@sjcrh/proteinpaint-client 2.63.0 → 2.63.2

package/dist/{tk-6a8e5bb0.js → tk-741d4674.js}

@@ -1 +1 @@
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e){const[e,a]=s.addRow();e.text(t.k);a.text(t.v)}}else{console.log("unknown return value")}return}const[n,i]=s.addRow();n.text(a.label);i.text(t.__value_missing?"NA":t.__value_use)}function yt(t,e,s){if(!t.htmlSections)return;if(!Array.isArray(t.htmlSections))throw"htmlSections[] is not array";for(const e of t.htmlSections){const[t,a]=s.addRow();if(e.key&&e.html){t.text(e.key);a.html(e.html)}}}function kt(t,e,s,a,n){if(!e){a.append("span").text(s);return}if(e.urlBase){a.append("a").text(s).attr("href",e.urlBase+s).attr("target","_blank");return}const i=a.append("span").text(s);if(e&&e.categories){const t=e.categories[s];if(t){i.style("padding","1px 4px").style("background",t.color);if(t.textcolor){i.style("color",t.textcolor)}}}}function xt(t,e){t.append("span").text(e.mname);t.append("span").style("margin-left","5px").style("color",i[e.class].color).style("font-size",".8em").text(i[e.class].label.toUpperCase())}function _t(t,e,s,a){const n=t.append("span").text(`${e.chr}:${e.pos+1} 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Mt(t,e){if(t.a.name)e.append("span").text(t.a.name).style("font-weight","bold").style("margin-right","5px");e.append("span").text(`${t.a.chr}:${t.a.pos} ${t.a.strand=="+"?"forward":"reverse"} > ${t.b.chr}:${t.b.pos} ${t.b.strand=="+"?"forward":"reverse"}`);if(t.b.name)e.append("span").text(t.b.name).style("font-weight","bold").style("margin-left","5px")}async function St(t,e,s){const a=e.append("div").text("Loading...");try{if(!t.pairlst)throw".pairlst[] missing";const n={a:{chr:t.pairlst[0].a.chr,position:t.pairlst[0].a.pos,strand:t.pairlst[0].a.strand},b:{chr:t.pairlst[0].b.chr,position:t.pairlst[0].b.pos,strand:t.pairlst[0].b.strand}};await Ct(n.a,s);await Ct(n.b,s);a.remove();const i=await import("./svgraph-3c5cd8d2.js");i.default({pairlst:[n],genome:s.genome,holder:e})}catch(t){a.text(t.message||t)}}async function Ct(t,e){const s=await u("isoformbycoord",{body:{genome:e.genome.name,chr:t.chr,pos:t.position}});if(s.error)throw s.error;const a=s.lst.find((t=>t.isdefault))||s.lst[0];if(a){t.name=a.name;t.gm={isoform:a.isoform}}}function qt(t,e,s){if(!e.mds.queries?.ld)return;const[a,n]=s.addRow();a.text("LD overlay");const i=e.mds.queries.ld.mOverlay?.m;if(i){const s=n.append("div").style("margin-bottom","5px");if(t.ssm_id==i.ssm_id){s.html(e.mds.queries.ld.mOverlay.ldtkname+" r<sup>2</sup> values against this variant are displayed on all the other variants.")}else{let a=null;for(const s of e.mds.queries.ld.mOverlay.data||[]){if(s.pos==t.pos&&s.alleles==t.ref+"."+t.alt){a=s.r2;break}}if(a==null){s.html("No r<sup>2</sup> value is found.")}else{s.html(e.mds.queries.ld.mOverlay.ldtkname+" r<sup>2</sup> = "+a)}}}n.append("div").html("Click a button to overlay LD r<sup>2</sup> values against this variant:").style("font-size",".8em").style("opacity",.5);for(const s of e.mds.queries.ld.tracks){const a=n.append("button").text(s.name);if(i&&i.ssm_id==t.ssm_id){if(s.name==e.mds.queries.ld.mOverlay.ldtkname){a.property("disabled",true);continue}}a.on("click",(()=>{e.itemtip.hide();e.mds.queries.ld.mOverlay={ldtkname:s.name,m:{chr:t.chr,pos:t.pos,ref:t.ref,alt:t.alt,ssm_id:t.ssm_id}};e.load()}))}}async function Lt(t){const e=t.div.append("div").text("Loading...").style("padding","10px").style("color","#8AB1D4").style("font-size","1.25em").style("font-weight","bold");t.tid2value_orig=new Set;if(t.tid2value)Object.keys(t.tid2value).forEach(t.tid2value_orig.add,t.tid2value_orig);try{t.querytype=t.tk.mds.variant2samples.type_samples;const s=await t.tk.mds.variant2samples.get(t);await zt(s.samples,t);e.remove()}catch(t){e.text("Error: "+(t.message||t));if(t.stack)console.log(t.stack)}}async function zt(t,e){if(t.length==1){return await $t(t[0],e)}const[s,a]=await Tt(t,e.tk);const n={rows:a,columns:s,div:e.div,resize:a.length>10,dataTestId:"sjpp_mds3tk_sampletable"};n.columnButtons=[];if(e.tk.mds.queries?.singleSampleMutation){const s={text:"Disco",dataTestId:"sja_sample_table_disco_button",callback:async(s,a)=>{e.tk.itemtip.hide();e.tk.menutip.hide();let n;if(t[a].ssm_id_lst?.[0]){n=(e.tk.skewer.rawmlst||e.tk.custom_variants).find((e=>e.ssm_id==t[a].ssm_id_lst[0]))}await It(e.tk,e.block,t[a],n)}};n.columnButtons.push(s)}if(e.tk.mds.queries?.singleSampleGenomeQuantification){for(const s in e.tk.mds.queries.singleSampleGenomeQuantification){const a={text:s,dataTestId:`${s}_button`,callback:async(a,n)=>{const i=h(e.tk.newChartHolder||e.block.holder0);i.header.text(t[n].sample_id);await(await import("./plot.ssgq-9d364d41.js")).plotSingleSampleGenomeQuantification(e.tk.mds,e.tk.mds.label,s,t[n],i.body.append("div").style("margin","20px"),e.block.genome,e.block.usegm?.name)}};n.columnButtons.push(a)}}if(e.tk.allow2selectSamples){n.buttons=[{text:e.tk.allow2selectSamples.buttonText,class:e.tk.allow2selectSamples.class,callback:s=>{Nt(e.tk,e.block,t,s);e.tk.itemtip.hide();e.tk.menutip.hide()}}]}return R(n)}async function Nt(t,e,s,a){const n=[...s];const i=a.map((t=>n[t]));t.allow2selectSamples.callback({samples:await t.mds.termdb.vocabApi.convertSampleId(i,t.allow2selectSamples.attributes),source:"Samples with "+Dt(e)})}async function $t(t,e){const s=e.singleSampleDiv||m({holder:e.div});if(t.sample_id){const[a,n]=s.addRow();a.text(e.tk.mds.termdbConfig?.lollipop?.sample||"Sample");let i;if(t.ssm_id_lst?.[0]){i=e.tk.skewer.rawmlst.find((e=>e.ssm_id==t.ssm_id_lst[0]))}Rt(t,e.tk,n,e.block,i)}if("caseIsOpenAccess"in t){const[e,a]=s.addRow();e.text("Access");a.text(t.caseIsOpenAccess?"Open":"Controlled")}if(e.tk.mds.variant2samples.twLst){for(const a of e.tk.mds.variant2samples.twLst){const[e,n]=s.addRow();e.text(a.term.name).style("text-overflow","ellipsis");n.style("text-overflow","ellipsis");if(a.term.id in t){if(Array.isArray(t[a.term.id])){if(a.baseURL){n.html(t[a.term.id].map((t=>`<a href=${a.baseURL+t} target=_blank>${t}</a>`)).join("<br>"))}else{n.html(t[a.term.id].join("<br>"))}}else{const e=Ot(t,a);if(a.baseURL){n.html(`<a href=${a.baseURL+e} target=_blank>${e}</a>`)}else{n.text(e)}}}}}if(t.ssmid2format){for(const a of t.ssm_id_lst){if(t.ssm_id_lst.length>1){const[t,n]=s.addRow();n.style("padding-top","20px");const i=e.tk.skewer.rawmlst.find((t=>t.ssm_id==a));if(i){if(i.dt==f){_t(n,i,e.tk,e.block)}else if(i.dt==r||i.dt==l){Mt(i.pairlst[0],n)}else{n.text(a)}}else{n.text(a)}}for(const n in t.ssmid2format[a]){const i=t.ssmid2format[a][n];const[o,r]=s.addRow();const l=e.tk.mds?.bcf?.format?.[n];o.text(l&&l.Description||n);r.html(Ft(l,i))}}}}function Ot(t,e){if(!(e.term.id in t))return"";const s=t[e.term.id];if(e.term.values?.