue}let n=null;if(e.usegm){const 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_=Q().innerRadius((t=>t.radius)).outerRadius((t=>t.radius+t.rimwidth)).startAngle(0).endAngle((t=>{t.rim1_startangle=Math.PI2t.rim1count/t.occurrence;return t.rim1_startangle}));x.append("path").attr("d",_).attr("fill",(t=>s(t.mlst[0]))).attr("class","sja_aa_discrim").attr("fill-opacity",0);const j=Q().innerRadius((t=>t.radius+.5)).outerRadius((t=>t.radius+.5+t.rimwidth)).startAngle((t=>t.rim1_startangle)).endAngle((t=>t.rim1_startangle+Math.PI2t.rim2count/t.occurrence));x.filter((t=>t.rim2count>0)).append("path").attr("d",j).attr("stroke",(t=>s(t.mlst[0]))).attr("fill","none").attr("class","sja_aa_discrim").attr("stroke-opacity",0);{let e=0;let s=0;for(const o of t.data){if(o.x-o.maxradius-o.maxrimwidth<s){e++}s=Math.max(s,o.x+o.width-o.maxradius-o.maxrimwidth)}t.stem1=e==0?0:u;t.stem2=R().domain([0,1,t.data.length]).range([0,u,u3])(e)}const M=u.7;let A=0;for(const e of t.data){for(const t of e.groups){A=Math.max(A,t.occurrence)}}t.stem3=Math.max(p+2,M+uMath.min(5,A));t.skewer.append("circle").attr("class","sja_aa_skkick").attr("fill","white").attr("fill-opacity",0).attr("stroke","none").attr("r",(t=>t.maxradius+1)).attr("cy",(e=>(t.aboveprotein?-1:1)e.maxradius)).attr("transform",(t=>"scale("+(t.showmode==oe?1:0)+")")).on("mouseover",((e,o)=>{je(t,o.mlst,true);const a=t.aboveprotein;let n=0;let r=0;const i=5;const l=a?7:14;for(const e of o.groups){e.pica_fontsize=Math.max(11,e.radius);n+=e.pica_fontsize+1;t.pica.g.append("text").text(e.mlst[0].mname+(e.occurrence>1?" x"+e.occurrence:"")).attr("font-size",e.pica_fontsize).each((function(){r=Math.max(r,this.getBBox().width)})).remove()}r+=i2;const c=n+5;t.pica.g.append("rect").attr("y",a?-c:0).attr("width",r).attr("height",c).attr("fill","white").attr("fill-opacity",.8).attr("stroke","#ccc").attr("shape-rendering","crispEdges");n=0;const 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p=t.pica.g.append("g").attr("transform","translate("+(i+d/2)+","+(a?1:-1)+")");p.append("line").attr("y2",(a?1:-1)l).attr("stroke","#858585").attr("shape-rendering","crispEdges");p.append("line").attr("x1",-1).attr("x2",-1).attr("y2",(a?1:-1)l).attr("stroke","white").attr("shape-rendering","crispEdges");p.append("line").attr("x1",1).attr("x2",1).attr("y2",(a?1:-1)l).attr("stroke","white").attr("shape-rendering","crispEdges")})).on("mouseout",((e,s)=>{t.pica.g.selectAll("").remove();je(t,s.mlst,false)})).on("click",((s,o)=>{t.pica.g.selectAll("").remove();xe([o],t,e)}));let z=0;for(const e of t.data){z=Math.max(z,e.occurrence)}const N=R().domain([1,z]).range([M,t.stem3-y]);t.skewer.attr("transform",(e=>{e.foldyoffset=N(e.occurrence);e.y=ge(e,t);return"translate("+e.x+","+e.y+")"}));if(d.length>0){t.skewer.filter((t=>t.hasstackbar)).selectAll().data((t=>{const e=[];for(const s of t.groups){if(s.stackbar){e.push(s.stackbar)}}return e})).enter().append("g").attr("class","sja_aa_stackbar_g").attr("transform",(e=>"translate(0,"+(t.aboveprotein?1:-1)(t.stem1-e.y)+")")).append("rect").attr("y",(e=>t.aboveprotein?-e.height:0)).attr("class","sja_aa_stackbar_rect").attr("width",0).attr("shape-rendering","crispEdges").attr("fill-opacity",.5).attr("stroke","none").attr("stroke-width",1).attr("height",(t=>t.height)).attr("fill",(t=>s(t.grp.mlst[0]))).on("mouseover",((e,a)=>{const n=s(a.grp.mlst[0]);C(e.target).attr("stroke",n);const i=t.pica;let l="wrong label";let c="wrong label, ";switch(a.grp.mlst[0].dt){case r:l=f[a.grp.mlst[0].class].desc;c=Math.ceil(a.grp.mlst[0].rnaduplength/3)+" aa, ";break;case o:l=f[a.grp.mlst[0].class].label;c=Math.ceil(a.grp.mlst[0].rnadellength/3)+" aa, ";break}if(a.grp.occurrence==1){const t=a.grp.mlst[0];if(t.sample){c+=t.sample}else if(t.patient){c+=t.patient}else{c+="1 sample"}}else{c+=a.grp.occurrence+" samples"}const d=14,p=10,u=2,m=4;let 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P=t.skewer.filter((t=>t.groups.length>1));P.append("rect").attr("class","sja_aa_ssk_bg").attr("shape-rendering","crispEdges").attr("fill-opacity",0).attr("height",t.stem1).attr("fill",(t=>s(t.groups[0].mlst[0]))).attr("width",(t=>{t.ssk_width=Math.max(t.occurrence.toString().length8+6,2(t.maxradius+t.maxrimwidth));return t.ssk_width})).attr("x",(t=>-t.ssk_width/2));P.append("text").attr("class","sja_aa_ssk_text").attr("fill","white").attr("fill-opacity",0).attr("font-weight","bold").attr("text-anchor","middle").attr("dominant-baseline","central").text((t=>t.occurrence)).each((e=>{e.ssk_fontsize=Math.min(t.stem1,e.ssk_width/(e.occurrence.toString().lengthS))})).attr("font-size",(t=>t.ssk_fontsize));P.append("rect").attr("class","sja_aa_ssk_kick").attr("fill","white").attr("fill-opacity",0).attr("stroke","none").attr("height",t.stem1).attr("x",(t=>-t.ssk_width/2)).attr("width",(t=>t.ssk_width)).on("mouseover",((e,s)=>{const o=C(e.target.parentNode);o.selectAll(".sja_aa_disckick").transition().attr("stroke-opacity",1);o.select(".sja_aa_ssk_bg").transition().attr("fill-opacity",1).attr("stroke-opacity",1);o.select(".sja_aa_ssk_text").transition().attr("fill-opacity",1);je(t,s.mlst,true)})).on("mouseout",(function(e,s){const o=C(e.target.parentNode);o.selectAll(".sja_aa_disckick").transition().attr("stroke-opacity",0);o.select(".sja_aa_ssk_bg").transition().attr("fill-opacity",0).attr("stroke-opacity",0);o.select(".sja_aa_ssk_text").transition().attr("fill-opacity",0);je(t,s.mlst,false)})).on("click",(async(s,o)=>{const a=s.target.getBoundingClientRect();if(o.occurrence>1){if(await Ut(o.occurrence,o.mlst,o.x,o.y+(t.aboveprotein?1:-1)t.stem1/2,t,e))return}$({mlst:o.mlst,pane:true,x:a.left-10,y:a.top-10,tk:t,block:e})}))}function he(t){t.aboveprotein=!t.aboveprotein;if(t.numericmode){return}const e=t.aboveprotein;const s=1e3;const o=t.skewer.filter((t=>t.hasstackbar));o.selectAll(".sja_aa_stackbar_g").transition().duration(s).attr("transform",(s=>{const o=s.grp.aa;return"translate("+(o.showmode==oe?0:o.x0-o.x)+","+(e?1:-1)(o.showmode==oe?t.stem1-s.y:t.stem1+t.stem2+t.stem3-s.y)+")"}));o.filter((t=>t.showmode==ae)).selectAll(".sja_aa_stackbar_rect").transition().duration(s).attr("y",(t=>e?-t.height:0));t.skewer.transition().duration(s).attr("transform",(e=>{e.y=ge(e,t);return"translate("+e.x+","+e.y+")"}));t.skewer.selectAll(".sja_aa_stem").transition().duration(s).attr("d",(e=>be(e,t)));t.skewer.selectAll(".sja_aa_discg").transition().duration(s).attr("transform",(t=>{t.y=(e?-1:1)(t.aa.showmode==oe?t.aa.maxradius:t.yoffset);return"translate(0,"+t.y+")"}));t.skewer.selectAll(".sja_aa_ssk_kick").attr("y",e?0:-t.stem1);t.skewer.selectAll(".sja_aa_ssk_bg").attr("y",e?0:-t.stem1);t.skewer.selectAll(".sja_aa_ssk_text").attr("y",(e?1:-1)t.stem1/2);t.skewer.selectAll(".sja_aa_skkick").attr("cy",(t=>(e?-1:1)t.maxradius));t.skewer.filter((t=>t.showmode==ae&&t.groups.length==1)).selectAll(".sja_aa_disclabel").transition().duration(s).attr("transform",(t=>"scale(1) 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t=e.skewer.filter((t=>r.has(t.x0)));t.transition().duration(o).attr("transform",(t=>"translate("+t.x+","+t.y+")"));t.selectAll(".sja_aa_discg").transition().duration(o).attr("transform",(t=>{t.y=t.yoffset(a?-1:1);return"translate(0,"+t.y+")"}));setTimeout((function(){t.selectAll(".sja_aa_disckick").attr("transform","scale(1)")}),o);t.selectAll(".sja_aa_discnum").transition().duration(o).attr("fill-opacity",1).attr("stroke-opacity",1);t.filter((t=>t.groups.length>1)).selectAll(".sja_aa_disclabel").transition().duration(o).attr("fill-opacity",1).attr("transform","scale(1)");t.selectAll(".sja_aa_discrim").transition().duration(o).attr("fill-opacity",1).attr("stroke-opacity",1);t.selectAll(".sja_aa_ssk_kick").attr("transform","scale(1)").attr("y",a?0:-e.stem1);t.selectAll(".sja_aa_ssk_bg").attr("transform","scale(1)").attr("y",a?0:-e.stem1);t.selectAll(".sja_aa_ssk_text").attr("transform","scale(1)").attr("y",(a?1:-1)e.stem1/2);t.selectAll(".sja_aa_skkick").attr("transform","scale(0)");t.filter((t=>t.hasstackbar)).selectAll(".sja_aa_stackbar_g").attr("transform",(t=>"translate(0,"+(a?1:-1)(e.stem1+e.stem2+e.stem3-t.y)+")"));let n=0;t.selectAll(".sja_aa_stem").transition().duration(o).attr("d",(t=>be(t,e))).each((()=>++n)).on("end",(()=>{if(! --n){ke(e,s)}}))}else{ke(e,s)}}function ke(t,e){const s=1e3;const o=t.aboveprotein;const a=[];const n=new Set;const r=0;const i=e.width;for(const e of t.data){if(e.x0<r\|\|e.x0>i)continue;if(e.showmode==ae){e.x=e.x0;a.push(e);n.add(e.x0)}}if(a.length==0){return}ve(a,t,e);for(const t of a){t.xoffset=t.x-t.x0}for(let e=0;e<a.length;e++){const s=a[e];if(s.groups.length>1)continue;const o=s.groups[0];if(t.slabel_forcerotate){s.slabelrotate=true}else{const t=a[e+1];const n=t?t.x-t.maxradius-t.maxrimwidth:i;s.slabelrotate=n-s.x-o.radius-o.rimwidth-1<s.slabelwidth}s.width=(o.radius+o.rimwidth)2+(s.slabelrotate?0:2+s.slabelwidth)}const l=t.skewer.filter((t=>n.has(t.x0)));l.transition().duration(s).attr("transform",(t=>"translate("+t.x+","+t.y+")"));l.selectAll(".sja_aa_stem").transition().duration(s).attr("d",(e=>be(e,t)));l.filter((t=>t.groups.length==1)).selectAll(".sja_aa_disclabel").transition().duration(s).attr("fill-opacity",1).attr("transform",(t=>"scale(1) rotate("+(t.aa.slabelrotate?(o?"-":"")+"90":"0")+")"));t.slabel_forcerotate=false;const c=l.filter((t=>t.hasstackbar));c.selectAll(".sja_aa_stackbar_g").transition().duration(s).attr("transform",(e=>"translate("+(e.grp.aa.x0-e.grp.aa.x)+","+(o?1:-1)(t.stem1+t.stem2+t.stem3-e.y)+")"));c.selectAll(".sja_aa_stackbar_rect").transition().duration(s).attr("width",(t=>t.pxspan)).attr("y",(t=>o?-t.height:0))}function ve(t,e,s){const o=0;const a=s.width;let n=o;let r=false;for(const e of t){if(e.x0<o\|\|e.x0>a)continue;if(e.groups.length==1){e.slabelrotate=true;const t=e.groups[0];e.width=(t.radius+t.rimwidth)2}const t=e.x-e.maxradius-e.maxrimwidth;if(t<n){r=true}if(t+e.width>a){r=true}n=Math.max(n,t+e.width)}if(!r){return false}n=o;for(const e of t){if(e.x0<o\|\|e.x0>a)continue;e.x=n+e.maxradius+e.maxrimwidth;n+=e.width}we(t,s.width)}function we(t,e){for(let s=0;s<t.length;s++){if(t[s].x0<0)continue;if(t[s].x0>e)break;while(1){let o=0,a=0;for(let n=s;n<t.length;n++){const s=t[n];if(s.x0>e){return}o+=Math.abs(s.x-s.x0);s.x++;a+=Math.abs(s.x-s.x0)}if(t[s].x>=t[s].x0){for(let e=s;e<t.length;e++){t[e].x--}break}const n=t[t.length-1];if(n.x+n.width/2>=e){return}if(a<=o);else{for(let o=s;o<t.length;o++){if(t[o].x0>e){break}t[o].x--}break}}}}function _e(t,e){if(t.length==0)return;const s=1e3;const o=e.aboveprotein;const a=new Set;for(const s of t){s.x=s.x0;a.add(s.x0);s.showmode=oe;s.y=ge(s,e)}const n=e.skewer.filter((t=>a.has(t.x0)));n.transition().duration(s).attr("transform",(t=>"translate("+t.x+","+t.y+")"));n.selectAll(".sja_aa_stem").transition().duration(s).attr("d",(t=>be(t,e)));n.selectAll(".sja_aa_discg").transition().duration(s).attr("transform",(t=>"translate(0,"+(o?"