[s]?.label)return e.term.values[s].label;const a=e.term.valueConversion;if(a)return p(s,a.fromUnit,a.toUnit,a.scaleFactor);return s}function Rt(t,e,s,a,n){const i=e.mds.termdbConfig?.urlTemplates?.sample;if(i){const e=s.append("a");e.attr("href",i.base+(t[i.namekey]||t.sample_id));e.attr("target","_blank");e.text(t.sample_id);e.style("word-break","break-word")}else{s.append("span").attr("class","pp_mds3_singleSampleNameSpan").text(t.sample_id)}const o=s.append("div");if(e.allow2selectSamples){const s=e.allow2selectSamples.buttonText;const n=o.append("button").style("margin-right","10px").text(s.endsWith("s")?s.substring(0,s.length-1):s).on("click",(()=>{Nt(e,a,[t],[0]);e.itemtip.hide();e.menutip.hide()}));if(e.allow2selectSamples.class)n.attr("class",e.allow2selectSamples.class)}if(e.mds.queries?.singleSampleMutation){o.append("button").style("margin-right","10px").text("Disco plot").attr("data-testid","proteinpaint_disc_table_disco_button").on("click",(async()=>{e.itemtip.hide();await It(e,a,t,n)}))}if(e.mds.queries?.singleSampleGenomeQuantification){for(const s in e.mds.queries.singleSampleGenomeQuantification){o.append("button").text(s).on("click",(async()=>{const n=h(e.newChartHolder||a.holder0);n.header.text(t.sample_id);await(await import("./plot.ssgq-9d364d41.js")).plotSingleSampleGenomeQuantification(e.mds,e.mds.label,s,t,n.body.append("div").style("margin","20px"),a.genome,a.usegm?.name)}))}}}async function It(t,e,s,a){const n=h(t.newChartHolder||e.holder0);const i=[s.sample_id];if(a){i.push(", with ");if(e.usegm){i.push(e.usegm.name)}else{i.push(a.isoform)}i.push(" "+a.mname)}n.header.text(i.join(""));try{(await import("./plot.disco-70d493f4.js")).default(t.mds,t.mds.label,s,n.body,e.genome,{downloadImgName:i.join("")+" Disco",Disco:{prioritizeGeneLabelsByGeneSets:true}})}catch(t){n.body.append("div").text("Error: "+(t.message||t));if(t.stack)console.log(t.stack)}}async function Tt(t,e){const s=t.some((t=>"caseIsOpenAccess"in t)),a=t.some((t=>t.ssm_id))||t.some((t=>t.ssm_id_lst)),n=t.some((t=>t.ssmid2format))&&e.mds?.bcf?.format;const o=new Set;const c=[{label:e.mds.termdbConfig?.lollipop?.sample||"Sample"}],d=[];if(s){c.push({label:"Access"})}if(e.mds.variant2samples.twLst){for(const t of e.mds.variant2samples.twLst){const e={label:t.term.name};c.push(e)}}if(a){c.push({label:"Mutations",isSsm:true})}if(n){for(const e of t){if(!e.ssmid2format)continue;for(const t in e.ssmid2format){for(const s in e.ssmid2format[t])o.add(s)}}for(const t in e.mds.bcf.format){if(!o.has(t))continue;const s=e.mds.bcf.format[t];c.push({label:s.Description||t})}}for(const c of t){const t=[{value:c.sample_id}];let m=c.ssm_id_lst;if(!m&&c.ssm_id)m=[c.ssm_id];{const s=e.mds.termdbConfig?.urlTemplates?.sample;if(s){t[0].url=s.base+(c[s.namekey]||c.sample_id)}}if(s){t.push({value:c.caseIsOpenAccess?"Open":"Controlled"})}if(e.mds.variant2samples.twLst){for(const s of e.mds.variant2samples.twLst){const e=Ot(c,s);if(s.baseURL){t.push({html:`<a href=${s.baseURL+e} target=_blank>${e}</a>`})}else{t.push({value:e})}}}if(a){if(m){const s=[];for(const t of m){const a=[];const n=(e.skewer.rawmlst||e.custom_variants).find((e=>e.ssm_id==t));if(n){if(n.dt==f){if(e.mds.queries&&e.mds.queries.snvindel&&e.mds.queries.snvindel.url){a.push(`<a href=${e.mds.queries.snvindel.url.base+n.ssm_id} target=_blank>${n.mname}</a>`)}else{a.push(n.mname)}}else if(n.dt==r||n.dt==l){const t=n.pairlst[0];a.push(`${t.a.name||""} ${t.a.chr}:${t.a.pos} ${t.a.strand=="+"?"forward":"reverse"} > ${t.b.name||""} ${t.b.chr}:${t.b.pos} ${t.b.strand=="+"?"forward":"reverse"}`)}else{throw"unknown dt"}a.push(`<span style="color:${g(i[n.class].color).darker()};font-size:0.8em;">${i[n.class].label}</span>`);s.push(a.join(" "))}else{s.push(t)}}t.push({html:s.join("<br>")})}else{t.push({value:""})}}if(n){if(!m)throw"ssm_id_lst missing, cannot show format";for(const s in e.mds.bcf.format){if(!o.has(s))continue;if(!c.ssmid2format){t.push({value:""});continue}const a=e.mds.bcf.format[s];const n=[];for(const t of m){const e=c.ssmid2format?.[t]?.[s];n.push(Ft(a,e))}t.push({html:n.join("<br>")})}}d.push(t)}return[c,d]}function Ft(t,e){if(t&&e&&t.Number=="R"&&t.Type=="Integer"){const t=e.split(",").map(Number);if(t.length==2){const[e,s]=t;if(e>=0&&s>=0&&e+s>0){return`${b(null,{f:s/(s+e)})} <span style="font-size:.8em">${s}/${s+e}</span>`}}}return e}function Dt(t){if(t.gmmode=="genomic"){const e=t.rglst[0];return"mutations from "+e.chr+":"+e.start+"-"+e.stop}if(t.usegm)return"mutations in "+t.usegm.name;return"mutations"}const Bt=10;async function Gt(t,e,s,a,n){try{if(e.click_snvindel){e.skewer.hlssmid=new Set(t.mlst.map((t=>t.ssm_id)));ie(e);e.click_snvindel(t.mlst[0]);return}if("occurrence"in t&&t.occurrence>=Bt&&e.mds.variant2samples&&e.mds.variant2samples.sunburst_twLst){await Ht(t,e,s,a);return}await Ut({mlst:t.mlst,tk:e,block:s,tippos:a})}catch(t){s.error(t.message||t);if(t.stack)console.log(t.stack)}}async function Ht(t,e,s,a){e.glider.style("cursor","wait");const n=await e.mds.variant2samples.get({mlst:t.mlst,querytype:e.mds.variant2samples.type_sunburst});e.glider.style("cursor","auto");const i={nodes:n.nodes,occurrence:t.occurrence,boxyoff:e.yoff,boxheight:Math.min(800,e.height),boxwidth:s.width,svgheight:Number.parseFloat(s.svg.attr("height")),g:e.skewer.g.append("g"),pica:e.pica,click_listbutton:(n,i)=>{Ut({mlst:t.mlst,tk:e,block:s,tippos:a})},click_ring:async(a,n)=>{e.itemtip.clear();const i={mlst:t.mlst,tk:e,block:s,div:e.itemtip.d,tid2value:{}};i.tid2value[n.data.id0]=n.data.v0;if(n.data.id1)i.tid2value[n.data.id1]=n.data.v1;if(n.data.id2)i.tid2value[n.data.id2]=n.data.v2;i.mlst=t.mlst.map((t=>{if(e.mds.variant2samples.variantkey=="ssm_id"){return{ssm_id:t.ssm_id,occurrence:0}}throw"unknown variant2samples.variantkey"}));i.mlst[0].occurrence=n.value;const o=a.clientX;const r=a.clientY;await Lt(i);e.itemtip.show2(o,r)}};if(t.aa){i.cx=t.aa.x;i.cy=Jt(t,e)+t.yoffset*(e.skewer.pointup?-1:1)}else{i.cx=t.x;i.cy=t.y+(e.skewer.pointup?1:-1)*e.skewer.stem1/2}if(t.mlst.length==1){i.chartlabel=t.mlst[0].mname}else{const e=new Set(t.mlst.map((t=>t.mname)));if(e.size==1){i.chartlabel=[...e][0]}else{i.chartlabel=t.mlst.reduce(((t,e)=>e.occurrence>t.occurrence?e:t)).mname+" etc"}}const o=await import("./sunburst-452df940.js");o.default(i)}async function Ut(t){t.tk.itemtip.clear().show(t.tippos.left-10,t.tippos.top-10);t.div=t.tk.itemtip.d;t.tipDiv=t.tk.itemtip.d;await pt(t)}const Pt=0;const Et=1;const Vt=.3;const Kt=1;const Wt=.6;const Xt="Arial";function Qt(t,e){const s=t.skewer;for(const t of s.data){t.x0=t.x;if(t.xoffset!