-":"")+t.aa.maxradius+")"));n.selectAll(".sja_aa_disckick").attr("transform","scale(0)");n.selectAll(".sja_aa_discnum").transition().duration(s).attr("fill-opacity",0).attr("stroke-opacity",0);n.selectAll(".sja_aa_disclabel").transition().duration(s).attr("fill-opacity",0).attr("transform","scale(0)");n.selectAll(".sja_aa_discrim").transition().duration(s).attr("fill-opacity",0).attr("stroke-opacity",0);n.selectAll(".sja_aa_ssk_kick").attr("transform","scale(0)");n.selectAll(".sja_aa_ssk_bg").attr("transform","scale(0)");n.selectAll(".sja_aa_ssk_text").attr("transform","scale(0)");n.selectAll(".sja_aa_skkick").transition().duration(s).attr("transform","scale(1)");const r=n.filter((t=>t.hasstackbar));r.selectAll(".sja_aa_stackbar_g").transition().duration(s).attr("transform",(t=>"translate(0,"+(o?1:-1)(e.stem1-t.y)+")"));r.selectAll(".sja_aa_stackbar_rect").transition().duration(s).attr("width",0)}function je(t,e,s){if(!t.eplst)return;for(const o of t.eplst){o.may_hl(e,s)}}function Me(t,e,s){if(!t.config){s.error("config missing for expression data in "+e.ds.label);return}if(t.config.maf){try{t.config.maf.get=new Function(...t.config.maf.get)}catch(t){s.error("invalid javascript for config.maf.get of "+e.ds.label);return}}const o=t.config;if(o.usecohort){o.cohort=e.ds.cohort}const a={data:t.lst,expp:o,block:s,genome:s.genome,genename:s.usegm.name,dsname:e.ds.label};if(s.samplecart){if(e.ds.sampleselectable){a.samplecart=s.samplecart}}return import("./ep-d017ec2f.js").then((t=>{e.eplst.push(new t.default(a))}))}function Ae(t,e,s){for(const f of t){switch(f.dt){case c:if(s.usegm){const t=_(f.pos,s.usegm);f.rnapos=t.rnapos;f.aapos=t.aapos}e.mlst.push(f);break;case l:case i:if(!f.pairlst){console.error("pairlst missing from sv/fusion");break}if(s.usegm&&f.dt==l){if(f.pairlst.length==1){const t=f.pairlst[0].a;const e=f.pairlst[0].b;if(t.chr!=null&&e.chr!=null&&t.chr==e.chr&&t.position!=null&&e.position!=null){if(t.position<e.position){if(s.usegm.strand=="+"){t.strand="+";e.strand="+"}else{t.strand="-";e.strand="-";f.pairlst[0].a=e;f.pairlst[0].b=t}}}}}if(s.usegm&&s.gmmode!=F.genomic){f.isoform=s.usegm.isoform;let t=true;for(let e=0;e<f.pairlst.length;e++){const o=f.pairlst[e];if(s.usegm.isoform==(o.a.isoform\|\|o.a.name)){f.useNterm=e==0;f.chr=s.usegm.chr;f.strand=o.a.strand;if(o.a.position==undefined){if(o.a.rnaposition==undefined){if(o.a.codon==undefined){console.error("no position/rnaposition/codon available for "+s.usegm.isoform);break}else{f.pos=U(o.a.codon,s.usegm);o.a.position=f.pos}}else{f.pos=E(o.a.rnaposition-1,s.usegm);if(f.pos==null){console.error("failed to convert rnaposition to genomic position: "+o.a.rnaposition);break}o.a.position=f.pos}}else{f.pos=o.a.position}const a=_(f.pos,s.usegm);f.rnapos=a.rnapos;f.aapos=a.aapos;if(o.a.codon){f.aapos=o.a.codon}f.mname=o.b.name;t=false;break}if(s.usegm.isoform==(o.b.isoform\|\|o.b.name)){f.useNterm=false;f.chr=s.usegm.chr;f.strand=o.b.strand;if(o.b.position==undefined){if(o.b.rnaposition==undefined){if(o.b.codon==undefined){console.error("no position/rnaposition/codon available for "+s.usegm.isoform);break}else{f.pos=U(o.b.codon,s.usegm);o.b.position=f.pos}}else{f.pos=E(o.b.rnaposition-1,s.usegm);if(f.pos==null){console.error("failed to convert rnaposition to genomic");break}o.b.position=f.pos}}else{f.pos=o.b.position}const e=_(f.pos,s.usegm);f.rnapos=e.rnapos;f.aapos=e.aapos;if(o.b.codon){f.aapos=o.b.codon}f.mname=o.a.name;t=false;break}}if(t){console.error("sv/fusion isoform no match to gm isoform: "+s.usegm.isoform)}else{e.mlst.push(f)}}else{for(const t of f.pairlst){let o=false,a=false;for(let e=s.startidx;e<=s.stopidx;e++){const n=s.rglst[e];if(t.a.chr==n.chr&&t.a.position>=n.start&&t.a.position<=n.stop){o=true}if(t.b.chr==n.chr&&t.b.position>=n.start&&t.b.position<=n.stop){a=true}}if(o){const s=G(f);const o=t.a;s.chr=o.chr;s.strand=o.strand;s.useNterm=o.strand=="+";s.pos=o.pos\|\|o.position;s.mname=t.b.name\|\|t.b.chr;if(!Number.isFinite(s.pos)){console.error("no genomic pos for breakend a")}else if(!s.chr){console.error("no chromosome for breakend a")}else{e.mlst.push(s)}}if(a){const s=G(f);const o=t.b;s.chr=o.chr;s.strand=o.strand;s.useNterm=o.strand=="+";s.pos=o.pos\|\|o.position;s.mname=t.a.name\|\|t.a.chr;if(!Number.isFinite(s.pos)){console.error("no genomic pos for breakend b")}else if(!s.chr){console.error("no chromosome for breakend b")}else{e.mlst.push(s)}}}}break;case r:case o:if(f.chrpos1&&f.chrpos2){let t=_(f.chrpos1,s.usegm);const e=t.rnapos;t=_(f.chrpos2,s.usegm);const a=t.rnapos;if(e<a){f.pos=f.chrpos1}else{f.pos=f.chrpos2}delete f.chrpos1;delete f.chrpos2;const n=Math.abs(e-a);if(f.dt==r){f.rnaduplength=n}else if(f.dt==o){f.rnadellength=n}}if(f.position){f.pos=f.position;delete f.position}if(!f.pos){if(f.dt==r){if(f.b){if(f.b.position){f.pos=f.b.position;f.chr=f.b.chr}}}}if(!f.pos){if(f.rnaposition){if(s.usegm){f.pos=E(f.rnaposition-1,s.usegm);f.chr=s.usegm.chr;if(f.pos==null){console.error("failed to convert rnaposition to genomic position: "+f.rnaposition);break}}}else if(f.aapos);}if(!f.pos){console.error("no genomic pos for itd");break}if(s.usegm){const t=_(f.pos,s.usegm);if(f.rnaposition){f.rnapos=f.rnaposition}else{f.rnapos=t.rnapos}f.aapos=t.aapos}if(f.dt==r){if(!f.rnaduplength){console.error("itd has no rnaduplength");f.rnaduplength=1}}else{if(!f.rnadellength){console.error("deletion has no rnadellength");f.rnadellength=1}}e.mlst.push(f);break;case n:case a:if(f.position){f.pos=f.position;delete f.position}if(!f.pos){if(f.rnaposition){if(s.usegm){f.pos=E(f.rnaposition-1,s.usegm);f.chr=s.usegm.chr;if(f.pos==null){console.error("failed to convert rnaposition to genomic position: "+f.rnaposition);break}}}else if(f.aapos);}if(!f.pos){console.error("no genomic pos for truncation");break}if(s.usegm){const t=_(f.pos,s.usegm);if(f.rnaposition){f.rnapos=f.rnaposition}else{f.rnapos=t.rnapos}f.aapos=t.aapos}e.mlst.push(f);break;default:console.error("unknown dt: "+f.dt)}}}function ze(t,e){const s=new Map;for(const t in f){s.set(f[t].label.toUpperCase(),t)}const o=[];for(const[a,n]of t.hlaachange){if(n==false){continue}if(!n.name){e.error("hlaachange item .name missing");continue}if(n.codon==undefined\|\|!Number.isFinite(n.codon)){e.error("hlaachange invalid codon for "+n.name);continue}if(!n.class){e.error("hlaachange .class missing");continue}const t=f[n.class]?n.class:s.get(n.class.toUpperCase());if(!t){e.error("hlaachange invalid class: "+n.class);continue}n.class=t;n.mname=n.name;delete n.name;n.chr=e.usegm.chr;n.pos=U(n.codon,e.usegm);delete n.codon;n.dt=c;n.isoform=e.usegm.isoform;o.push(n)}if(o.length){const t={label:"Highlight",type:D.ds,iscustom:true,bulkdata:{}};t.bulkdata[e.usegm.name.toUpperCase()]=o;e.ownds[t.label]=t;const s=e.block_addtk_template({type:D.ds,ds:t});ne(s,e)}}function Ne(t,e){if(!t.vcfinfofilter)return;for(const s of t.vcfinfofilter.lst){s.holder.selectAll("").remove();if(s.numericfilter){for(const t of s.numericfilter){t.count=0}for(const e of t.mlst){const[t,o]=Se(s,e);if(t){continue}if(!o)continue;const a=o[0];if(!Number.isFinite(a))continue;for(const t of s.numericfilter){if(t.side=="<"){if(a<t.value){t.count++}}else{if(a>t.value){t.count++}}}}for(const o of s.numericfilter){const a=s.holder.append("div").style("display","inline-block").style("padding","10px").attr("class","sja_clb").on("click",(()=>{if(s.numericCutoff==o.value&&s.numericCutoffSide==o.side){delete s.numericCutoff}else{s.numericCutoff=o.value;s.numericCutoffSide=o.side}fe(t,e)}));if(s.numericCutoff==o.value&&s.numericCutoffSide==o.side){a.style("border-bottom","solid 2px #ccc").style("background-color","#f1f1f1")}if(o.count>0){a.append("div").style("display","inline-block").attr("class","sja_mcdot").style("padding","1px 5px").style("background-color","#ccc").style("color","white").html(o.count>1?o.count:" ").style("margin-right","5px")}a.append("span").text(o.side+o.value)}continue}if(!s.categories){continue}const o=new Map;let a=0;for(const e of t.mlst){const[t,n]=Se(s,e);if(t){continue}if(n==undefined){a++}else{for(const t of n){if(!o.has(t)){o.set(t,0)}o.set(t,o.get(t)+1)}}}const n=[...o];if(a){n.push([$t,a])}n.sort(((t,e)=>e[1]-t[1]));for(const[o,a]of n){const n=s.categories[o]\|\|{color:"black",label:o};const r=s.holder.append("div").style("display","inline-block").style("padding","10px").attr("class","sja_clb").on("click",(()=>{t.vcfinfofilter.tip.showunder(r.node());Ce(s,o,t,e)}));r.append("div").style("display","inline-block").attr("class","sja_mcdot").style("padding","1px 5px").style("background-color",n.color).style("color","white").html(a>1?a:" ").style("margin-right","5px");const i=r.append("span").text(n.label).style("color",n.color);if(s.categoryhidden[o]){i.style("text-decoration","line-through")}}}}function Pe(t,e){if(!t.vcfinfofilter)return;for(const e of t.vcfinfofilter.lst){if(e.numericfilter){continue}if(!e.autocategory){continue}const s=new Map;for(const o of t.mlst){const[t,a]=Se(e,o);if(t){continue}if(a!=undefined){for(const t of a){if(!s.has(t)){s.set(t,0)}s.set(t,s.get(t)+1)}}}const o=[...s];o.sort(((t,e)=>e[1]-t[1]));const a=M(Z);e.categories={};for(const[t,s]of o){e.categories[t]={label:t,color:a(t)}}}}function Se(t,e){if(t.altalleleinfo){if(!e.altinfo)return["no .altinfo"];const s=e.altinfo[t.altalleleinfo.key];if(s==undefined){if(t.numericfilter){return[null,[0]]}return[null,undefined]}let o=Array.isArray(s)?s:[s];if(t.altalleleinfo.separator){o=o[0].split(t.altalleleinfo.separator)}return[null,o]}if(t.locusinfo){if(!e.info)return["no .info"];const s=e.info[t.locusinfo.key];if(s==undefined){if(t.numericfilter){return[null,[0]]}return[null,undefined]}let o=Array.isArray(s)?s:[s];if(t.locusinfo.separator){o=o[0].split(t.locusinfo.separator)}return[null,o]}return["no trigger"]}function Ce(t,e,s,o){const a=s.vcfinfofilter.tip;a.clear();const n=t.categoryhidden[e];a.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show alone').on("click",(()=>{a.hide();t.categoryhidden={};for(const s in t.categories){if(s!=e){t.categoryhidden[s]=1}}if(e!=$t){t.categoryhidden[$t]=1}fe(s,o)}));if(n){a.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show').on("click",(()=>{a.hide();delete t.categoryhidden[e];fe(s,o)}))}else{a.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">×</div> hide').on("click",(()=>{a.hide();t.categoryhidden[e]=1;fe(s,o)}))}let r=0;for(const e in t.categoryhidden){r++}if(r>1){a.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show all').on("click",(()=>{a.hide();t.categoryhidden={};fe(s,o)}))}}function Fe(t,e){if(!t.vcfid)return[".vcfid missing"];if(!t.sampledata)return[".sampledata missing"];const s=e.ds.id2vcf[t.vcfid];if(!s)return["no vcf"];if(!s.samples\|\|s.samples.length==0)return["vcf no samples"];let o=0;for(const e of t.sampledata){if(!e.gtallref)o++}return[null,o/s.samples.length]}function Re(t,e){if(!t.populationfrequencyfilter)return;for(const e of t.populationfrequencyfilter.lst){e.count=0}for(const e of t.mlst){const[s,o]=Fe(e,t);if(s){continue}for(const e of t.populationfrequencyfilter.lst){if(o<e.value){e.count++}}}t.populationfrequencyfilter.holder.selectAll("").remove();for(const s of t.populationfrequencyfilter.lst){const o=t.populationfrequencyfilter.holder.append("div").style("display","inline-block").style("padding","10px").attr("class","sja_clb").on("click",(()=>{if(t.populationfrequencyfilter.cutoff==s.value){delete t.populationfrequencyfilter.cutoff}else{t.populationfrequencyfilter.cutoff=s.value}fe(t,e)}));if(t.populationfrequencyfilter.cutoff==s.value){o.style("border-bottom","solid 2px #ccc").style("background-color","#f1f1f1")}o.append("div").style("display","inline-block").attr("class","sja_mcdot").style("padding","1px 5px").style("background-color","#ccc").style("color","white").html(s.count>1?s.count:" ").style("margin-right","5px");o.append("span").text("< "+s.value)}}function Ie(t,e){if(!t.ds\|\|!t.ds.cohort\|\|!t.ds.cohort.sampleattribute)return;if(!t.ds.cohort.annotation)return".ds.cohort.annotation missing";if(!t.ds.cohort.key4annotation)return".ds.cohort.key4annotation missing";const s=t.ds.cohort.sampleattribute;if(!s.lst)return".lst missing";if(!s.holder)return".holder missing";s.holder.selectAll("").remove();if(t.mlst.length==0){return}for(const t of s.lst){if(!t.k)return".k missing for an attribute";if(!t.hiddenvalues)t.hiddenvalues=new Set}const o=[];if(t.mlst[0].sampledata){for(const e of s.lst){let s=0;const a=new Map;for(const o of t.mlst){if(!o.sampledata)continue;for(const n of o.sampledata){const o=n.sampleobj[t.ds.cohort.key4annotation];if(!o)continue;const r=t.ds.cohort.annotation[o];if(!r)continue;const i=r[e.k];if(i==undefined)continue;s++;if(!a.has(i)){a.set(i,0)}a.set(i,a.get(i)+1)}}if(s==0){continue}o.push({samplecount:s,key:e,lst:[...a].sort(((t,e)=>e[1]-t[1])).map((t=>({value:t[0],count:t[1]})))})}}else{for(const e of s.lst){let s=0;const a=new Map;for(const o of t.mlst){const n=o[t.ds.cohort.key4annotation];if(!n)continue;const 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all').on("click",(()=>{s.hide();e.key.hiddenvalues.clear();fe(o,a)}))}}function qe(t,e,s){let o=0;let a=0;let n=[];let r=[];for(const i of t.mlst){delete i.__x;if(e.legend&&e.legend.mclasses.has(i.class)&&e.legend.mclasses.get(i.class).hidden){continue}if(e.legend&&e.legend.morigins.has(i.origin)&&e.legend.morigins.get(i.origin).hidden){continue}if(i.origin&&s.has(i.origin)){continue}if(e.gmmode==V.protein&&e.usegm.codingstart&&e.usegm.codingstop){if(i.pos<e.usegm.codingstart\|\|i.pos>e.usegm.codingstop)continue}if(t.vcfinfofilter){let e=false;for(const s of t.vcfinfofilter.lst){const[t,o]=Se(s,i);if(t){continue}const a=o==undefined?[$t]:o;if(s.numericCutoff!=undefined){const t=Number.parseFloat(a[0]);if(Number.isNaN(t)){e=true;break}if(s.numericCutoffSide=="<"){if(t>=s.numericCutoff){e=true;break}}else if(s.numericCutoffSide==">"){if(t<=s.numericCutoff){e=true;break}}}else if(s.categoryhidden){let t=false;for(const e of a){if(!s.categoryhidden[e]){t=true;break}}if(!t){e=true;break}}}if(e){continue}}if(t.populationfrequencyfilter&&t.populationfrequencyfilter.cutoff){const[e,s]=Fe(i,t);if(e);else{if(s>t.populationfrequencyfilter.cutoff){continue}}}if(t.ds&&t.ds.cohort&&t.ds.cohort.annotation&&t.ds.cohort.key4annotation&&t.ds.cohort.sampleattribute&&t.ds.cohort.sampleattribute.runtimelst){let e=0;for(const s of t.ds.cohort.sampleattribute.runtimelst){if(s.key&&s.key.hiddenvalues){e+=s.key.hiddenvalues.size}}if(e>0){if(t.ds.vcfcohorttrack);else if(i.sampledata){let e=0;for(const s of i.sampledata){if(!O(s.genotype,i.alt)){continue}const o=s.sampleobj[t.ds.cohort.key4annotation];if(o){const e=t.ds.cohort.annotation[o];if(e){let s=false;for(const o of t.ds.cohort.sampleattribute.runtimelst){const t=e[o.key.k];if(t!=undefined){if(o.key.hiddenvalues.has(t)){s=true;break}}}if(s){continue}}}e++}if(e==0){continue}}else{const e=i[t.ds.cohort.key4annotation];if(e){const s=t.ds.cohort.annotation[e];if(s){let e=false;for(const o of t.ds.cohort.sampleattribute.runtimelst){const t=s[o.key.k];if(t!=undefined){if(o.key.hiddenvalues.has(t)){e=true;break}}}if(e){continue}}}}}}if(!i.chr){a++;continue}if(!Number.isInteger(i.pos)){o++;continue}const l=e.seekcoord(i.chr,i.pos);if(l.length==0){n.push(i);continue}if(l.length==1){i.__x=l[0].x}else{i.__x=l[0].x}if(i.__x<-1\|\|i.__x>e.width+1){continue}r.push(i)}const i=[];t.tklabel.each((function(){i.push(this.getBBox().width)}));if(r.length==0){t.label_mcount.text("")}else{t.label_mcount.text(r.length<t.mlst.length?r.length+" of "+t.mlst.length+" "+t.itemlabelname+"s":r.length+" "+t.itemlabelname+(r.length>1?"s":"")).each((function(){i.push(this.getBBox().width)}))}if(t.label_stratify){for(const e of t.label_stratify){let s;if(e.bycohort){const e=new Set;for(const s of r){let o="";for(const e of t.ds.cohort.levels){const t=s[e.k];if(t){o+=t}}e.add(o)}s=e.size}else{const t=new Set;for(const s of r){let o=s[e.attr1.k];if(!o)continue;if(e.attr2){const t=s[e.attr2.k];if(t){o+=t}}if(e.attr3){const t=s[e.attr3.k];if(t){o+=t}}t.add(o)}s=t.size}if(s==0){e.svglabel.text("")}else{e.svglabel.text(s+" "+e.label+(s>1?"s":"")).each((function(){i.push(this.getBBox().width)}))}}}t.leftLabelMaxwidth=Math.max(...i);if(o+a>0){e.tkerror(t,o+a+" items have no chromosome or genomic position")}if(n.length){console.error(n.length+" items not mapped to any region");for(const t of n)console.log(t)}return r}function De(t,e){for(const s of t.data){if(s.isbin){let t=0;for(const o of s.mlst){const s=e.seekcoord(o.chr,o.pos);if(o.usehitidx!=undefined&&s[o.usehitidx]){t+=s[o.usehitidx].x}else if(s.length==1){t+=s[0].x}else{console.log("cannot map item");console.log(o)}}s.x0=t/s.mlst.length;s.x=s.x0+(s.xoffset!=undefined?s.xoffset:0)}else{const t=e.seekcoord(s.chr,s.pos);if(t.length>0){s.x0=t[0].x;s.x=s.x0+(s.xoffset!=undefined?s.xoffset:0)}else{console.log("cannot map group of item");console.log(s)}}}}function Le(t,e){t.height_main=t.toppad+e.labelfontsize+t.bottompad;if(t.label_mcount&&t.label_mcount.text().length>0){t.height_main+=t.labyspace+e.labelfontsize}if(t.label_stratify){for(const s of t.label_stratify){if(s.svglabel.text().length>0){t.height_main+=t.labyspace+e.labelfontsize}}}t.glider.selectAll("").remove();t.leftaxis.selectAll("").remove();if(t.viewrangeupperlimit_above){e.tkerror(t,t.name+": zoom in under "+T(t.viewrangeupperlimit)+" to view data")}else{let s;if(!t.skewer.data\|\|t.skewer.data.length==0){if(e.pannedpx!=undefined\|\|e.zoomedin==true){s="view range"}else if(e.usegm&&e.gmmode!="genomic"){s=e.usegm.name\|\|e.usegm.isoform}}e.tkerror(t,t.name+": no mutation in "+s)}if(t.hlaachange){ze(t,e);delete t.hlaachange}}function Ee(t,e){if(!t.stratifycount)return;for(const[s,o]of t.stratifycount){const t=e.label_stratify.find((t=>t.label==s));if(!t){console.error("unknown strat label: "+s);continue}t.servercount=o}}const Ue=new H({padding:"0px"});function Ge(t,e){const s=t.legend.holder.append("tr");const o=s.append("td").text(e).style("padding-right","10px").style("text-align","right").style("color","#555").style("border-right","solid 1px "+t.legend.legendcolor);const a=s.append("td");return[s,a,o]}function Ve(t){if(!t.legend){return}const e=new Set;for(const[s,o]of t.legend.mclasses){if(o.hidden){e.add(s)}}const s=new Map;for(const e of t.tklst){if(e.hidden\|\|e.type!=D.ds)continue;if(!e.mlst){continue}for(const t of e.mlst){if(t.class){if(!s.has(t.class)){s.set(t.class,{count:0})}s.get(t.class).count++}}}const o=[];for(const[t,a]of s){if(e.has(t)){s.get(t).hidden=true}o.push({key:t,count:a.count})}t.legend.mclasses=s;if(s.size==0){t.legend.tr_mclass.style("display","none");return}t.legend.tr_mclass.style("display","table-row");o.sort(((t,e)=>e.count-t.count));t.legend.td_mclass.selectAll("").remove();for(const s of o){const o=t.legend.td_mclass.append("div").style("display","inline-block").style("white-space","nowrap").style("padding",t.legend.vpad+" 20px "+t.legend.vpad+" 0px").classed("sja_clb",true).on("click",(()=>{Ue.clear();Ue.showunder(o.node());Ue.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show alone').on("click",(()=>{Ue.hide();t.pannedpx=undefined;for(const e of t.legend.mclasses.values()){e.hidden=true}t.legend.mclasses.get(s.key).hidden=false;for(const e of t.tklst){if(!e.hidden&&e.type==D.ds){fe(e,t)}}}));if(t.legend.mclasses.get(s.key).hidden){Ue.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show').on("click",(()=>{Ue.hide();t.pannedpx=undefined;t.legend.mclasses.get(s.key).hidden=false;for(const e of t.tklst){if(!e.hidden&&e.type==D.ds){fe(e,t)}}}))}else{Ue.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">×</div> hide').on("click",(()=>{Ue.hide();t.pannedpx=undefined;t.legend.mclasses.get(s.key).hidden=true;for(const e of t.tklst){if(!e.hidden&&e.type==D.ds){fe(e,t)}}}))}if(e.size>1){Ue.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show all').on("click",(()=>{Ue.hide();t.pannedpx=undefined;for(const e of t.legend.mclasses.values()){e.hidden=false}for(const e of t.tklst){if(!e.hidden&&e.type==D.ds){fe(e,t)}}}))}const a=Ue.d.append("div").style("margin","20px");a.append("div").text(f[s.key].label.toUpperCase()).style("color",f[s.key].color).style("font-size",".8em");a.append("div").html(f[s.key].desc).style("color","#858585").style("font-size",".8em").style("width","210px")}));o.append("div").style("display","inline-block").style("background-color",f[s.key].color).style("margin-right","5px").style("border-radius","15px").style("padding","4px 8px").style("color","white").style("font-size",".8em").text(s.count);const a=o.append("div").style("display","inline-block").style("color",f[s.key].color).text(f[s.key].label);if(e.has(s.key)){a.style("text-decoration","line-through")}}}function Oe(t){if(!t.legend){return}const e=new Set;for(const[s,o]of t.legend.morigins){if(o.hidden){e.add(s)}}const s=new Map;for(const o of t.tklst){if(o.hidden\|\|o.type!