=undefined){t.x=t.x0+t.xoffset}for(const e of t.groups){e.aa=t}}const a=Math.max(14,e.width/110);let n=0;for(const t of s.data){for(const e of t.groups){n=Math.max(n,e.occurrence)}}let i=0;const o=Math.pow(a/2,2)*Math.PI;if(n<=10)i=o*n*.9;else if(n<=100)i=o*10;else if(n<=1e3)i=o*14;else i=o*20;const c=d().domain([1,n*.5,n*.6,n*.7,n*.8,n]).range([o,o+(i-o)*.8,o+(i-o)*.85,o+(i-o)*.9,o+(i-o)*.95,i]);let m=a/2;s.maxheight=0;for(const t of s.data){if(t.showmode==undefined)t.showmode=Pt;if(t.slabelrotate==undefined)t.slabelrotate=false;t.maxradius=0;t.maxrimwidth=0;t.width=0;t.slabelwidth=0;for(const e of t.groups){if(e.occurrence<=1){e.radius=a/2}else{const t=e.occurrence.toString().length;e.radius=Math.max(Math.sqrt(c(e.occurrence)/Math.PI),t*5)}t.maxradius=Math.max(t.maxradius,e.radius);m=Math.max(m,e.radius);e.rimwidth=e.rim1count+e.rim2count==0?0:Math.max(2,e.radius/6);t.maxrimwidth=Math.max(t.maxrimwidth,e.rimwidth)}let e=0;for(const s of t.groups){s.yoffset=e+s.radius+s.rimwidth;e+=(s.radius+s.rimwidth)*2}s.maxheight=Math.max(s.maxheight,e)}s.selection=s.g.selectAll().data(s.data).enter().append("g").attr("class","sja_skg").each((function(t){t.skewer=this}));const u=s.selection.selectAll().data((t=>t.groups)).enter().append("g").attr("transform",(e=>"translate(0,"+(e.aa.showmode==Pt?0:e.yoffset*(t.skewer.pointup?-1:1))+")")).attr("class","sja_aa_discg").each((function(t){t.g=this}));const p=u.append("circle");p.filter((t=>t.dt==f||t.dt==r||t.dt==l)).attr("fill",(e=>t.color4disc(e.mlst[0]))).attr("stroke","white").attr("r",(t=>t.radius-.5));u.filter((t=>t.dt==l||t.dt==r)).append("path").attr("fill","white").attr("stroke","none").attr("d",(t=>I()({innerRadius:0,outerRadius:t.radius-2,startAngle:t.useNterm?0:Math.PI,endAngle:t.useNterm?Math.PI:Math.PI*2})));const h=u.filter((t=>t.occurrence>1)).append("text").text((t=>t.occurrence)).attr("font-family",Xt).attr("class","sja_aa_discnum").attr("fill-opacity",(t=>t.aa.showmode==Pt?0:1)).attr("stroke-opacity",(t=>t.aa.showmode==Pt?0:1)).attr("text-anchor","middle").each((t=>{const 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t.mlst){if(!o.has(e.dt))o.set(e.dt,[]);o.get(e.dt).push(e)}}if(t.cnv?.cnvLst){o.set(s,t.cnv.cnvLst)}if(o.size==1){const e=t.menutip.d.append("div").style("margin","10px");await pt({div:e,mlst:o.get([...o.keys()][0]),tk:t,block:a,doNotListSample4multim:true});return}const r=[];for(const[t,s]of o){r.push({label:s.length+" "+e[t]})}new A({holder:t.menutip.d.append("div").attr("class","sja_pp_vlb_dttabdiv").style("margin","10px"),tabs:r}).main();let l=0;for(const[e,s]of o){pt({div:r[l++].contentHolder.append("div").style("margin-left","10px"),mlst:s,tk:t,block:a,doNotListSample4multim:true})}}function He(t,e){if(!t.skewer)return;if(t.skewer.viewModes.length<=1){return}const s=[];for(const[e,a]of t.skewer.viewModes.entries()){const t={label:Ue(a),value:e};if(a.inuse)t.checked=true;s.push(t)}D({holder:t.menutip.d.append("div").attr("class","sja_pp_vlb_viewmoderadiodiv").style("margin","10px"),options:s,callback:async s=>{for(const e of 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t;e.menutip=new t({padding:""});e.load=_s(e,s);e.mnamegetter=t=>{if(e.mds.queries?.snvindel?.vcfid4skewerName&&t.vcf_id)return t.vcf_id;const s=t.mname;if(!s)return"";if(s.length>25){return s.substr(0,20)+"..."}return s};await hs(e,s);await bs(e,s);await ys(e,s);ws(e,s);vs(e,s);fs(e);ms(e);await zs(e);e.tklabel.text(e.mds.label||e.name);e.clear=()=>{if(e.skewer)e.skewer.g.selectAll("*").remove()};X(e,s);ps(e);e.color4disc=t=>{if(e.mutationColorBy){if(e.mutationColorBy=="hardcode"){if(t.color)return t.color}}if(e.mds.queries?.ld?.mOverlay?.data){const s=e.mds.queries.ld.mOverlay.m;if(t.chr==s.chr&&t.pos==s.pos&&t.ref==s.ref&&t.alt==s.alt){return e.mds.queries.ld.overlay.color_1}for(const s of e.mds.queries.ld.mOverlay.data){if(s.pos==t.pos&&s.alleles==t.ref+"."+t.alt){return e.mds.queries.ld.colorScale(s.r2)}}return e.mds.queries.ld.overlay.color_0}if(e.vcfinfofilter&&e.vcfinfofilter.setidx4mclass!=undefined){const s=e.vcfinfofilter.lst[e.vcfinfofilter.setidx4mclass];const[a,n]=js(s,t);if(a||n==undefined)return"black";for(const t of n){if(s.categories[t]){return s.categories[t].color}else{return"black"}}}if(i[t.class]){return i[t.class].color}return"black"};ds(e);if(e.hlssmid){e.skewer.hlssmid=new Set(e.hlssmid.split(","));delete e.hlssmid}try{Ls(e)}catch(t){console.error(t)}}function cs(t,e){return s=>{t.legend?.headTd.text(t.name+(t.filterObj?" - "+ts(t.filterObj):""));if(t.cnv){t.cnv.g.transition().attr("transform",`translate(0,${t.subtk2height.skewer||0})`)}if(s){if(s.error){t.subtk2height.skewer=40}else{let a=0;if(s.skewer)a=s.skewer.length;if(s.cnv)a+=s.cnv.length;if(a==0){let s="view range";if(e.usegm&&e.gmmode!="genomic")s=e.usegm.name||e.usegm.isoform;t.skewer.g.append("text").text("No mutation in "+s).attr("y",25).attr("x",e.width/2).attr("text-anchor","middle").attr("dominant-baseline","center");t.subtk2height.skewer=40}}}t.height_main=Math.max(t.subtk2height.leftlabels||0,t.subtk2height.skewer+(t.subtk2height.cnv||0))+t.toppad+t.bottompad;if(s){st(s,t)}t.leftLabelMaxwidth=Math.max(t.leftlabels.maxwidth+t.leftlabels.xoff,t.skewer?t.skewer.maxwidth:0);e.tkcloakoff(t,{error:s?s.error:null});e.block_setheight();e.setllabel();if(typeof t.callbackOnRender=="function"){t.callbackOnRender(t,e)}}}function ds(t){const e=M();if(t.skewer){if(e.has("hlaachange")){t.hlaachange=e.get("hlaachange")}if(e.has("hlssmid")){t.hlssmid=e.get("hlssmid").split(",")}}}function fs(t){if(!t.mds.has_skewer)return;t.skewer={g:t.glider.append("g"),hlBoxColor:t.mds.hlBoxColor||"red",hideDotLabels:false,pointup:true};us(t)}function ms(t){const e=t.mds.termdbConfig?.queries?.cnv;if(!e)return;t.cnv={g:t.glider.append("g"),cnvMaxLength:e.cnvMaxLength,cnvGainCutoff:e.cnvGainCutoff,cnvLossCutoff:e.cnvLossCutoff,absoluteValueRenderMax:e.absoluteValueRenderMax||5,gainColor:e.gainColor||"#D6683C",lossColor:e.lossColor||"#67a9cf"}}function us(t){t.skewer.viewModes=t.skewerModes;delete t.skewerModes;if(!t.skewer.viewModes)t.skewer.viewModes=[];const e=t.skewer.viewModes;if(!Array.isArray(e))throw"skewerModes[] is not array";if(t.mds.skewerModes){for(const s of t.mds.skewerModes)e.push(s)}if(!e.find((t=>t.type=="skewer")))e.push({type:"skewer"});for(const t of e){if(typeof t!="object")throw"one of skewerModes[] is not object";if(t.type=="skewer"){if(!t.label)t.label="lollipops"}else if(t.type=="numeric"){if(t.byAttribute){if(!t.label)t.label=t.byAttribute}else if(t.byInfo);else{throw"unknown data method for a type=numeric mode"}}else{throw"unknown type from a skewerModes[]"}}if(!e.find((t=>t.inuse)))e[0].inuse=true}function ps(t){if(t.mds.hiddenmclass){for(const e of t.mds.hiddenmclass)t.legend.mclass.hiddenvalues.add(e)}}async function hs(t,e){if(t.dslabel){const s=await u("getDataset",{body:{genome:e.genome.name,dsname:t.dslabel}});if(s.error)throw"Error: "+s.error;if(!s.ds)throw"data.ds{} missing";t.mds=s.ds;t.name=s.ds.label;return}if(!t.name)t.name="Custom data";t.mds={};if(t.bcf){if(!t.bcf.file&&!t.bcf.url)throw"file or url missing for tk.bcf{}";t.mds.has_skewer=true;await qs(t,e.genome)}else if(t.custom_variants){t.mds.has_skewer=true;As(t,e);Cs(t)}else{throw"unknown data source for custom track"}gs(t)}function gs(t){if(!t.sampleAnnotation)return;if(!Array.isArray(t.sampleAnnotation.terms))throw"sampleAnnotation.terms is not array";if(!t.mds.termdb)t.mds.termdb={};t.mds.termdb.terms=t.sampleAnnotation.terms;t.mds.termdb.annotations=t.sampleAnnotation.annotations}async