=D.ds)continue;if(!o.mlst){continue}for(const t of o.mlst){if(!t.origin)continue;if(!s.has(t.origin)){let o=false;if(L[t.origin]&&L[t.origin].hidden){o=true;e.add(t.origin)}s.set(t.origin,{count:0,hidden:o})}s.get(t.origin).count++}}const o=[];for(const[t,a]of s){if(e.has(t)){s.get(t).hidden=true}o.push({key:t,count:a.count})}t.legend.morigins=s;if(s.size==0){t.legend.tr_morigin.style("display","none");return}t.legend.tr_morigin.style("display","table-row");o.sort(((t,e)=>e.count-t.count));t.legend.td_morigin.selectAll("*").remove();for(const s of o){const o=t.legend.td_morigin.append("div").style("display","inline-block").style("white-space","nowrap").style("padding",t.legend.vpad+" 20px "+t.legend.vpad+" 0px").classed("sja_clb",true).on("click",(()=>{Ue.clear();Ue.showunder(o.node());Ue.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show alone').on("click",(()=>{Ue.hide();t.pannedpx=undefined;for(const e of t.legend.morigins.values()){e.hidden=true}t.legend.morigins.get(s.key).hidden=false;L[s.key].hidden=false;for(const e of t.tklst){if(!e.hidden&&e.type==D.ds){fe(e,t)}}}));if(t.legend.morigins.get(s.key).hidden){Ue.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show').on("click",(()=>{Ue.hide();t.pannedpx=undefined;t.legend.morigins.get(s.key).hidden=false;L[s.key].hidden=false;for(const e of t.tklst){if(!e.hidden&&e.type==D.ds){fe(e,t)}}}))}else{Ue.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">×</div> hide').on("click",(()=>{Ue.hide();t.pannedpx=undefined;t.legend.morigins.get(s.key).hidden=true;for(const e of t.tklst){if(!e.hidden&&e.type==D.ds){fe(e,t)}}}))}if(e.size>1){Ue.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show all').on("click",(()=>{Ue.hide();t.pannedpx=undefined;for(const e of t.legend.morigins.values()){e.hidden=false}for(const e of t.tklst){if(!e.hidden&&e.type==D.ds){fe(e,t)}}}))}const a=Ue.d.append("div").style("margin","20px");a.append("div").text(L[s.key].label.toUpperCase()).style("color",L[s.key].color).style("font-size",".8em");a.append("div").html(L[s.key].desc).style("color","#858585").style("font-size",".8em").style("width","210px")}));o.append("svg").style("margin-right","5px").attr("width",19).attr("height",19).html(L[s.key].legend);const a=o.append("div").style("display","inline-block").style("color","#858585").text(L[s.key].label+", "+s.count);if(e.has(s.key)){a.style("text-decoration","line-through")}}}export{fe as a,ht as b,bt as c,ne as d,yt as e,_e as f,mt as g,he as h,$ as i,Ve as j,Oe as k,Ge as l,Ut as m,gt as r,ye as s};
1	+ import{Z as t,B as e,ap as s,aP as o,aQ as a,aR as n,ar as r,at as i,as as l,ak as c,z as f,a9 as d,p,ac as u,b6 as m,b7 as h,aN as g,q as b,b8 as y,j as x,b9 as k,ba as v,a7 as w,aG as _,bb as j,a8 as M,af as A,aM as z,aL as N,r as P,aW as S,d as C,aF as F,I as R,ah as I,W as B,ag as q,ad as D,O as L,aJ as E,bc as U,bd as G,be as V,bf as O,ae as T,M as H}from"./app-2cd97738.js";import{v as X,a as Y}from"./vcf-145bf5dd.js";import{p as J}from"./partition-db811f6b.js";import{d as Q}from"./arc-3d6751aa.js";import{b as W}from"./axis-747c801e.js";import{s as Z}from"./legacy-d3-polyfill-bdb2d792.js";const K="__";function $(f){const{mlst:d,tk:p,block:u}=f;if(!d\|\|d.length==0)return;let m;if(f.pane){const e=t({x:f.x,y:f.y});e.header.html(tt(d));m=e.body}else{m=f.holder}if(!m){console.error("no holder provided for showing table");return}const h=new Map;for(const t of d){if(!h.has(t.dt)){h.set(t.dt,[])}h.get(t.dt).push(t)}delete p.__singlevariant_table;for(const[t,f]of h){const d=m.append("div").style("margin","10px");if(h.size>1){d.append("p").text(e[t]).style("color","#858585")}switch(t){case c:et(f,d,p,u);break;case l:case i:ct(f,d,p,u);break;case r:dt(f,d,p,u.genome);break;case n:case a:ut(f,d,p,u.genome);break;case o:pt(f,d,p,u.genome);break;case s:d.append("p").text("cnv not supported yet");break;default:d.append("p").text("unknown dt: "+t)}}Ft(d,m,p,u)}function tt(t){if(t.length==1){const e=t[0];const d=f[e.class];if(e.dt==c){return'<span style="font-weight:bold;color:'+d.color+'">'+(e.mname?e.mname:e.pos?e.chr+":"+(e.pos+1):"")+'</span> <span style="font-size:80%">'+d.label+"</span>"}if(e.dt==l\|\|e.dt==i){const t=[];for(let s=0;s<e.pairlst.length;s++){if(s==0)t.push(e.pairlst[s].a.name?e.pairlst[s].a.name:e.pairlst[s].a.chr);t.push(e.pairlst[s].b.name?e.pairlst[s].b.name:e.pairlst[s].b.chr)}return t.join(" - ")+'  <span style="font-size:80%">'+d.label+"</span>"}if(e.dt==n\|\|e.dt==a\|\|e.dt==r\|\|e.dt==o\|\|e.dt==s){return'<span style="font-size:80%">'+d.label+"</span>"}return"unknown dt "+e.dt}const d=new Set;for(const e of t){d.add(e.dt)}if(d.size==1){const s=[...d][0];return t.length+" "+e[s]}return t.length+" mutations"}function et(e,s,o,a){if(o.ds&&o.ds.id2vcf){if(e.length==1){const t=o.ds.id2vcf[e[0].vcfid];if(!t){s.append("p").text("No vcf config file (id: "+e[0].vcfid+")");return}at(e[0],t,s,o,a);return}for(const n of e){const e=o.ds.id2vcf[n.vcfid];if(!e){s.append("p").text("No vcf config file (id: "+n.vcfid+")");continue}const r=s.append("div").attr("class","sja_menuoption").on("click",(s=>{const r=t({x:s.clientX+100,y:Math.max(100,s.clientY-100)});at(n,e,r.body,o,a)}));if(n.mname){r.append("span").html(n.mname+'\t<span style="font-size:80%;color:#858585">'+f[n.class].label+"</span>")}else if(n.csq){r.append("span").html(n.csq[0]._mname+'\t<span style="font-size:80%;color:#858585">'+n.csq[0].Consequence+"</span>")}r.append("span").html("  "+n.chr+":"+(n.pos+1)+' <span style="font-size:70%">REF</span> 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n=e.append("table").style("font-size","90%").style("border-spacing","2px").style("border-collapse","separate");const r=n.append("tr");for(const t of s.svattr){r.append("td").text(t.label)}st(t,n,s.svattr,s,(t=>{a.selectAll("").remove();ft(t.pairlst,o,a)}));if(s.eplst){const o=e.append("div").style("margin-top","5px");for(const e of s.eplst){lt(e,o,t)}}}function ft(t,e,s){for(const e of t){if(e.a.isoform){e.a.gm={isoform:e.a.isoform}}if(e.b.isoform){e.b.gm={isoform:e.b.isoform}}}const o={jwt:e.jwt,hostURL:e.hostURL,pairlst:t,genome:e.genome,holder:s};import("./svgraph-6ab3011b.js").then((t=>{t.default(o)}))}function dt(t,e,s,o){if(!s.itdattr){bt(s,t)}if(t.length==1){const o=t[0];const a=[];for(const t of s.itdattr){a.push({k:t.label,v:t.get(o)})}d(e,a);if(s.eplst){const o=e.append("div").style("margin-top","10px");for(const e of s.eplst){lt(e,o,t)}}return}const a=e.append("table").style("font-size","90%").style("border-spacing","2px").style("border-collapse","separate");const 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Wt(t,e){if(t.mlst.length==1){return"M0,0v"+e.stem1+"l"+-t.xoffset+","+e.stem2+"v"+e.stem3}return"M0,0"+"v"+e.stem1+"l"+-t.xoffset+","+e.stem2+"v"+e.stem3+"v-"+e.stem3+"l"+(t.stemw+t.xoffset-1)+",-"+e.stem2+"v-"+e.stem1}function Zt(t,e){t.numericmode;const s=100;let o=0;for(const e of t.data){let t=0;for(const s of e.mlst){t+=2(s.radius+s.rimwidth)}if(e.mlst.length==1){e.width=t}else{e.width=Math.min(s,t);const o=e.mlst[0];const a=e.mlst[e.mlst.length-1];e.fixedgew=o.radius+o.rimwidth+a.radius+a.rimwidth}o+=e.width}if(o<=e.width){let s=0;for(const e of t.data){e.x=s+e.mlst[0].radius+e.mlst[0].rimwidth;s+=e.width;if(e.mlst.length==1){e.stemw=0}else{e.stemw=e.width-e.fixedgew}}Kt(t.data,e.width);for(const e of t.data){e.xoffset=e.x-e.x0;if(e.mlst.length==1){e.mlst[0].xoff=0;e.stemw=0}else{e.stemw=e.width-e.fixedgew;const t=e.stemw/(e.mlst.length-1);for(let s=0;s<e.mlst.length;s++){e.mlst[s].xoff=ts}}}return true}else{for(const e of t.data){e.x=e.x0;e.xoffset=0;for(const t of e.mlst){t.xoff=0}}return false}}function Kt(t,e){for(let s=0;s<t.length;s++){if(t[s].x0<0)continue;if(t[s].x0>e)break;while(1){let o=0,a=0;for(let n=s;n<t.length;n++){const s=t[n];if(s.x0>e){return}o+=Math.abs(s.x-s.x0-s.stemw/2);s.x++;a+=Math.abs(s.x-s.x0-s.stemw/2)}if(t[s].x>t[s].x0-t[s].stemw/2){for(let e=s;e<t.length;e++){t[e].x--}break}const n=t[t.length-1];if(n.x+n.width/2>=e){return}if(a<=o);else{for(let o=s;o<t.length;o++){if(t[o].x0>e){break}t[o].x--}break}}}}const $t="Not annotated";const te=.3;const ee=1;const se=4;const oe=0;const ae=1;async function ne(t,e){try{if(!t)throw"no tk";if(!t.ds)throw"no ds";if(!e.gmmode\|\|e.gmmode==F.genomic){if(e.viewrangeabovelimit(t.viewrangeupperlimit)){t.mlst=[];t.viewrangeupperlimit_above=true;fe(t,e);return}}delete t.viewrangeupperlimit_above;if(t.isvcf){e.tkcloakon(t);Rt(e,t);return}if(e.ds2handle[t.ds.label]){t.__handlesays=e.ds2handle[t.ds.label].handlesays}if(t.ds.bulkdata\|\|t.ds.mlst){return await ie(t,e)}await le(t,e);re(t,e);t.ds.busy=false;e.tkcloakoff(t,{})}catch(s){if(s.stack)console.log(s.stack);t.ds.busy=false;e.tkcloakoff(t,{error:s.message\|\|s});e.setllabel(t);e.block_setheight()}}function re(t,e){if(!t.legacyDsFilter)return;if(!t.legacyDsFilter.key\|\|!t.legacyDsFilter.value)throw"legacyDsFilter is not {key,value}";const s=t.mlst.filter((e=>e[t.legacyDsFilter.key]==t.legacyDsFilter.value));const o={label:t.ds.label+" - "+t.legacyDsFilter.value,bulkdata:{},parentname:t.ds.label,iscustom:true,sampleselectable:t.ds.sampleselectable};o.bulkdata[e.usegm.name.toUpperCase()]=s;e.addchilddsnoload(o);const a=e.block_addtk_template({type:D.ds,ds:o});ne(a,e)}async function ie(t,e){if(e.usegm){if(t.__handlesays){t.__handlesays.style("background-color","#ddd").style("color","black")}let s=[];if(t.ds.bulkdata){const o=t.ds.bulkdata[e.usegm.name.toUpperCase()];if(o){s=[...o]}}if(t.ds.mlst){for(const o of t.ds.mlst){if(o.gene.toUpperCase()==e.usegm.name.toUpperCase()){s.push(o)}}}if(s.length){const o=[];for(const t of s){if(t.isoform&&t.isoform==e.usegm.isoform){o.push(t)}}if(o.length){ce([{lst:o}],e,t)}else{throw"No data from "+t.ds.label+" for "+e.usegm.isoform}}else{throw"No data from "+t.ds.label+" for "+e.usegm.name}if(t.ds.dbexpression&&(!t.eplst\|\|t.eplst.length==0)){const s={jwt:e.jwt,db:t.ds.dbexpression.dbfile,tablename:t.ds.dbexpression.tablename,keyname:t.ds.dbexpression.keyname,key:e.usegm.name};const o=await w("dbdata",{method:"POST",body:JSON.stringify(s)});if(o.error)throw o.error;if(!t.eplst)t.eplst=[];if(t.ds.dbexpression.tidy)t.ds.dbexpression.tidy(o.rows);const a={data:o.rows,expp:t.ds.dbexpression.config,block:e,genome:e.genome,genename:e.usegm.name,dsname:t.ds.label};const n=await import("./ep-a5c1ee3a.js");t.eplst.push(new n.default(a))}}else{const s=[];const f=new Map;for(const t of e.rglst){if(!f.has(t.chr)){f.set(t.chr,[])}f.get(t.chr).push(t)}const d=[];if(t.ds.bulkdata){for(const e in t.ds.bulkdata){d.push(...t.ds.bulkdata[e])}}if(t.ds.mlst){d.push(...t.ds.mlst)}for(const t of d){switch(t.dt){case c:case r:case o:case n:case a:if(!t.pos){break}if(!t.chr&&!f.has(t.chr)){break}for(const e of f.get(t.chr)){if(t.pos>=e.start&&t.pos<e.stop){s.push(t);break}}break;case l:case i:if(!t.pairlst){break}let e=false;for(const s of t.pairlst){if(s.a.chr&&f.has(s.a.chr)){const t=s.a.position\|\|s.a.pos;if(t){for(const o of f.get(s.a.chr)){if(t>=o.start&&t<o.stop){e=true;break}}}}if(s.b.chr&&f.has(s.b.chr)){const t=s.b.position\|\|s.b.pos;if(t){for(const o of f.get(s.b.chr)){if(t>=o.start&&t<o.stop){e=true;break}}}}}if(e){s.push(t)}break}}if(s.length){ce([{lst:s}],e,t)}}}async function le(t,e){if(t.