function bs(t,e){const s=t.mds.termdb;if(!s)return;{const a={};if(t.mds.label){a.vocab={genome:e.genome.name,dslabel:t.mds.label}}else if(s.terms){a.vocab={terms:s.terms,sampleannotation:s.annotations}}else{throw"do not know how to init vocab"}const n=await import("./FilterRxComp-0e75dd8d.js").then((function(t){return t.z}));s.vocabApi=n.vocabInit(a)}t.mds.termdbConfig=await s.vocabApi.getTermdbConfig();if(t.mds.termdb.allowCaseDetails){t.mds.termdb.allowCaseDetails.get=async t=>{}}}function ws(t,e){if(!t.mds.queries?.snvindel?.m2csq)return;t.mds.queries.snvindel.m2csq.get=async s=>{const a={genome:e.genome.name,dslabel:t.mds.label,m2csq:1};if(t.mds.queries.snvindel.m2csq.by=="ssm_id"){a.ssm_id=s.ssm_id}else{return{error:"unknown query method"}}const n={"Content-Type":"application/json",Accept:"application/json"};if(t.token)n["X-Auth-Token"]=t.token;return await u("mds3",{body:a,headers:n},{serverData:t.cache})}}function vs(t,e){if(!t.mds.queries?.singleSampleMutation)return;t.mds.queries.singleSampleMutation.get=async s=>{const a={genome:e.genome.name,dslabel:t.mds.label,sample:s};const n={"Content-Type":"application/json",Accept:"application/json"};if(t.token)n["X-Auth-Token"]=t.token;const i=await u("termdb/singleSampleMutation",{body:a,headers:n});if(i.error)throw i.error;if(!Array.isArray(i.mlst))throw"data.mlst is not array";return i.mlst}}async function ys(t,e){if(!t.mds.variant2samples)return;if(t.custom_variants){ks(t)}else{xs(t,e)}if(t.mds.variant2samples.twLst){if(!Array.isArray(t.mds.variant2samples.twLst))throw"v2s.twLst[] not array";if(!t.mds.termdb?.vocabApi)throw"mds.termdb.vocabApi should be present for initiating v2s.twLst";for(const e of t.mds.variant2samples.twLst)await E(e,t.mds.termdb.vocabApi)}}function ks(t,e){t.mds.variant2samples.get=e=>{if(e.querytype==t.mds.variant2samples.type_samples){const t=[];for(const s of e.mlst){if(!s.samples)continue;for(const e of s.samples){const a=JSON.parse(JSON.stringify(e));a.ssm_id=s.ssm_id;t.push(a)}}return{samples:t}}if(e.querytype==t.mds.variant2samples.type_summary){throw"todo: summary"}if(e.querytype==t.mds.variant2samples.type_sunburst){throw"todo: sunburst"}throw"unknown querytype"};t.mds.getSamples=()=>{const e=new Map;for(const s of t.custom_variants){if(!s.samples)continue;for(const t of s.samples){if(e.has(t.sample_id)){e.get(t.sample_id).ssm_id_lst.push(s.ssm_id)}else{const a=JSON.parse(JSON.stringify(t));a.ssm_id_lst=[s.ssm_id];e.set(t.sample_id,a)}}}return{samples:[...e.values()]}}}function xs(t,e){t.mds.variant2samples.get=async s=>{const a={genome:e.genome.name,variant2samples:1,get:s.querytype};if(t.mds.label){a.dslabel=t.mds.label}else if(t.bcf){if(t.bcf.file)a.bcffile=t.bcf.file;else if(t.bcf.url)a.bcfurl=t.bcf.url;else throw"tk.bcf{}: file/url missing"}else{throw"no dslabel or tk.bcf"}if(s.groupSsmBySample){a.groupSsmBySample=1}if(s.mlst){if(t.mds.variant2samples.variantkey=="ssm_id"){a.ssm_id_lst=s.mlst.map((t=>t.ssm_id)).join(",")}else{throw"unknown variantkey for variant2samples"}}if(s.isoform){a.isoform=s.isoform}if(s.rglst){a.rglst=s.rglst}const n={"Content-Type":"application/json",Accept:"application/json"};if(t.set_id)a.set_id=t.set_id;if(t.token)n["X-Auth-Token"]=t.token;if(t.filter0)a.filter0=t.filter0;if(t.filterObj)a.filterObj=t.filterObj;if(s.tid2value)a.tid2value=s.tid2value;if(s.querytype==t.mds.variant2samples.type_sunburst){if(t.mds.variant2samples.sunburst_twLst){a.twLst=t.mds.variant2samples.sunburst_twLst}}else if(s.querytype==t.mds.variant2samples.type_samples){if(t.mds.variant2samples.twLst)a.twLst=t.mds.variant2samples.twLst}else if(s.querytype==t.mds.variant2samples.type_summary){if(t.mds.variant2samples.twLst)a.twLst=t.mds.variant2samples.twLst}else{throw"unknown querytype"}a.skewerRim=t.mds.queries.snvindel?.skewerRim;if(t.legend.formatFilter){const e={};for(const s in t.legend.formatFilter){if(t.legend.formatFilter[s].hiddenvalues.size){e[s]=[...t.legend.formatFilter[s].hiddenvalues]}}if(Object.keys(e).length){a.formatFilter=e}}if(t.legend.mclass?.hiddenvalues?.size){a.hiddenmclasslst=[...t.legend.mclass.hiddenvalues].join(",")}const i=await u("mds3",{body:a,headers:n},{serverData:t.cache});if(i.error)throw i.error;const o=i.variant2samples;if(!o)throw"result error";if(s.querytype==t.mds.variant2samples.type_sunburst){if(!Array.isArray(o.nodes))throw"nodes[] not array from return"}else if(s.querytype==t.mds.variant2samples.type_samples){if(!Array.isArray(o.samples))throw"samples[] not array from return"}else if(s.querytype==t.mds.variant2samples.type_summary){if(!Array.isArray(o.summary))throw"summary[] not array from return"}else{throw"unknown querytype"}return o};t.mds.getSamples=async(s={})=>{if(s.isSummary){s.querytype=t.mds.variant2samples.type_summary}else{s.querytype=t.mds.variant2samples.type_samples;s.groupSsmBySample=1}Ds(t,e,s);return await t.mds.variant2samples.get(s)}}function _s(t,e){return async()=>await Is(t,e)}function js(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 a=Array.isArray(s)?s:[s];if(t.altalleleinfo.separator){a=a[0].split(t.altalleleinfo.separator)}return[null,a]}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 a=Array.isArray(s)?s:[s];if(t.locusinfo.separator){a=a[0].split(t.locusinfo.separator)}return[null,a]}return["no trigger"]}function As(t,e){for(const s of t.custom_variants){if(s.dt==f){Ms(s);continue}if(s.dt==l||s.dt==r){Ss(s,e);continue}throw"unknown dt for a custom variant"}}function Ms(t){if(!t.chr)throw".chr missing for custom snvindel";if(!Number.isInteger(t.pos))throw".pos not integer for custom snvindel";if(!t.ssm_id){t.ssm_id=t.chr+"."+t.pos+"."+(t.ref&&t.alt?t.ref+"."+t.alt:t.mname)}}function Ss(t,e){if(t.pairlst);else{if(!t.chr1)throw".chr1 missing for custom sv/fusion";if(!Number.isInteger(t.pos1))throw".pos1 not integer for custom svfusion";if(t.strand1!="+"&&t.strand1!="-")throw".strand1 not +/- for custom svfusion";if(!t.chr2)throw".chr1 missing for custom sv/fusion";if(!Number.isInteger(t.pos2))throw".pos1 not integer for custom svfusion";if(t.strand2!="+"&&t.strand2!="-")throw".strand1 not +/- for custom svfusion";t.pairlst=[{a:{chr:t.chr1,pos:t.pos1,strand:t.strand1,name:t.gene1||""},b:{chr:t.chr2,pos:t.pos2,strand:t.strand2,name:t.gene2||""}}];delete t.chr1;delete t.pos1;delete t.strand1;delete t.gene1;delete t.chr2;delete t.pos2;delete t.strand2;delete t.gene2}const s=[t.dt];const a=e.seekcoord(t.pairlst[0].a.chr,t.pairlst[0].a.pos);if(a.length&&a[0].x>0&&a[0].x<e.width){s.push(...[t.pairlst[0].a.chr,t.pairlst[0].a.pos,t.pairlst[0].a.strand,0,t.pairlst[0].a.name]);t.mname=t.pairlst[0].b.name||"";t.chr=t.pairlst[0].a.chr;t.pos=t.pairlst[0].a.pos;t.pairlstIdx=0}else{const a=e.seekcoord(t.pairlst[0].b.chr,t.pairlst[0].b.pos);if(a.length&&a[0].x>0&&a[0].x<e.width){s.push(...[t.pairlst[0].b.chr,t.pairlst[0].b.pos,t.pairlst[0].b.strand,1,t.pairlst[0].b.name]);t.mname=t.pairlst[0].a.name||"";t.chr=t.pairlst[0].b.chr;t.pos=t.pairlst[0].b.pos;t.pairlstIdx=1}}t.ssm_id=s.join(".")