__handlesays)t.__handlesays.text("Loading...");t.ds.busy=true;e.tkcloakon(t);const s={genome:e.genome.name,dsname:t.ds.label,range:e.tkarg_maygm(t)[0]};if(e.usegm){s.genename=e.usegm.name;s.isoform=e.usegm.isoform}if(t.eplst){s.noexpression=1}if(e.hidedatasetexpression){s.noexpression=1}const o=await w("dsdata",{method:"POST",body:JSON.stringify(s)});if(t.__handlesays){t.__handlesays.text(t.ds.label).style("background-color","#ddd").style("color","black")}if(o.error)throw o.error;ce(o.data,e,t)}function ce(t,e,s){if(s.dsuninitiated){for(let t=0;t<e.tklst.length;t++){if(e.tklst[t].tkid==s.tkid){e.tklst.splice(t,1);break}}delete s.dsuninitiated;let t=-1;for(let s=0;s<e.tklst.length;s++){const o=e.tklst[s];if(o.type==D.usegm&&!o.hidden){t=s;break}}let o=true;if(t==-1){o=true;e.tklst.push(s)}else{let a=false;for(let s=0;s<t;s++){const t=e.tklst[s];if(!t.hidden&&t.type==D.ds){a=true;break}}if(a){o=false;e.tklst.splice(t+1,0,s)}else{o=true;if(t==0){e.tklst.unshift(s)}else{e.tklst.splice(t-1,0,s)}}}if(s.aboveprotein==undefined){s.aboveprotein=o}s.eplst=[]}s.mlst=[];const o=[];for(const a of t){if(a.isgeneexpression){o.push(Me(a,s,e));continue}if(a.vcfid){It(a,s,e);continue}if(a.lst){Ae(a.lst,s,e);Ee(a,s);continue}e.error("unknown data/query type from "+s.ds.label);return}Promise.all(o).then((()=>{if(s.eplst.length>1){for(let t=1;t<s.eplst.length;t++){const e=s.eplst[t];e.pane.pane.style("left",Number.parseInt(s.eplst[0].pane.pane.style("left"))+50t+"px");e.pane.pane.style("top",Number.parseInt(s.eplst[0].pane.pane.style("top"))+50t+"px")}}}));fe(s,e)}function fe(t,e){e.tkcloakoff(t,{});de(t);if(t.vcfinfofilter&&t.vcfinfofilter.setidx4numeric!=undefined){if(!t.numericmode){t.numericmode={axisheight:t.axisheight}}}else{delete t.numericmode}const s=new Set;for(const t in L){if(L[t].hidden){s.add(t)}}Pe(t);if(t.numericmode){Ot(t,e,s)}else{pe(t,e,s)}e.setllabel(t);e.block_setheight();e.tkchangeaffectlegend(t);Ne(t,e);Re(t,e);{const s=Ie(t,e);if(s)console.log("showlegend_sampleattribute: "+s)}}function de(t){if(t.vcfinfofilter&&t.vcfinfofilter.setidx4occurrence!=undefined){const e=t.vcfinfofilter.lst[t.vcfinfofilter.setidx4occurrence];if(!e)throw"mcset not found by setidx4occurrence";for(const s of t.mlst){const[t,o]=Se(e,s);if(t\|\|o==undefined){s.occurrence=1}else{s.occurrence=o[0]}}}else{for(const e of t.mlst){e.occurrence=1}}}function pe(t,e,s){t.leftaxis.selectAll("").remove();if(e.usegm&&e.gmmode!=F.genomic&&e.pannedpx!=undefined&&t.skewer){De(t,e);t.skewer.attr("transform",(t=>"translate("+t.x+","+t.y+")"));ye(t,e)}else{t.glider.selectAll("").remove();qe(t,e,s);const o=new Map;for(const e of t.mlst){if(e.__x==undefined){continue}if(!o.has(e.__x)){o.set(e.__x,[])}o.get(e.__x).push(e)}const a=[];if(e.exonsf>=se){for(const[t,e]of o){a.push({chr:e[0].chr,pos:e[0].pos,mlst:e,x:t,groups:ue(e)})}}else{if(e.usegm&&e.usegm.coding&&e.gmmode!=F.genomic){const t=new Map;for(const[s,a]of o){if(a[0].chr!=e.usegm.chr){continue}let n=undefined;for(const t of a){if(Number.isFinite(t.aapos))n=t.aapos}if(n==undefined){n=_(a[0].pos,e.usegm).aapos}if(n==undefined){console.error("data item cannot map to aaposition");console.log(a[0]);continue}o.delete(s);if(!t.has(n)){t.set(n,[])}let r=true;for(const s of t.get(n)){if(Math.abs(s[0].__x-a[0].__x)<=e.exonsf3){for(const t of a){s.push(t)}r=false;break}}if(r){t.get(n).push(a)}}e.usegm.utr5?e.usegm.utr5.reduce(((t,e)=>t+e[1]-e[0]),0):0;for(const e of t.values()){for(const t of e){let e=null;for(const s of t){if(Number.isFinite(s.rnapos))e=s}if(e==null){console.log("trying to map mlst to codon, but no rnapos found");for(const e of t){console.log(e)}continue}a.push({chr:t[0].chr,pos:e.pos,mlst:t,x:t[0].__x,groups:ue(t)})}}}const t=[];const s=2;for(const[e,a]of o){const o=Math.floor(e/s);if(!t[o]){t[o]=[]}t[o]=[...t[o],...a]}for(const e of t){if(!e)continue;const t=e.reduce(((t,e)=>t+e.__x),0);a.push({isbin:true,chr:e[0].chr,pos:e[0].pos,mlst:e,x:t/e.length,groups:ue(e)})}}a.sort(((t,e)=>t.x-e.x));if(t.data&&e.pannedpx!=undefined&&(!e.usegm\|\|e.gmmode==F.genomic)){const e={};for(const s of t.data){e[s.chr+"."+s.pos]={mode:s.showmode,xoffset:s.xoffset,slabelrotate:s.slabelrotate}}for(const t of a){const s=t.chr+"."+t.pos;if(e[s]){t.showmode=e[s].mode;t.xoffset=e[s].xoffset;t.slabelrotate=e[s].slabelrotate}}}t.data=a;for(const e of t.data){e.occurrence=e.groups.reduce(((t,e)=>t+e.occurrence),0)}me(t,e);t.height_main=t.toppad+t.maxskewerheight+t.stem1+t.stem2+t.stem3+t.bottompad}if(!t.data\|\|t.data.length==0){Le(t,e);return}if(t.hlaachange\|\|t.hlvariants){const s=[];const o=[];if(t.hlaachange){for(const e of t.data){let a=false;for(const s of e.groups){if(t.hlaachange.has(s.mlst[0].mname)){a=true;t.hlaachange.delete(s.mlst[0].mname);break}}if(a){o.push(e)}else{s.push(e)}}if(t.hlaachange.size){if(!e.usegm){e.error("cannot add items from hlaachange: not in gene-mode")}else{ze(t,e)}}delete t.hlaachange}if(t.hlvariants){const e={};for(const s of t.hlvariants){e[s.chr+"."+s.pos+"."+s.ref+"."+s.alt]=1}for(const a of t.data){let t=false;for(const s of a.groups){if(t){break}for(const o of s.mlst){if(e[o.chr+"."+o.pos+"."+o.ref+"."+o.alt]){t=true;break}}}if(t){o.push(a)}else{s.push(a)}}}_e(s,t);xe(o,t,e)}else{ye(t,e)}}function ue(t,e){const s=new Map;for(const e of t){switch(e.dt){case c:if(!s.has(e.dt)){s.set(e.dt,new Map)}if(!s.get(e.dt).has(e.class)){s.get(e.dt).set(e.class,new Map)}const t=e.mname\|\|"";if(!s.get(e.dt).get(e.class).has(t)){s.get(e.dt).get(e.class).set(t,[])}s.get(e.dt).get(e.class).get(t).push(e);break;case l:case i:if(!s.has(e.dt)){s.set(e.dt,new Map)}if(!s.get(e.dt).has(e.class)){s.get(e.dt).set(e.class,{use5:new Map,use3:new Map})}if(e.useNterm){if(!s.get(e.dt).get(e.class).use5.has(e.mname)){s.get(e.dt).get(e.class).use5.set(e.mname,[])}s.get(e.dt).get(e.class).use5.get(e.mname).push(e)}else{if(!s.get(e.dt).get(e.class).use3.has(e.mname)){s.get(e.dt).get(e.class).use3.set(e.mname,[])}s.get(e.dt).get(e.class).use3.get(e.mname).push(e)}break;case r:case o:case n:case a:if(!s.has(e.dt)){s.set(e.dt,[])}s.get(e.dt).push(e);break;default:console.log("unknown datatype: "+e.dt);console.log(e);return}}const f=[];for(const[t,e]of s){switch(t){case c:for(const s of e.values()){for(const e of s.values()){f.push({dt:t,mlst:e})}}break;case l:case i:for(const s of e.values()){for(const e of s.use5.values()){f.push({dt:t,useNterm:true,mlst:e})}for(const e of s.use3.values()){f.push({dt:t,useNterm:false,mlst:e})}}break;case r:case o:case n:case a:f.push({dt:t,mlst:e})}}for(const t of f){let e=0,s=0;for(const o of t.mlst){if(o.isrim1)e++;else if(o.isrim2)s++}t.rim1count=e;t.rim2count=s;t.occurrence=t.mlst.reduce(((t,e)=>t+e.occurrence),0)}f.sort(((t,e)=>e.occurrence-t.occurrence));return f}function me(t,e){delete t.skewer2;const s=e=>{if(t.vcfinfofilter&&t.vcfinfofilter.setidx4mclass!=undefined){const s=t.vcfinfofilter.lst[t.vcfinfofilter.setidx4mclass];const[o,a]=Se(s,e);if(o\|\|a==undefined)return"black";for(const t of a){if(s.categories[t]){return s.categories[t].color}else{return"black"}}}if(f[e.class]){return f[e.class].color}return"black"};const d=[];for(const s of t.data){s.x0=s.x;if(s.xoffset!=undefined){s.x=s.x0+s.xoffset}for(const t of s.groups){t.aa=s;let a=null;if(t.dt==r){a=t.mlst[0].rnaduplength;for(const e of t.mlst){a=Math.max(a,e.rnaduplength)}}else if(t.dt==o){a=t.mlst[0].rnadellength;for(const e of t.mlst){a=Math.max(a,e.rnadellength)}}else{continue}if(!Number.isFinite(a)\|\|a<0){console.log("no rnaspan for stack bar from itd/del");console.log(t.mlst);continue}let n=null;if(e.usegm){const o=t.mlst[0].rnapos;const r=E(o+a,e.usegm);const i=e.seekcoord(e.usegm.chr,r);if(i.length>0){n=i[0].x-s.x}else{console.log(r+" no hit on rglst")}}if(!Number.isFinite(n)){console.log("no pxspan for stack bar from itd/del");console.log(t.mlst);continue}t.stackbar={aa:s.mlst[0].aapos,pxspan:n,height:4,grp:t};s.hasstackbar=true;d.push(t.stackbar)}}let p=0;if(d.length>0){let t=1;for(let e=0;e<d.length;e++){const s=d[e];const o=[];for(let t=0;t<e;t++){const e=d[t];if(Math.max(s.aa,e.aa)<Math.min(s.pxspan+s.aa,e.pxspan+e.aa)){o.push(e)}}s.y=2;for(const e of o){if(Math.max(s.y,e.y)<Math.min(s.y+s.height,e.y+e.height)){s.y=e.y+e.height+t}}p=Math.max(p,s.y+s.height)}}const u=Math.max(14,e.width/110);let m=0;for(const e of t.data){for(const t of e.groups){m=Math.max(m,t.occurrence)}}let h=0;const g=Math.pow(u/2,2)Math.PI;if(m<=10)h=gm.9;else if(m<=100)h=g10;else if(m<=1e3)h=g14;else h=g20;const b=R().domain([1,m.5,m.6,m.7,m.8,m]).range([g,g+(h-g).8,g+(h-g).85,g+(h-g).9,g+(h-g).95,h]);let y=u/2;t.maxskewerheight=0;t.skewer=t.glider.selectAll().data(t.data).enter().append("g").attr("class","sja_skg").each((function(e){e.skewer=this;if(e.showmode==undefined){e.showmode=oe}e.maxradius=0;e.maxrimwidth=0;e.width=0;e.slabelrotate=false;e.slabelwidth=0;for(const t of e.groups){if(t.occurrence==1){t.radius=u/2}else{const e=t.occurrence.toString().length;t.radius=Math.max(Math.sqrt(b(t.occurrence)/Math.PI),e5)}e.maxradius=Math.max(e.maxradius,t.radius);y=Math.max(y,t.radius);t.rimwidth=t.rim1count+t.rim2count==0?0:Math.max(2,t.radius/6);e.maxrimwidth=Math.max(e.maxrimwidth,t.rimwidth)}let s=0;for(const t of e.groups){t.yoffset=s+t.radius+t.rimwidth;s+=(t.radius+t.rimwidth)2}t.maxskewerheight=Math.max(t.maxskewerheight,s)}));const x=t.skewer.selectAll().data((t=>t.groups)).enter().append("g").attr("transform",(e=>"translate(0,"+(e.aa.showmode==oe?0:e.yoffset(t.aboveprotein?-1:1))+")")).attr("class","sja_aa_discg").each((function(t){t.g=this}));const 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e.groups){A=Math.max(A,t.occurrence)}}t.stem3=Math.max(p+2,M+uMath.min(5,A));t.skewer.append("circle").attr("class","sja_aa_skkick").attr("fill","white").attr("fill-opacity",0).attr("stroke","none").attr("r",(t=>t.maxradius+1)).attr("cy",(e=>(t.aboveprotein?