}function Cs(t){if(t.custom_variants.find((t=>t.occurrence!=undefined))){return}for(const e of t.custom_variants){if(e.sample){e.sample_id=e.sample;delete e.sample}}if(!t.custom_variants.find((t=>t.sample_id))){return}const e=new Map;for(const s of t.custom_variants){const t=s.mname+"."+s.chr+"."+s.pos+"."+s.ref+"."+s.alt;const a=e.get(t);if(a){a.occurrence++;a.samples.push({sample_id:s.sample_id})}else{s.occurrence=1;s.samples=[{sample_id:s.sample_id}];delete s.sample_id;e.set(t,s)}}t.custom_variants=[];for(const s of e.values())t.custom_variants.push(s);if(!t.mds.variant2samples)t.mds.variant2samples={};const s=t.mds.variant2samples;s.type_samples="samples";s.type_summary="summary";s.type_sunburst="sunburst"}async function qs(t,e){const s={genome:e.name};if(t.bcf.file){s.file=t.bcf.file}else{s.url=t.bcf.url;if(t.bcf.indexURL)s.indexURL=t.bcf.indexURL}const a=await u("vcfheader",{body:s});if(a.error)throw a.error;const[n,i,o,r]=B(a.metastr.split("\n"));if(r)throw"Error parsing VCF meta lines: "+r.join("; ");t.mds.bcf={info:n,format:i};if(o?.length){t.mds.bcf.samples=o;t.mds.variant2samples={type_samples:"samples",variantkey:"ssm_id"}}if(!t.mds.queries)t.mds.queries={};t.mds.queries.snvindel={forTrack:true}}function Ls(t){const e=t.allow2selectSamples;if(!e)return;if(!e.buttonText)e.buttonText="Select samples";if(typeof e.buttonText!="string")throw"allow2selectSamples.buttonText value is not string";if(!e.attributes)e.attributes=[{from:"sample_id",to:"sample_id"}];if(!Array.isArray(e.attributes))throw"allow2selectSamples.attributes[] is not array";if(e.attributes.length==0)throw"allow2selectSamples.attributes[] blank array";for(const t of e.attributes){if(typeof t.from!="string"||!t.from)throw"allow2selectSamples.attributes.from is not string";if(typeof t.to!="string"||!t.to)throw"allow2selectSamples.attributes.to is not string"}if(typeof e.callback!="function")throw"allow2selectSamples.callback() is not function";e._cart=[]}async function zs(t){if(!t.filterObj)return;if(typeof t.filterObj!="object")throw"tk.filterObj{} is set but is not object";await e(t.filterObj);async function e(s){if(s.type=="tvs"){if(!s.tvs?.term)throw"tvs.tvs.term missing";if(!s.tvs.term.id)throw"tvs.tvs.term.id missing";s.tvs.term=await t.mds.termdb.vocabApi.getterm(s.tvs.term.id);return}if(s.type=="tvslst"){if(!Array.isArray(s.lst))throw"tvslst.lst[] not array";for(const t of s.lst)await e(t);return}throw"type not tvs or tvslst"}}function Ns(t,e,s){e.cnv?.g.selectAll("*").remove();if(!t.cnv){delete e.subtk2height.cnv;return}const[a,n,i]=$s(t,e,s);e.cnv.cnvLst=n;e.cnv.absoluteMax=i;e.cnv.colorScale=d([-i,0,i],[e.cnv.lossColor,"white",e.cnv.gainColor]).clamp(true);const[o,r]=Rs(a);let l=0;for(const t of a){for(const a of t.cnvs){const n=Math.max(0,a.x1),i=Math.min(a.x2,s.width);e.cnv.g.append("rect").attr("x",n).attr("y",l).attr("width",i-n).attr("height",o).attr("fill",e.cnv.colorScale(a.value)).on("mouseover",(s=>{s.target.setAttribute("stroke","black");e.itemtip.clear().show(s.clientX,s.clientY);const n=m({holder:e.itemtip.d});const i=structuredClone(a);i.samples=[{sample_id:t.sample_id}];At({mlst:[i],tk:e},n)})).on("mouseout",(t=>{t.target.setAttribute("stroke","");e.itemtip.hide()}))}l+=o+r}e.subtk2height.cnv=l}function $s(t,e,s){let a=0;const n=new Map;const i=[];for(const e of t.cnv){if(!e.chr)continue;if(!Number.isFinite(e.value)){if(typeof e.class=="string"){if(e.class==S){e.value=1}else if(e.class==C){e.value=-1}else{continue}}else{continue}}if(!Number.isInteger(e.start)||!Number.isInteger(e.stop))continue;const t=s.seekcoord(e.chr,e.start)[0];if(!t)continue;const o=s.seekcoord(e.chr,e.stop)[0];if(!o)continue;const r={chr:e.chr,start:e.start,stop:e.stop,value:e.value,dt:e.dt};if(t.x>o.x){r.x1=o.x;r.x2=t.x}else{r.x1=t.x;r.x2=o.x}if(!Array.isArray(e.samples))continue;i.push(e);for(const t of e.samples){if(!n.has(t.sample_id))n.set(t.sample_id,[]);n.get(t.sample_id).push(structuredClone(r))}a=Math.max(a,Math.abs(e.value))}const o=[];for(const[t,e]of n){o.push({sample_id:t,cnvs:e,x1:Math.min(...e.map((t=>t.x1))),x2:Math.max(...e.map((t=>t.x2)))})}o.sort(((t,e)=>t.x1-e.x1));return[o,i,Math.min(e.cnv.absoluteValueRenderMax,a)]}const Os=d([40,120],[10,1]);function Rs(t,e){if(t.length>120)return[1,0];if(t.length<40)return[10,1];return[Math.ceil(Os(t.length)),1]}async function Is(t,e){e.tkcloakon(t);e.block_setheight();try{if(!t.mds||t.uninitialized){await ls(t,e)}const s=await Fs(t,e);if(t.uninitialized){t.clear();delete t.uninitialized}Ne(s,t,e);Ns(s,t,e);await Ke(s,t,e);t._finish(s)}catch(e){if(t.clear)t.clear();if(t.subtk2height)t.subtk2height.skewer=50;if(t._finish)t._finish({error:e.message||e});if(e.stack)console.log(e.stack);return}}function Ts(t,e){const s={genome:e.genome.name,forTrack:1,skewerRim:t.mds.queries?.snvindel?.skewerRim};const a={"Content-Type":"application/json",Accept:"application/json"};if(t.mds.has_skewer){s.skewer=1}if(t.set_id){s.set_id=t.set_id}if(t.filter0){s.filter0=t.filter0}if(t.filterObj){if(t.filterObj?.lst.length){s.filterObj=t.filterObj}}if(t.token){a["X-Auth-Token"]=t.token}if(t.mds.label){s.dslabel=t.mds.label}else{if(t.bcf){if(t.bcf.file){s.bcffile=t.bcf.file}else if(t.bcf.url){s.bcfurl=t.bcf.url;if(t.bcf.indexURL)s.bcfindexURL=t.bcf.indexURL}else{throw".file and .url missing for tk.bcf{}"}}}Ds(t,e,s);if(t.legend.mclass.hiddenvalues.size){s.hiddenmclasslst=[...t.legend.mclass.hiddenvalues].join(",")}if(t.legend.bcfInfo){const e={};for(const s in t.legend.bcfInfo){if(t.legend.bcfInfo[s].hiddenvalues.size){e[s]=[...t.legend.bcfInfo[s].hiddenvalues]}}if(Object.keys(e).length){s.infoFilter=e}}if(t.legend.formatFilter){const e={};for(const s in t.legend.formatFilter){if(t.legend.formatFilter[s].hiddenvalues.size){e[s]=[...t.legend.formatFilter[s].hiddenvalues]}}if(Object.keys(e).length){s.formatFilter=e}}if(t.cnv){if(t.cnv.cnvMaxLength)s.cnvMaxLength=t.cnv.cnvMaxLength;if(t.cnv.cnvGainCutoff)s.cnvGainCutoff=t.cnv.cnvGainCutoff;if(t.cnv.cnvLossCutoff)s.cnvLossCutoff=t.cnv.cnvLossCutoff}return[s,a]}async function Fs(t,e){let s;if(t.custom_variants){s=await Bs(t,e)}else{const[a,n]=Ts(t,e);s=await u("mds3",{body:a,headers:n})}if(s.error)throw s.error;return s}function Ds(t,e,s){if(typeof s!="object")throw"par{} is not object";let a=[];if(e.usegm){const t={chr:e.rglst[0].chr,reverse:e.rglst[0].reverse,width:0,start:null,stop:null};for(let s=e.startidx;s<=e.stopidx;s++){const a=e.rglst[s];t.width+=a.width+e.regionspace;t.start=t.start==null?a.start:Math.min(t.start,a.start);t.stop=t.stop==null?a.stop:Math.max(t.stop,a.stop)}a.push(t);if(e.gmmode=="genomic");else{s.isoform=e.usegm.isoform;s.gene=e.usegm.name}}else{a=e.tkarg_rglst(t)}let n=0;for(const t of a){t.xoff=0;n+=t.width+e.regionspace}if(e.subpanels.length==t.subpanels.length){for(const t of e.subpanels){a.push({chr:t.chr,start:t.start,stop:t.stop,width:t.width,exonsf:t.exonsf,xoff:n});n+=t.width+t.leftpad}}s.rglst=a}async function Bs(t,e){const s={skewer:[]};let a=null,n;for(let t=e.startidx;t<=e.stopidx;t++){if(a==null){a=e.rglst[t].start;n=e.rglst[t].stop}else{a=Math.min(a,e.rglst[t].start);n=Math.max(n,e.rglst[t].stop)}}const o=new Map;for(const r of t.custom_variants){if(r.chr!