-1:1)e.maxradius)).attr("transform",(t=>"scale("+(t.showmode==oe?1:0)+")")).on("mouseover",((e,o)=>{je(t,o.mlst,true);const a=t.aboveprotein;let n=0;let r=0;const i=5;const l=a?7:14;for(const e of o.groups){e.pica_fontsize=Math.max(11,e.radius);n+=e.pica_fontsize+1;t.pica.g.append("text").text(e.mlst[0].mname+(e.occurrence>1?" x"+e.occurrence:"")).attr("font-size",e.pica_fontsize).each((function(){r=Math.max(r,this.getBBox().width)})).remove()}r+=i2;const c=n+5;t.pica.g.append("rect").attr("y",a?-c:0).attr("width",r).attr("height",c).attr("fill","white").attr("fill-opacity",.8).attr("stroke","#ccc").attr("shape-rendering","crispEdges");n=0;const 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g=u3+d+p;i.x=a.grp.aa.x0+3;i.y=t.aboveprotein?t.height_main-t.toppad-t.bottompad-a.y-a.height-3-g:a.y+a.height+3;i.g.attr("transform","translate("+i.x+","+i.y+")");i.g.append("rect").attr("width",h+m2).attr("height",g).attr("stroke",n).attr("stroke-width",1).attr("shape-rendering","crispEdges").attr("fill","white").attr("fill-opacity",.8);i.g.append("text").text(l).attr("x",m).attr("y",u+d/2).attr("dominant-baseline","middle").attr("font-size",d).attr("font-family",I).attr("fill",n);i.g.append("text").text(c).attr("x",m).attr("y",u2+d+p/2).attr("dominant-baseline","middle").attr("font-size",p).attr("font-family",I).attr("fill","#858585")})).on("mouseout",((e,s)=>{C(e.target).attr("stroke","none");t.pica.g.selectAll("").remove()})).on("click",((s,o)=>{$({mlst:o.grp.mlst,pane:true,x:s.clientX,y:s.clientY,tk:t,block:e})}))}t.skewer.append("path").attr("class","sja_aa_stem").attr("d",(e=>be(e,t))).attr("stroke",(t=>s(t.groups[0].mlst[0]))).attr("fill","none");const P=t.skewer.filter((t=>t.groups.length>1));P.append("rect").attr("class","sja_aa_ssk_bg").attr("shape-rendering","crispEdges").attr("fill-opacity",0).attr("height",t.stem1).attr("fill",(t=>s(t.groups[0].mlst[0]))).attr("width",(t=>{t.ssk_width=Math.max(t.occurrence.toString().length8+6,2(t.maxradius+t.maxrimwidth));return t.ssk_width})).attr("x",(t=>-t.ssk_width/2));P.append("text").attr("class","sja_aa_ssk_text").attr("fill","white").attr("fill-opacity",0).attr("font-weight","bold").attr("text-anchor","middle").attr("dominant-baseline","central").text((t=>t.occurrence)).each((e=>{e.ssk_fontsize=Math.min(t.stem1,e.ssk_width/(e.occurrence.toString().lengthS))})).attr("font-size",(t=>t.ssk_fontsize));P.append("rect").attr("class","sja_aa_ssk_kick").attr("fill","white").attr("fill-opacity",0).attr("stroke","none").attr("height",t.stem1).attr("x",(t=>-t.ssk_width/2)).attr("width",(t=>t.ssk_width)).on("mouseover",((e,s)=>{const 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o=t.skewer.filter((t=>t.hasstackbar));o.selectAll(".sja_aa_stackbar_g").transition().duration(s).attr("transform",(s=>{const 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t=e.skewer.filter((t=>r.has(t.x0)));t.transition().duration(o).attr("transform",(t=>"translate("+t.x+","+t.y+")"));t.selectAll(".sja_aa_discg").transition().duration(o).attr("transform",(t=>{t.y=t.yoffset(a?-1:1);return"translate(0,"+t.y+")"}));setTimeout((function(){t.selectAll(".sja_aa_disckick").attr("transform","scale(1)")}),o);t.selectAll(".sja_aa_discnum").transition().duration(o).attr("fill-opacity",1).attr("stroke-opacity",1);t.filter((t=>t.groups.length>1)).selectAll(".sja_aa_disclabel").transition().duration(o).attr("fill-opacity",1).attr("transform","scale(1)");t.selectAll(".sja_aa_discrim").transition().duration(o).attr("fill-opacity",1).attr("stroke-opacity",1);t.selectAll(".sja_aa_ssk_kick").attr("transform","scale(1)").attr("y",a?0:-e.stem1);t.selectAll(".sja_aa_ssk_bg").attr("transform","scale(1)").attr("y",a?0:-e.stem1);t.selectAll(".sja_aa_ssk_text").attr("transform","scale(1)").attr("y",(a?1:-1)e.stem1/2);t.selectAll(".sja_aa_skkick").attr("transform","scale(0)");t.filter((t=>t.hasstackbar)).selectAll(".sja_aa_stackbar_g").attr("transform",(t=>"translate(0,"+(a?1:-1)(e.stem1+e.stem2+e.stem3-t.y)+")"));let n=0;t.selectAll(".sja_aa_stem").transition().duration(o).attr("d",(t=>be(t,e))).each((()=>++n)).on("end",(()=>{if(! --n){ke(e,s)}}))}else{ke(e,s)}}function ke(t,e){const s=1e3;const o=t.aboveprotein;const a=[];const n=new Set;const r=0;const i=e.width;for(const e of t.data){if(e.x0<r\|\|e.x0>i)continue;if(e.showmode==ae){e.x=e.x0;a.push(e);n.add(e.x0)}}if(a.length==0){return}ve(a,t,e);for(const t of a){t.xoffset=t.x-t.x0}for(let e=0;e<a.length;e++){const s=a[e];if(s.groups.length>1)continue;const o=s.groups[0];if(t.slabel_forcerotate){s.slabelrotate=true}else{const t=a[e+1];const n=t?t.x-t.maxradius-t.maxrimwidth:i;s.slabelrotate=n-s.x-o.radius-o.rimwidth-1<s.slabelwidth}s.width=(o.radius+o.rimwidth)2+(s.slabelrotate?0:2+s.slabelwidth)}const l=t.skewer.filter((t=>n.has(t.x0)));l.transition().duration(s).attr("transform",(t=>"translate("+t.x+","+t.y+")"));l.selectAll(".sja_aa_stem").transition().duration(s).attr("d",(e=>be(e,t)));l.filter((t=>t.groups.length==1)).selectAll(".sja_aa_disclabel").transition().duration(s).attr("fill-opacity",1).attr("transform",(t=>"scale(1) rotate("+(t.aa.slabelrotate?(o?"-":"")+"90":"0")+")"));t.slabel_forcerotate=false;const c=l.filter((t=>t.hasstackbar));c.selectAll(".sja_aa_stackbar_g").transition().duration(s).attr("transform",(e=>"translate("+(e.grp.aa.x0-e.grp.aa.x)+","+(o?1:-1)(t.stem1+t.stem2+t.stem3-e.y)+")"));c.selectAll(".sja_aa_stackbar_rect").transition().duration(s).attr("width",(t=>t.pxspan)).attr("y",(t=>o?-t.height:0))}function ve(t,e,s){const o=0;const a=s.width;let n=o;let r=false;for(const e of t){if(e.x0<o\|\|e.x0>a)continue;if(e.groups.length==1){e.slabelrotate=true;const t=e.groups[0];e.width=(t.radius+t.rimwidth)2}const t=e.x-e.maxradius-e.maxrimwidth;if(t<n){r=true}if(t+e.width>a){r=true}n=Math.max(n,t+e.width)}if(!r){return false}n=o;for(const e of t){if(e.x0<o\|\|e.x0>a)continue;e.x=n+e.maxradius+e.maxrimwidth;n+=e.width}we(t,s.width)}function we(t,e){for(let s=0;s<t.length;s++){if(t[s].x0<0)continue;if(t[s].x0>e)break;while(1){let o=0,a=0;for(let n=s;n<t.length;n++){const s=t[n];if(s.x0>e){return}o+=Math.abs(s.x-s.x0);s.x++;a+=Math.abs(s.x-s.x0)}if(t[s].x>=t[s].x0){for(let e=s;e<t.length;e++){t[e].x--}break}const n=t[t.length-1];if(n.x+n.width/2>=e){return}if(a<=o);else{for(let o=s;o<t.length;o++){if(t[o].x0>e){break}t[o].x--}break}}}}function _e(t,e){if(t.length==0)return;const s=1e3;const o=e.aboveprotein;const a=new Set;for(const s of t){s.x=s.x0;a.add(s.x0);s.showmode=oe;s.y=ge(s,e)}const n=e.skewer.filter((t=>a.has(t.x0)));n.transition().duration(s).attr("transform",(t=>"translate("+t.x+","+t.y+")"));n.selectAll(".sja_aa_stem").transition().duration(s).attr("d",(t=>be(t,e)));n.selectAll(".sja_aa_discg").transition().duration(s).attr("transform",(t=>"translate(0,"+(o?"-":"")+t.aa.maxradius+")"));n.selectAll(".sja_aa_disckick").attr("transform","scale(0)");n.selectAll(".sja_aa_discnum").transition().duration(s).attr("fill-opacity",0).attr("stroke-opacity",0);n.selectAll(".sja_aa_disclabel").transition().duration(s).attr("fill-opacity",0).attr("transform","scale(0)");n.selectAll(".sja_aa_discrim").transition().duration(s).attr("fill-opacity",0).attr("stroke-opacity",0);n.selectAll(".sja_aa_ssk_kick").attr("transform","scale(0)");n.selectAll(".sja_aa_ssk_bg").attr("transform","scale(0)");n.selectAll(".sja_aa_ssk_text").attr("transform","scale(0)");n.selectAll(".sja_aa_skkick").transition().duration(s).attr("transform","scale(1)");const r=n.filter((t=>t.hasstackbar));r.selectAll(".sja_aa_stackbar_g").transition().duration(s).attr("transform",(t=>"translate(0,"+(o?1:-1)(e.stem1-t.y)+")"));r.selectAll(".sja_aa_stackbar_rect").transition().duration(s).attr("width",0)}function je(t,e,s){if(!t.eplst)return;for(const o of t.eplst){o.may_hl(e,s)}}function Me(t,e,s){if(!t.config){s.error("config missing for expression data in "+e.ds.label);return}if(t.config.maf){try{t.config.maf.get=new Function(...t.config.maf.get)}catch(t){s.error("invalid javascript for config.maf.get of "+e.ds.label);return}}const o=t.config;if(o.usecohort){o.cohort=e.ds.cohort}const a={data:t.lst,expp:o,block:s,genome:s.genome,genename:s.usegm.name,dsname:e.ds.label};if(s.samplecart){if(e.ds.sampleselectable){a.samplecart=s.samplecart}}return import("./ep-a5c1ee3a.js").then((t=>{e.eplst.push(new t.default(a))}))}function Ae(t,e,s){for(const f of t){switch(f.dt){case c:if(s.usegm){const t=_(f.pos,s.usegm);f.rnapos=t.rnapos;f.aapos=t.aapos}e.mlst.push(f);break;case l:case i:if(!f.pairlst){console.error("pairlst missing from sv/fusion");break}if(s.usegm&&f.dt==l){if(f.pairlst.length==1){const t=f.pairlst[0].a;const e=f.pairlst[0].b;if(t.chr!=null&&e.chr!=null&&t.chr==e.chr&&t.position!=null&&e.position!=null){if(t.position<e.position){if(s.usegm.strand=="+"){t.strand="+";e.strand="+"}else{t.strand="-";e.strand="-";f.pairlst[0].a=e;f.pairlst[0].b=t}}}}}if(s.usegm&&s.gmmode!=F.genomic){f.isoform=s.usegm.isoform;let t=true;for(let e=0;e<f.pairlst.length;e++){const o=f.pairlst[e];if(s.usegm.isoform==(o.a.isoform\|\|o.a.name)){f.useNterm=e==0;f.chr=s.usegm.chr;f.strand=o.a.strand;if(o.a.position==undefined){if(o.a.rnaposition==undefined){if(o.a.codon==undefined){console.error("no position/rnaposition/codon available for "+s.usegm.isoform);break}else{f.pos=U(o.a.codon,s.usegm);o.a.position=f.pos}}else{f.pos=E(o.a.rnaposition-1,s.usegm);if(f.pos==null){console.error("failed to convert rnaposition to genomic position: "+o.a.rnaposition);break}o.a.position=f.pos}}else{f.pos=o.a.position}const a=_(f.pos,s.usegm);f.rnapos=a.rnapos;f.aapos=a.aapos;if(o.a.codon){f.aapos=o.a.codon}f.mname=o.b.name;t=false;break}if(s.usegm.isoform==(o.b.isoform\|\|o.b.name)){f.useNterm=false;f.chr=s.usegm.chr;f.strand=o.b.strand;if(o.b.position==undefined){if(o.b.rnaposition==undefined){if(o.b.codon==undefined){console.error("no position/rnaposition/codon available for "+s.usegm.isoform);break}else{f.pos=U(o.b.codon,s.usegm);o.b.position=f.pos}}else{f.pos=E(o.b.rnaposition-1,s.usegm);if(f.pos==null){console.error("failed to convert rnaposition to genomic");break}o.b.position=f.pos}}else{f.pos=o.b.position}const e=_(f.pos,s.usegm);f.rnapos=e.rnapos;f.aapos=e.aapos;if(o.b.codon){f.aapos=o.b.codon}f.mname=o.a.name;t=false;break}}if(t){console.error("sv/fusion isoform no match to gm isoform: "+s.usegm.isoform)}else{e.mlst.push(f)}}else{for(const t of f.pairlst){let o=false,a=false;for(let e=s.startidx;e<=s.stopidx;e++){const n=s.rglst[e];if(t.a.chr==n.chr&&t.a.position>=n.start&&t.a.position<=n.stop){o=true}if(t.b.chr==n.chr&&t.b.position>=n.start&&t.b.position<=n.stop){a=true}}if(o){const s=G(f);const