=e.rglst[0].chr)continue;if(r.pos<=a||r.pos>=n)continue;if(!r.class)r.class="X";if(!i[r.class])r.class="X";o.set(r.class,1+(o.get(r.class)||0));if(t.legend.mclass.hiddenvalues.has(r.class))continue;s.skewer.push(r)}if(s.skewer.some((t=>t.samples))){const t=new Set;for(const e of s.skewer){if(e.samples){for(const s of e.samples)t.add(s.sample_id)}}s.sampleTotalNumber=t.size}s.mclass2variantcount=[...o];await Gs(t,s.skewer);return s}async function Gs(t){if(!t.mds.queries?.ld?.mOverlay)return;if(!t.mds.termdb?.vocabApi)return;delete t.mds.queries.ld.mOverlay.data;const e=await t.mds.termdb.vocabApi.getLDdata(t.mds.queries.ld.mOverlay.ldtkname,t.mds.queries.ld.mOverlay.m);if(e.error||!Array.isArray(e.lst))return;t.mds.queries.ld.mOverlay.data=e.lst}export{Is as loadTk,Ds as rangequery_rglst};
+import{M as t,O as e,af as s,be as a,I as n,E as i,bc as o,K as r,J as l,bP as c,l as d,L as f,bo as m,S as u,aN as p,a1 as h,x as g,B as b,q as w,ar as v,t as y,f as k,G as x,H as _,F as j,aR as A,bn as M,bH as S,bG as C}from"./app-71453429.js";import{l as q}from"./block.legend-cec87c6f.js";import{s as L,m as z}from"./regression.results-25008028.js";import{a as N}from"./axisstyle-fac7f76b.js";import{d as $,b as O}from"./axis-6cb4f314.js";import{r as R}from"./table-1dae543a.js";import{d as I}from"./arc-3d6751aa.js";import{m as T}from"./block-4f585abe.js";import{t as F}from"./downloadTextfile-5723af95.js";import{m as D}from"./radiobutton-09bff425.js";import{v as B}from"./vcf-16ba1e06.js";import{f as G}from"./FilterStateless-8f30f856.js";import{g as H}from"./FilterRxComp-fc769f34.js";import{v as U}from"./violinRenderer-71c9f3ab.js";import{n as P}from"./niceNumLabels-ddb76164.js";import{f as E}from"./termsetting-636d2271.js";import"./partition-db811f6b.js";import"./legacy-d3-polyfill-bdb2d792.js";import"./ColorScale-9800a609.js";import"./log-ca1e2a74.js";import"./constant-426a1483.js";import"./math-2fb199c6.js";import"./checkbox-0e5c659f.js";import"./pointer-c7475677.js";import"./brush-bb4566a3.js";import"./nodrag-bed2488c.js";import"./line-264f8f9e.js";import"./basis-3870f5ba.js";import"path";const V="white",K="black";const W="Unannotated";function X(e,s){if(!e.legend)e.legend={};e.legend.tip=new t({padding:"0px"});const[a,n,i]=q(s,e.name);e.legend.headTd=i;e.tr_legend=a;const o=n.append("table").style("border-spacing","5px").style("border-collapse","separate");e.legend.table=o;Q(e,s);J(e);Y(e);Z(e);ot(e);dt(e);mt(e)}function Q(t,e){if(!t.legend.mclass)t.legend.mclass={};if(!t.legend.mclass.hiddenvalues)t.legend.mclass.hiddenvalues=new Set;t.legend.mclass.row=t.legend.table.append("tr");t.legend.mclass.row.append("td").style("text-align","right").style("opacity",.7).text(e.mclassOverride?e.mclassOverride.className||"Mutation":"Mutation");t.legend.mclass.holder=t.legend.mclass.row.append("td")}function J(t){if(!t.variantShapeName)return;const e=t.legend.table.append("tr").append("td").attr("colspan",2);const s=t.legend.variantShapeName={};{const a=e.append("div");a.append("span").html(`<svg style="display:inline-block" width=12 height=12>\n\t\t\t<circle cx=6 cy=6 r=6 fill=gray></circle></svg> n=`);s.dotCount=a.append("span");if(t.variantShapeName.dot)a.append("span").text(", "+t.variantShapeName.dot);s.dotDiv=a}{const a=e.append("div");a.append("span").html(`<svg style="display:inline-block" width=12 height=12>\n\t\t\t<path d="M 6 0 L 0 12 h 12 Z" fill=gray></path></svg> n=`);s.triangleCount=a.append("span");if(t.variantShapeName.triangle)a.append("span").text(", "+t.variantShapeName.triangle);s.triangleDiv=a}{const a=e.append("div");a.append("span").html(`<svg style="display:inline-block" width=13 height=13>\n\t\t\t<circle cx=6.5 cy=6.5 r=6 stroke=gray fill=none></circle></svg> n=`);s.circleCount=a.append("span");if(t.variantShapeName.circle)a.append("span").text(", "+t.variantShapeName.circle);s.circleDiv=a}}function Y(t){if(!t.mds.bcf?.info)return;const e=[];for(const s in t.mds.bcf.info){const a=t.mds.bcf.info[s];if(a.categories){e.push(s)}}if(!e.length)return;if(!t.legend.bcfInfo)t.legend.bcfInfo={};for(const s of e){const e=t.legend.table.append("tr");e.append("td").style("text-align","right").style("opacity",.7).text(t.mds.bcf.info[s].name||s);t.legend.bcfInfo[s]={hiddenvalues:new Set,row:e,holder:e.append("td")}}}function Z(t){if(!t.mds.bcf?.format)return;const e=[];for(const s in t.mds.bcf.format){if(t.mds.bcf.format[s].isFilter)e.push(s)}if(!e.length)return;if(!t.legend.formatFilter)t.legend.formatFilter={};for(const s of e){const e=t.legend.table.append("tr");e.append("td").style("text-align","right").style("opacity",.7).text(t.mds.bcf.format[s].Description);t.legend.formatFilter[s]={hiddenvalues:new Set,row:e,holder:e.append("td")}}}function tt(t,e){if(!e.legend.formatFilter)return;if(!t.skewer){console.log("data.skewer[] is not present and cannot show INFO legend");return}for(const s in e.legend.formatFilter){e.legend.formatFilter[s].holder.selectAll("*").remove();const a=new Map;let n=0;for(const e of t.skewer){if(!e.formatK2count?.[s])continue;for(const t in e.formatK2count[s].v2c){a.set(t,e.formatK2count[s].v2c[t]+(a.get(t)||0))}n+=e.formatK2count[s].unannotatedCount||0}const i=[...a];i.sort(((t,e)=>e[1]-t[1]));if(n){i.push([W,n])}for(const[t,a]of i){const n=e.legend.formatFilter[s].holder.append("div").attr("class","sja_clb").style("display","inline-block").on("click",(()=>{e.legend.tip.clear().showunder(n.node()).d.append("div").attr("class","sja_menuoption").text("Hide").on("click",(()=>{e.legend.formatFilter[s].hiddenvalues.add(t);et(e)}));e.legend.tip.d.append("div").attr("class","sja_menuoption").text("Show only").on("click",(()=>{for(const t of i){e.legend.formatFilter[s].hiddenvalues.add(t[0])}e.legend.formatFilter[s].hiddenvalues.delete(t);et(e)}));if(e.legend.formatFilter[s].hiddenvalues.size){e.legend.tip.d.append("div").attr("class","sja_menuoption").text("Show all").on("click",(()=>{e.legend.formatFilter[s].hiddenvalues.clear();et(e)}))}}));n.append("div").style("display","inline-block").attr("class","sja_mcdot").style("background","#aaa").style("margin-right","5px").html(a>1?a:"&nbsp;");n.append("div").style("display","inline-block").text(t)}for(const t of e.legend.formatFilter[s].hiddenvalues){let a=false;e.legend.formatFilter[s].holder.append("div").style("display","inline-block").attr("class","sja_clb").style("text-decoration","line-through").style("opacity",.7).text(t).on("click",(async()=>{if(a)return;a=true;e.legend.formatFilter[s].hiddenvalues.delete(t);et(e)}))}}}function et(t){t.legend.tip.hide();t.load()}function