o=t.a;s.chr=o.chr;s.strand=o.strand;s.useNterm=o.strand=="+";s.pos=o.pos\|\|o.position;s.mname=t.b.name\|\|t.b.chr;if(!Number.isFinite(s.pos)){console.error("no genomic pos for breakend a")}else if(!s.chr){console.error("no chromosome for breakend a")}else{e.mlst.push(s)}}if(a){const s=G(f);const o=t.b;s.chr=o.chr;s.strand=o.strand;s.useNterm=o.strand=="+";s.pos=o.pos\|\|o.position;s.mname=t.a.name\|\|t.a.chr;if(!Number.isFinite(s.pos)){console.error("no genomic pos for breakend b")}else if(!s.chr){console.error("no chromosome for breakend b")}else{e.mlst.push(s)}}}}break;case r:case o:if(f.chrpos1&&f.chrpos2){let t=_(f.chrpos1,s.usegm);const e=t.rnapos;t=_(f.chrpos2,s.usegm);const a=t.rnapos;if(e<a){f.pos=f.chrpos1}else{f.pos=f.chrpos2}delete f.chrpos1;delete f.chrpos2;const n=Math.abs(e-a);if(f.dt==r){f.rnaduplength=n}else if(f.dt==o){f.rnadellength=n}}if(f.position){f.pos=f.position;delete f.position}if(!f.pos){if(f.dt==r){if(f.b){if(f.b.position){f.pos=f.b.position;f.chr=f.b.chr}}}}if(!f.pos){if(f.rnaposition){if(s.usegm){f.pos=E(f.rnaposition-1,s.usegm);f.chr=s.usegm.chr;if(f.pos==null){console.error("failed to convert rnaposition to genomic position: "+f.rnaposition);break}}}else if(f.aapos);}if(!f.pos){console.error("no genomic pos for itd");break}if(s.usegm){const t=_(f.pos,s.usegm);if(f.rnaposition){f.rnapos=f.rnaposition}else{f.rnapos=t.rnapos}f.aapos=t.aapos}if(f.dt==r){if(!f.rnaduplength){console.error("itd has no rnaduplength");f.rnaduplength=1}}else{if(!f.rnadellength){console.error("deletion has no rnadellength");f.rnadellength=1}}e.mlst.push(f);break;case n:case a:if(f.position){f.pos=f.position;delete f.position}if(!f.pos){if(f.rnaposition){if(s.usegm){f.pos=E(f.rnaposition-1,s.usegm);f.chr=s.usegm.chr;if(f.pos==null){console.error("failed to convert rnaposition to genomic position: "+f.rnaposition);break}}}else if(f.aapos);}if(!f.pos){console.error("no genomic pos for truncation");break}if(s.usegm){const t=_(f.pos,s.usegm);if(f.rnaposition){f.rnapos=f.rnaposition}else{f.rnapos=t.rnapos}f.aapos=t.aapos}e.mlst.push(f);break;default:console.error("unknown dt: "+f.dt)}}}function ze(t,e){const s=new Map;for(const t in f){s.set(f[t].label.toUpperCase(),t)}const o=[];for(const[a,n]of t.hlaachange){if(n==false){continue}if(!n.name){e.error("hlaachange item .name missing");continue}if(n.codon==undefined\|\|!Number.isFinite(n.codon)){e.error("hlaachange invalid codon for "+n.name);continue}if(!n.class){e.error("hlaachange .class missing");continue}const t=f[n.class]?n.class:s.get(n.class.toUpperCase());if(!t){e.error("hlaachange invalid class: "+n.class);continue}n.class=t;n.mname=n.name;delete n.name;n.chr=e.usegm.chr;n.pos=U(n.codon,e.usegm);delete n.codon;n.dt=c;n.isoform=e.usegm.isoform;o.push(n)}if(o.length){const t={label:"Highlight",type:D.ds,iscustom:true,bulkdata:{}};t.bulkdata[e.usegm.name.toUpperCase()]=o;e.ownds[t.label]=t;const s=e.block_addtk_template({type:D.ds,ds:t});ne(s,e)}}function Ne(t,e){if(!t.vcfinfofilter)return;for(const s of t.vcfinfofilter.lst){s.holder.selectAll("").remove();if(s.numericfilter){for(const t of s.numericfilter){t.count=0}for(const e of t.mlst){const[t,o]=Se(s,e);if(t){continue}if(!o)continue;const a=o[0];if(!Number.isFinite(a))continue;for(const t of s.numericfilter){if(t.side=="<"){if(a<t.value){t.count++}}else{if(a>t.value){t.count++}}}}for(const o of s.numericfilter){const a=s.holder.append("div").style("display","inline-block").style("padding","10px").attr("class","sja_clb").on("click",(()=>{if(s.numericCutoff==o.value&&s.numericCutoffSide==o.side){delete s.numericCutoff}else{s.numericCutoff=o.value;s.numericCutoffSide=o.side}fe(t,e)}));if(s.numericCutoff==o.value&&s.numericCutoffSide==o.side){a.style("border-bottom","solid 2px #ccc").style("background-color","#f1f1f1")}if(o.count>0){a.append("div").style("display","inline-block").attr("class","sja_mcdot").style("padding","1px 5px").style("background-color","#ccc").style("color","white").html(o.count>1?o.count:" ").style("margin-right","5px")}a.append("span").text(o.side+o.value)}continue}if(!s.categories){continue}const o=new Map;let a=0;for(const e of t.mlst){const[t,n]=Se(s,e);if(t){continue}if(n==undefined){a++}else{for(const t of n){if(!o.has(t)){o.set(t,0)}o.set(t,o.get(t)+1)}}}const n=[...o];if(a){n.push([$t,a])}n.sort(((t,e)=>e[1]-t[1]));for(const[o,a]of n){const n=s.categories[o]\|\|{color:"black",label:o};const r=s.holder.append("div").style("display","inline-block").style("padding","10px").attr("class","sja_clb").on("click",(()=>{t.vcfinfofilter.tip.showunder(r.node());Ce(s,o,t,e)}));r.append("div").style("display","inline-block").attr("class","sja_mcdot").style("padding","1px 5px").style("background-color",n.color).style("color","white").html(a>1?a:" ").style("margin-right","5px");const i=r.append("span").text(n.label).style("color",n.color);if(s.categoryhidden[o]){i.style("text-decoration","line-through")}}}}function Pe(t,e){if(!t.vcfinfofilter)return;for(const e of t.vcfinfofilter.lst){if(e.numericfilter){continue}if(!e.autocategory){continue}const s=new Map;for(const o of t.mlst){const[t,a]=Se(e,o);if(t){continue}if(a!=undefined){for(const t of a){if(!s.has(t)){s.set(t,0)}s.set(t,s.get(t)+1)}}}const o=[...s];o.sort(((t,e)=>e[1]-t[1]));const a=M(Z);e.categories={};for(const[t,s]of o){e.categories[t]={label:t,color:a(t)}}}}function Se(t,e){if(t.altalleleinfo){if(!e.altinfo)return["no .altinfo"];const s=e.altinfo[t.altalleleinfo.key];if(s==undefined){if(t.numericfilter){return[null,[0]]}return[null,undefined]}let o=Array.isArray(s)?s:[s];if(t.altalleleinfo.separator){o=o[0].split(t.altalleleinfo.separator)}return[null,o]}if(t.locusinfo){if(!e.info)return["no .info"];const s=e.info[t.locusinfo.key];if(s==undefined){if(t.numericfilter){return[null,[0]]}return[null,undefined]}let o=Array.isArray(s)?s:[s];if(t.locusinfo.separator){o=o[0].split(t.locusinfo.separator)}return[null,o]}return["no trigger"]}function Ce(t,e,s,o){const a=s.vcfinfofilter.tip;a.clear();const n=t.categoryhidden[e];a.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show alone').on("click",(()=>{a.hide();t.categoryhidden={};for(const s in t.categories){if(s!=e){t.categoryhidden[s]=1}}if(e!=$t){t.categoryhidden[$t]=1}fe(s,o)}));if(n){a.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show').on("click",(()=>{a.hide();delete t.categoryhidden[e];fe(s,o)}))}else{a.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">×</div> hide').on("click",(()=>{a.hide();t.categoryhidden[e]=1;fe(s,o)}))}let r=0;for(const e in t.categoryhidden){r++}if(r>1){a.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show all').on("click",(()=>{a.hide();t.categoryhidden={};fe(s,o)}))}}function Fe(t,e){if(!t.vcfid)return[".vcfid missing"];if(!t.sampledata)return[".sampledata missing"];const s=e.ds.id2vcf[t.vcfid];if(!s)return["no vcf"];if(!s.samples\|\|s.samples.length==0)return["vcf no samples"];let o=0;for(const e of t.sampledata){if(!e.gtallref)o++}return[null,o/s.samples.length]}function Re(t,e){if(!t.populationfrequencyfilter)return;for(const e of t.populationfrequencyfilter.lst){e.count=0}for(const e of t.mlst){const[s,o]=Fe(e,t);if(s){continue}for(const e of t.populationfrequencyfilter.lst){if(o<e.value){e.count++}}}t.populationfrequencyfilter.holder.selectAll("").remove();for(const s of t.populationfrequencyfilter.lst){const o=t.populationfrequencyfilter.holder.append("div").style("display","inline-block").style("padding","10px").attr("class","sja_clb").on("click",(()=>{if(t.populationfrequencyfilter.cutoff==s.value){delete t.populationfrequencyfilter.cutoff}else{t.populationfrequencyfilter.cutoff=s.value}fe(t,e)}));if(t.populationfrequencyfilter.cutoff==s.value){o.style("border-bottom","solid 2px #ccc").style("background-color","#f1f1f1")}o.append("div").style("display","inline-block").attr("class","sja_mcdot").style("padding","1px 5px").style("background-color","#ccc").style("color","white").html(s.count>1?s.count:" ").style("margin-right","5px");o.append("span").text("< "+s.value)}}function Ie(t,e){if(!t.ds\|\|!t.ds.cohort\|\|!t.ds.cohort.sampleattribute)return;if(!t.ds.cohort.annotation)return".ds.cohort.annotation missing";if(!t.ds.cohort.key4annotation)return".ds.cohort.key4annotation missing";const s=t.ds.cohort.sampleattribute;if(!s.lst)return".lst missing";if(!s.holder)return".holder missing";s.holder.selectAll("").remove();if(t.mlst.length==0){return}for(const t of s.lst){if(!t.k)return".k missing for an attribute";if(!t.hiddenvalues)t.hiddenvalues=new Set}const o=[];if(t.mlst[0].sampledata){for(const e of s.lst){let s=0;const a=new Map;for(const o of t.mlst){if(!o.sampledata)continue;for(const n of o.sampledata){const o=n.sampleobj[t.ds.cohort.key4annotation];if(!o)continue;const r=t.ds.cohort.annotation[o];if(!r)continue;const i=r[e.k];if(i==undefined)continue;s++;if(!a.has(i)){a.set(i,0)}a.set(i,a.get(i)+1)}}if(s==0){continue}o.push({samplecount:s,key:e,lst:[...a].sort(((t,e)=>e[1]-t[1])).map((t=>({value:t[0],count:t[1]})))})}}else{for(const e of s.lst){let s=0;const a=new Map;for(const o of t.mlst){const n=o[t.ds.cohort.key4annotation];if(!n)continue;const r=t.ds.cohort.annotation[n];if(!r)continue;const i=r[e.k];if(i==undefined)continue;s++;if(!a.has(i)){a.set(i,0)}a.set(i,a.get(i)+1)}if(s==0){continue}o.push({samplecount:s,key:e,lst:[...a].sort(((t,e)=>e[1]-t[1])).map((t=>({value:t[0],count:t[1]})))})}}if(o.length==0){delete s.runtimelst;return}s.runtimelst=o;const a=s.holder.append("table").style("border-spacing","5px");for(const n of o){const o=a.append("tr");o.append("td").style("color","#858585").style("text-align","right").text(n.key.label\|\|n.key.k);const r=o.append("td");for(const o of n.lst){const a=r.append("div").style("display","inline-block").style("padding","5px").attr("class","sja_clb").on("click",(()=>{s.tip.showunder(a.node());Be(o,n,s.tip,t,e)}));a.append("div").style("display","inline-block").attr("class","sja_mcdot").style("padding","1px 3px").style("background-color","#858585").style("color","white").html(o.count>1?o.count:" ").style("margin-right","5px");const i=a.append("span").text(o.value);if(n.key.hiddenvalues.has(o.value)){i.style("text-decoration","line-through")}}}return null}function Be(t,e,s,o,a){s.clear();s.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show alone').on("click",(()=>{s.hide();for(const t of e.lst){e.key.hiddenvalues.add(t.value)}e.key.hiddenvalues.delete(t.value);fe(o,a)}));if(e.key.hiddenvalues.has(t.value)){s.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show').on("click",(()=>{s.hide();e.key.hiddenvalues.delete(t.value);fe(o,a)}))}else{s.