st(t,e,s){if(!e.legend){return}e.legend.mclass.currentData=t.mclass2variantcount;it(e);at(t,e);nt(t,e);tt(t,e);lt(t,e);ft(e);ut(e)}function at(t,e){if(!e.variantShapeName)return;let s=0,a=0,n=0;for(const e of t.skewer){if(e.shapeTriangle)a++;else if(e.shapeCircle)n++;else s++}const i=e.legend.variantShapeName;i.dotDiv.style("display",s?"block":"none");i.triangleDiv.style("display",a?"block":"none");i.circleDiv.style("display",n?"block":"none");i.dotCount.text(s);i.triangleCount.text(a);i.circleCount.text(n)}function nt(t,e){if(!e.legend.bcfInfo)return;if(!t.skewer){console.log("data.skewer[] is not present and cannot show INFO legend");return}for(const s in e.legend.bcfInfo){e.legend.bcfInfo[s].holder.selectAll("*").remove();if(e.mds.bcf.info[s].Type=="String"){const a=new Map;for(const e of t.skewer){const t=s in e.info?e.info[s]:W;if(Array.isArray(t)){for(const e of t){a.set(e,1+(a.get(e)||0))}}else{a.set(t,1+(a.get(t)||0))}}const n=[...a].sort(((t,e)=>e[1]-t[1]));for(const[t,a]of n){const i=e.legend.bcfInfo[s].holder.append("div").attr("class","sja_clb").style("display","inline-block").on("click",(()=>{e.legend.tip.clear().showunder(i.node()).d.append("div").attr("class","sja_menuoption").text("Hide").on("click",(()=>{e.legend.bcfInfo[s].hiddenvalues.add(t);et(e)}));e.legend.tip.d.append("div").attr("class","sja_menuoption").text("Show only").on("click",(()=>{for(const t of n){e.legend.bcfInfo[s].hiddenvalues.add(t[0])}e.legend.bcfInfo[s].hiddenvalues.delete(t);et(e)}));if(e.legend.bcfInfo[s].hiddenvalues.size){e.legend.tip.d.append("div").attr("class","sja_menuoption").text("Show all").on("click",(()=>{e.legend.bcfInfo[s].hiddenvalues.clear();et(e)}))}const a=e.mds.bcf.info[s].categories?.[t]?.desc;if(a){e.legend.tip.d.append("div").style("padding","10px").style("font-size",".8em").style("width","150px").html(a)}}));i.append("div").style("display","inline-block").attr("class","sja_mcdot").style("background",e.mds.bcf.info[s].categories?.[t]?.color||V).html(a>1?a:"&nbsp;");i.append("div").style("display","inline-block").style("color",e.mds.bcf.info[s].categories?.[t]?.color||K).html("&nbsp;"+e.mds.bcf.info[s].categories?.[t]?.label||t)}for(const t of e.legend.bcfInfo[s].hiddenvalues){let a=false;e.legend.bcfInfo[s].holder.append("div").style("display","inline-block").attr("class","sja_clb").style("text-decoration","line-through").style("opacity",0).text(t).on("click",(async()=>{if(a)return;a=true;e.legend.bcfInfo[s].hiddenvalues.delete(t);et(e)}))}}}}function it(t){if(!t.legend.mclass.currentData||t.legend.mclass.currentData.length==0)return;t.legend.mclass.holder.selectAll("*").remove();const c=[],d=[];for(const[e,s]of t.legend.mclass.currentData){const a={k:e,count:s};if(t.legend.mclass.hiddenvalues.has(e)){d.push(a)}else{c.push(a)}}c.sort(((t,e)=>e.count-t.count));d.sort(((t,e)=>e.count-t.count));for(const e of t.legend.mclass.hiddenvalues){if(!d.find((t=>t.k==e))){d.push({k:e})}}for(const f of c){let m,u,p="#858585";if(Number.isInteger(f.k)){m=e[f.k];if(f.k==s){u="Copy number variation."}else if(f.k==a){u="Loss of heterozygosity."}else if(f.k==n){p=i[o].color;u="Internal tandem duplication."}else if(f.k==r){u="Structural variation of DNA."}else if(f.k==l){u="Fusion gene from RNA-seq."}}else{m=i[f.k].label;p=i[f.k].color;u=i[f.k].desc}const h=t.legend.mclass.holder.append("div").attr("class","sja_clb").style("display","inline-block").on("click",(e=>{t.legend.tip.clear().showunder(e.target).d.append("div").attr("class","sja_menuoption").text("Hide").on("click",(()=>{t.legend.mclass.hiddenvalues.add(f.k);et(t)}));t.legend.tip.d.append("div").attr("class","sja_menuoption").text("Show only").on("click",(()=>{for(const e of c){t.legend.mclass.hiddenvalues.add(e.k)}t.legend.mclass.hiddenvalues.delete(f.k);et(t)}));if(d.length){t.legend.tip.d.append("div").attr("class","sja_menuoption").text("Show all").on("click",(()=>{t.legend.mclass.hiddenvalues.clear();et(t)}))}t.legend.tip.d.append("div").style("padding","10px").style("font-size",".8em").style("width","150px").html(u)}));h.append("div").style("display","inline-block").attr("class","sja_mcdot").style("background",p).html(f.count>1?f.count:"&nbsp;");h.append("div").style("display","inline-block").style("color",p).html("&nbsp;"+m)}for(const s of d){let a=false;t.legend.mclass.holder.append("div").style("display","inline-block").attr("class","sja_clb").style("text-decoration","line-through").style("opacity",.7).text((s.count?"("+s.count+") ":"")+(Number.isInteger(s.k)?e[s.k]:i[s.k].label)).on("click",(async e=>{if(a)return;a=true;t.legend.mclass.hiddenvalues.delete(s.k);e.target.innerHTML="Updating...";await t.load()}))}}function ot(t,e){if(!t.mds.queries?.snvindel?.skewerRim)return;const s=t.legend.skewerRim={};if(!t.mds.queries.snvindel.skewerRim.hiddenvaluelst)t.mds.queries.snvindel.skewerRim.hiddenvaluelst=[];s.row=t.legend.table.append("tr");s.headerTd=s.row.append("td").style("text-align","right").style("opacity",.7);s.holder=s.row.append("td")}function rt(t){const e=t.mds.queries.snvindel.skewerRim;if(e.type=="format"){if(!e.formatKey)throw"skewerRim.formatKey missing";return t.mds.bcf?.format?.[e.formatKey]?.Description||e.formatKey}return"unknown skewerRim.type"}function lt(t,e){const s=e.mds.queries?.snvindel?.skewerRim;if(!s)return;let a=0,n=0;for(const e of t.skewer){const t=e.rim1count||0;a+=t;n+=e.occurrence-t}const i=e.legend.skewerRim;i.headerTd.text(rt(e));i.holder.selectAll("*").remove();if(a>0){i.holder.append("div").attr("class","sja_clb").style("display","inline-block").html(`${ct(1)}${s.rim1value}, n=${a}`).on("click",(t=>{e.legend.tip.clear().showunder(t.target).d.append("div").attr("class","sja_menuoption").text("Hide").on("click",(()=>{s.hiddenvaluelst.push(s.rim1value);et(e)}))}))}if(n>0){i.holder.append("div").attr("class","sja_clb").style("display","inline-block").html(`${ct()}${s.noRimValue}, n=${n}`).on("click",(t=>{e.legend.tip.clear().showunder(t.target).d.append("div").attr("class","sja_menuoption").text("Hide").on("click",(()=>{s.hiddenvaluelst.push(s.noRimValue);et(e)}))}))}for(const t of s.hiddenvaluelst){let a=false;i.holder.append("div").style("display","inline-block").attr("class","sja_clb").style("text-decoration","line-through").style("opacity",.7).text(t).on("click",(async n=>{if(a)return;a=true;s.hiddenvaluelst.splice(s.hiddenvaluelst.indexOf(t),1);n.target.innerHTML="Updating...";await e.load()}))}}function ct(t){return'<svg width="19" height="19" style="margin-right: 5px;">'+'<circle cx="7" cy="12" r="7" fill="#b1b1b1"></circle>'+(t==1?'