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">×</div> hide').on("click",(()=>{s.hide();e.key.hiddenvalues.add(t.value);fe(o,a)}))}if(e.key.hiddenvalues.size>1){s.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show all').on("click",(()=>{s.hide();e.key.hiddenvalues.clear();fe(o,a)}))}}function qe(t,e,s){let o=0;let a=0;let n=[];let r=[];for(const i of t.mlst){delete i.__x;if(e.legend&&e.legend.mclasses.has(i.class)&&e.legend.mclasses.get(i.class).hidden){continue}if(e.legend&&e.legend.morigins.has(i.origin)&&e.legend.morigins.get(i.origin).hidden){continue}if(i.origin&&s.has(i.origin)){continue}if(e.gmmode==V.protein&&e.usegm.codingstart&&e.usegm.codingstop){if(i.pos<e.usegm.codingstart\|\|i.pos>e.usegm.codingstop)continue}if(t.vcfinfofilter){let e=false;for(const s of t.vcfinfofilter.lst){const[t,o]=Se(s,i);if(t){continue}const a=o==undefined?[$t]:o;if(s.numericCutoff!=undefined){const t=Number.parseFloat(a[0]);if(Number.isNaN(t)){e=true;break}if(s.numericCutoffSide=="<"){if(t>=s.numericCutoff){e=true;break}}else if(s.numericCutoffSide==">"){if(t<=s.numericCutoff){e=true;break}}}else if(s.categoryhidden){let t=false;for(const e of a){if(!s.categoryhidden[e]){t=true;break}}if(!t){e=true;break}}}if(e){continue}}if(t.populationfrequencyfilter&&t.populationfrequencyfilter.cutoff){const[e,s]=Fe(i,t);if(e);else{if(s>t.populationfrequencyfilter.cutoff){continue}}}if(t.ds&&t.ds.cohort&&t.ds.cohort.annotation&&t.ds.cohort.key4annotation&&t.ds.cohort.sampleattribute&&t.ds.cohort.sampleattribute.runtimelst){let e=0;for(const s of t.ds.cohort.sampleattribute.runtimelst){if(s.key&&s.key.hiddenvalues){e+=s.key.hiddenvalues.size}}if(e>0){if(t.ds.vcfcohorttrack);else if(i.sampledata){let e=0;for(const s of i.sampledata){if(!O(s.genotype,i.alt)){continue}const o=s.sampleobj[t.ds.cohort.key4annotation];if(o){const e=t.ds.cohort.annotation[o];if(e){let s=false;for(const o of t.ds.cohort.sampleattribute.runtimelst){const t=e[o.key.k];if(t!=undefined){if(o.key.hiddenvalues.has(t)){s=true;break}}}if(s){continue}}}e++}if(e==0){continue}}else{const e=i[t.ds.cohort.key4annotation];if(e){const s=t.ds.cohort.annotation[e];if(s){let e=false;for(const o of t.ds.cohort.sampleattribute.runtimelst){const t=s[o.key.k];if(t!=undefined){if(o.key.hiddenvalues.has(t)){e=true;break}}}if(e){continue}}}}}}if(!i.chr){a++;continue}if(!Number.isInteger(i.pos)){o++;continue}const l=e.seekcoord(i.chr,i.pos);if(l.length==0){n.push(i);continue}if(l.length==1){i.__x=l[0].x}else{i.__x=l[0].x}if(i.__x<-1\|\|i.__x>e.width+1){continue}r.push(i)}const i=[];t.tklabel.each((function(){i.push(this.getBBox().width)}));if(r.length==0){t.label_mcount.text("")}else{t.label_mcount.text(r.length<t.mlst.length?r.length+" of "+t.mlst.length+" "+t.itemlabelname+"s":r.length+" "+t.itemlabelname+(r.length>1?"s":"")).each((function(){i.push(this.getBBox().width)}))}if(t.label_stratify){for(const e of t.label_stratify){let s;if(e.bycohort){const e=new Set;for(const s of r){let o="";for(const e of t.ds.cohort.levels){const t=s[e.k];if(t){o+=t}}e.add(o)}s=e.size}else{const t=new Set;for(const s of r){let o=s[e.attr1.k];if(!o)continue;if(e.attr2){const t=s[e.attr2.k];if(t){o+=t}}if(e.attr3){const t=s[e.attr3.k];if(t){o+=t}}t.add(o)}s=t.size}if(s==0){e.svglabel.text("")}else{e.svglabel.text(s+" "+e.label+(s>1?"s":"")).each((function(){i.push(this.getBBox().width)}))}}}t.leftLabelMaxwidth=Math.max(...i);if(o+a>0){e.tkerror(t,o+a+" items have no chromosome or genomic position")}if(n.length){console.error(n.length+" items not mapped to any region");for(const t of n)console.log(t)}return r}function De(t,e){for(const s of t.data){if(s.isbin){let t=0;for(const o of s.mlst){const s=e.seekcoord(o.chr,o.pos);if(o.usehitidx!=undefined&&s[o.usehitidx]){t+=s[o.usehitidx].x}else if(s.length==1){t+=s[0].x}else{console.log("cannot map item");console.log(o)}}s.x0=t/s.mlst.length;s.x=s.x0+(s.xoffset!=undefined?s.xoffset:0)}else{const t=e.seekcoord(s.chr,s.pos);if(t.length>0){s.x0=t[0].x;s.x=s.x0+(s.xoffset!=undefined?s.xoffset:0)}else{console.log("cannot map group of item");console.log(s)}}}}function Le(t,e){t.height_main=t.toppad+e.labelfontsize+t.bottompad;if(t.label_mcount&&t.label_mcount.text().length>0){t.height_main+=t.labyspace+e.labelfontsize}if(t.label_stratify){for(const s of t.label_stratify){if(s.svglabel.text().length>0){t.height_main+=t.labyspace+e.labelfontsize}}}t.glider.selectAll("").remove();t.leftaxis.selectAll("").remove();if(t.viewrangeupperlimit_above){e.tkerror(t,t.name+": zoom in under "+T(t.viewrangeupperlimit)+" to view data")}else{let s;if(!t.skewer.data\|\|t.skewer.data.length==0){if(e.pannedpx!=undefined\|\|e.zoomedin==true){s="view range"}else if(e.usegm&&e.gmmode!="genomic"){s=e.usegm.name\|\|e.usegm.isoform}}e.tkerror(t,t.name+": no mutation in "+s)}if(t.hlaachange){ze(t,e);delete t.hlaachange}}function Ee(t,e){if(!t.stratifycount)return;for(const[s,o]of t.stratifycount){const t=e.label_stratify.find((t=>t.label==s));if(!t){console.error("unknown strat label: "+s);continue}t.servercount=o}}const Ue=new H({padding:"0px"});function Ge(t,e){const s=t.legend.holder.append("tr");const o=s.append("td").text(e).style("padding-right","10px").style("text-align","right").style("color","#555").style("border-right","solid 1px "+t.legend.legendcolor);const a=s.append("td");return[s,a,o]}function Ve(t){if(!t.legend){return}const e=new Set;for(const[s,o]of t.legend.mclasses){if(o.hidden){e.add(s)}}const s=new Map;for(const e of t.tklst){if(e.hidden\|\|e.type!=D.ds)continue;if(!e.mlst){continue}for(const t of e.mlst){if(t.class){if(!s.has(t.class)){s.set(t.class,{count:0})}s.get(t.class).count++}}}const o=[];for(const[t,a]of s){if(e.has(t)){s.get(t).hidden=true}o.push({key:t,count:a.count})}t.legend.mclasses=s;if(s.size==0){t.legend.tr_mclass.style("display","none");return}t.legend.tr_mclass.style("display","table-row");o.sort(((t,e)=>e.count-t.count));t.legend.td_mclass.selectAll("").remove();for(const s of o){const o=t.legend.td_mclass.append("div").style("display","inline-block").style("white-space","nowrap").style("padding",t.legend.vpad+" 20px "+t.legend.vpad+" 0px").classed("sja_clb",true).on("click",(()=>{Ue.clear();Ue.showunder(o.node());Ue.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show alone').on("click",(()=>{Ue.hide();t.pannedpx=undefined;for(const e of t.legend.mclasses.values()){e.hidden=true}t.legend.mclasses.get(s.key).hidden=false;for(const e of t.tklst){if(!e.hidden&&e.type==D.ds){fe(e,t)}}}));if(t.legend.mclasses.get(s.key).hidden){Ue.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show').on("click",(()=>{Ue.hide();t.pannedpx=undefined;t.legend.mclasses.get(s.key).hidden=false;for(const e of t.tklst){if(!e.hidden&&e.type==D.ds){fe(e,t)}}}))}else{Ue.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">×</div> hide').on("click",(()=>{Ue.hide();t.pannedpx=undefined;t.legend.mclasses.get(s.key).hidden=true;for(const e of t.tklst){if(!e.hidden&&e.type==D.ds){fe(e,t)}}}))}if(e.size>1){Ue.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show all').on("click",(()=>{Ue.hide();t.pannedpx=undefined;for(const e of t.legend.mclasses.values()){e.hidden=false}for(const e of t.tklst){if(!e.hidden&&e.type==D.ds){fe(e,t)}}}))}const a=Ue.d.append("div").style("margin","20px");a.append("div").text(f[s.key].label.toUpperCase()).style("color",f[s.key].color).style("font-size",".8em");a.append("div").html(f[s.key].desc).style("color","#858585").style("font-size",".8em").style("width","210px")}));o.append("div").style("display","inline-block").style("background-color",f[s.key].color).style("margin-right","5px").style("border-radius","15px").style("padding","4px 8px").style("color","white").style("font-size",".8em").text(s.count);const a=o.append("div").style("display","inline-block").style("color",f[s.key].color).text(f[s.key].label);if(e.has(s.key)){a.style("text-decoration","line-through")}}}function Oe(t){if(!t.legend){return}const e=new Set;for(const[s,o]of t.legend.morigins){if(o.hidden){e.add(s)}}const s=new Map;for(const o of t.tklst){if(o.hidden\|\|o.type!=D.ds)continue;if(!o.mlst){continue}for(const t of o.mlst){if(!t.origin)continue;if(!s.has(t.origin)){let o=false;if(L[t.origin]&&L[t.origin].hidden){o=true;e.add(t.origin)}s.set(t.origin,{count:0,hidden:o})}s.get(t.origin).count++}}const o=[];for(const[t,a]of s){if(e.has(t)){s.get(t).hidden=true}o.push({key:t,count:a.count})}t.legend.morigins=s;if(s.size==0){t.legend.tr_morigin.style("display","none");return}t.legend.tr_morigin.style("display","table-row");o.sort(((t,e)=>e.count-t.count));t.legend.td_morigin.selectAll("*").remove();for(const s of o){const o=t.legend.td_morigin.append("div").style("display","inline-block").style("white-space","nowrap").style("padding",t.legend.vpad+" 20px "+t.legend.vpad+" 0px").classed("sja_clb",true).on("click",(()=>{Ue.clear();Ue.showunder(o.node());Ue.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show alone').on("click",(()=>{Ue.hide();t.pannedpx=undefined;for(const e of t.legend.morigins.values()){e.hidden=true}t.legend.morigins.get(s.key).hidden=false;L[s.key].hidden=false;for(const e of t.tklst){if(!e.hidden&&e.type==D.ds){fe(e,t)}}}));if(t.legend.morigins.get(s.key).hidden){Ue.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show').on("click",(()=>{Ue.hide();t.pannedpx=undefined;t.legend.morigins.get(s.key).hidden=false;L[s.key].hidden=false;for(const e of t.tklst){if(!e.hidden&&e.type==D.ds){fe(e,t)}}}))}else{Ue.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">×</div> hide').on("click",(()=>{Ue.hide();t.pannedpx=undefined;t.legend.morigins.get(s.key).hidden=true;for(const e of t.tklst){if(!e.hidden&&e.type==D.ds){fe(e,t)}}}))}if(e.size>1){Ue.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">✓</div> show all').on("click",(()=>{Ue.hide();t.pannedpx=undefined;for(const e of t.legend.morigins.values()){e.hidden=false}for(const e of t.tklst){if(!e.hidden&&e.type==D.ds){fe(e,t)}}}))}const a=Ue.d.append("div").style("margin","20px");a.append("div").text(L[s.key].label.toUpperCase()).style("color",L[s.key].color).style("font-size",".8em");a.append("div").html(L[s.key].desc).style("color","#858585").style("font-size",".8em").style("width","210px")}));o.append("svg").style("margin-right","5px").attr("width",19).attr("height",19).html(L[s.key].legend);const a=o.append("div").style("display","inline-block").style("color","#858585").text(L[s.key].label+", "+s.count);if(e.has(s.key)){a.style("text-decoration","line-through")}}}export{fe as a,ht as b,bt as c,ne as d,yt as e,_e as f,mt as g,he as h,$ as i,Ve as j,Oe as k,Ge as l,Ut as m,gt as r,ye as s};