<path d="M6.735557395310443e-16,-11A11,11 0 0,1 11,0L9,0A9,9 0 0,0 5.51091059616309e-16,-9Z" transform="translate(7,12)" fill="#858585" stroke="none"></path>':t==2?"":"")+"</svg>"}function dt(t,e){if(!t.mds.queries?.ld)return;t.mds.queries.ld.colorScale=c(t.mds.queries.ld.overlay.color_0,t.mds.queries.ld.overlay.color_1);const s=t.legend.ld={};s.row=t.legend.table.append("tr");s.headerTd=s.row.append("td").style("text-align","right").style("opacity",.7);s.holder=s.row.append("td");s.showHolder=s.holder.append("div").style("display","none");L(s.showHolder,t.mds.queries.ld.colorScale);s.showHolder.append("span").text("Cancel overlay").style("font-size",".7em").attr("class","sja_clbtext").on("click",(()=>{delete t.mds.queries.ld.mOverlay;if(t.skewer?.hlssmid)delete t.skewer.hlssmid;t.load()}))}function ft(t){if(!t.mds.queries?.ld?.mOverlay){if(t.legend.ld){t.legend.ld.headerTd.html("");t.legend.ld.showHolder.style("display","none")}return}t.legend.ld.headerTd.html(t.mds.queries.ld.mOverlay.ldtkname+" LD r<sup>2</sup>");t.legend.ld.showHolder.style("display","block")}function mt(t,e){if(!t.cnv)return;const s=t.legend.cnv={};s.row=t.legend.table.append("tr");s.headerTd=s.row.append("td").style("text-align","right").style("opacity",.7).text("CNV");s.holder=s.row.append("td");s.showHolder=s.holder.append("div").style("display","none")}function ut(t){if(!t.cnv)return;t.legend.cnv.holder.selectAll("*").remove();const e=t.legend.cnv.holder.append("svg");const s=20;const a=15;const n=10;const i=150;N({axis:e.append("g").attr("transform","translate("+n+","+s+")").call($().scale(d().domain([-t.cnv.absoluteMax,t.cnv.absoluteMax]).range([0,i])).ticks(4)),fontsize:12});const o="grad"+Math.random();const r=e.append("defs").append("linearGradient").attr("id",o);r.append("stop").attr("offset","0%").attr("stop-color",t.cnv.lossColor);r.append("stop").attr("offset","50%").attr("stop-color","white");r.append("stop").attr("offset","100%").attr("stop-color",t.cnv.gainColor);e.append("rect").attr("x",n).attr("y",s).attr("width",i).attr("height",a).attr("fill",`url(#${o})`);e.attr("width",n*2+i).attr("height",s+a)}async function pt(t){for(const e of t.mlst){if(e.dt!=f&&e.dt!=l&&e.dt!=r&&e.dt!=s)throw"mlst[] contains unknown dt"}if(t.mlst.length==1){await gt(t)}else{await bt(t)}ht(t)}function ht(t){if(!t.tipDiv){return}const e=[];for(const s of t.div.selectAll("div").selectAll("table")){if(s)e.push(s)}if(!e.length)return;let s=0;for(const t of e){const e=t.firstChild;if(e.tagName!="THEAD")continue;const a=e.firstChild;if(a.tagName!="TR")continue;s=Math.max(s,a.childNodes?.length)}if(s>5){t.tipDiv.style("left","50px")}}async function gt(t){const e=m({holder:t.div});const a=t.mlst[0];if(a.dt==f){wt(t,e)}else if(a.dt==r||a.dt==l){await jt(t,e)}else if(a.dt==s){At(t,e)}else{throw"oneItem: unknown dt"}t.singleSampleDiv=e;if(t.tk.mds.variant2samples){if(a.occurrence){await Lt(t)}}}async function bt(t){const e=t.div.append("div").style("margin-bottom","10px").style("display","none");e.append("span").html("&#8810; Back to list").attr("class","sja_clbtext").on("click",(()=>{u.style("display","");e.style("display","none");a.style("display","none")}));const a=t.div.append("div").style("display","none");const n=[{label:"Click a variant to see details"}];const o=t.mlst.some((t=>t.occurrence));if(o){n.push({label:"Occurrence"})}let c=null;if(t.tk.mds.bcf?.info){c=[];for(const e in t.tk.mds.bcf.info){if(t.tk.mds.bcf.info[e].categories){c.push(e);n.push({label:t.tk.mds.bcf.info[e].name||e})}}if(c.length==0)c=null}const d=t.tk.skewer.viewModes.find((t=>t.inuse&&t.type=="numeric"&&t.byAttribute!="occurrence"));if(d){n.push({label:d.label})}t.mlst.sort(((t,e)=>t.__x-e.__x));const m=[];for(const e of t.mlst){const s=[{}];if(o){s.push({value:"occurrence"in e?e.occurrence:""})}if(c){for(const a of c){const n=e.info[a];if(n==undefined){s.push({})}else{const e=t.tk.mds.bcf.info[a].categories[n];if(e?.color){s.push({html:`<span style="background:${e.color}">&nbsp;&nbsp;</span> ${e.label||n}`})}else{s.push({value:n})}}}}if(d){s.push({value:e[d.byAttribute]})}m.push(s)}const u=t.div.append("div");R({div:u,columns:n,rows:m,striped:false,resize:true});for(const[n,o]of t.mlst.entries()){const c=m[n][0].__td.append("div").attr("class","sja_menuoption").on("click",(()=>{u.style("display","none");e.style("display","");a.style("display","").selectAll("*").remove();const s=Object.assign({},t);s.mlst=[o];s.div=a;pt(s)}));if(o.dt==f){c.append("span").text(t.tk.mnamegetter(o));c.append("span").text(i[o.class].label).style("font-size",".8em").style("margin-left","10px").style("color",i[o.class].color);c.append("span").text(`${o.chr}:${o.pos+1}${o.ref?", "+o.ref+">"+o.alt:""}`).style("font-size",".8em").style("margin-left","10px")}else if(o.dt==r||o.dt==l){c.append("span").text(i[o.class].label).style("font-size",".7em").style("margin-right","8px");Mt(o.pairlst[0],c)}else if(o.dt==s){c.append("span").style("background",t.tk.cnv.colorScale(o.value)).text(o.value).style("font-size",".8em").style("padding","0px 3px");c.append("span").style("margin-left","10px").text(`${o.chr}:${o.start}-${o.stop}`)}else{c.text("error: unknown m.dt")}}if(!t.doNotListSample4multim&&t.tk.mds.variant2samples){const e=t.mlst.reduce(((t,e)=>t+(e.occurrence||0)),0);if(e){t.div.append("div").style("margin-top","10px").append("span").attr("class","sja_clbtext").text("List all 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Mt(t,e){if(t.a.name)e.append("span").text(t.a.name).style("font-weight","bold").style("margin-right","5px");e.append("span").text(`${t.a.chr}:${t.a.pos} ${t.a.strand=="+"?"forward":"reverse"} > ${t.b.chr}:${t.b.pos} ${t.b.strand=="+"?"forward":"reverse"}`);if(t.b.name)e.append("span").text(t.b.name).style("font-weight","bold").style("margin-left","5px")}async function St(t,e,s){const a=e.append("div").text("Loading...");try{if(!t.pairlst)throw".pairlst[] missing";const n={a:{chr:t.pairlst[0].a.chr,position:t.pairlst[0].a.pos,strand:t.pairlst[0].a.strand},b:{chr:t.pairlst[0].b.chr,position:t.pairlst[0].b.pos,strand:t.pairlst[0].b.strand}};await Ct(n.a,s);await Ct(n.b,s);a.remove();const i=await import("./svgraph-a12d89da.js");i.default({pairlst:[n],genome:s.genome,holder:e})}catch(t){a.text(t.message||t)}}async function Ct(t,e){const s=await u("isoformbycoord",{body:{genome:e.genome.name,chr:t.chr,pos:t.position}});if(s.error)throw s.error;const a=s.lst.find((t=>t.isdefault))||s.lst[0];if(a){t.name=a.name;t.gm={isoform:a.isoform}}}function qt(t,e,s){if(!e.mds.queries?.ld)return;const[a,n]=s.addRow();a.text("LD overlay");const i=e.mds.queries.ld.mOverlay?.m;if(i){const s=n.append("div").style("margin-bottom","5px");if(t.ssm_id==i.ssm_id){s.html(e.mds.queries.ld.mOverlay.ldtkname+" r<sup>2</sup> values against this variant are displayed on all the other variants.")}else{let a=null;for(const s of e.mds.queries.ld.mOverlay.data||[]){if(s.pos==t.pos&&s.alleles==t.ref+"."+t.alt){a=s.r2;break}}if(a==null){s.html("No r<sup>2</sup> value is found.")}else{s.html(e.mds.queries.ld.mOverlay.ldtkname+" r<sup>2</sup> = "+a)}}}n.append("div").html("Click a button to overlay LD r<sup>2</sup> values against this variant:").style("font-size",".8em").style("opacity",.5);for(const s of e.mds.queries.ld.tracks){const a=n.append("button").text(s.name);if(i&&i.ssm_id==t.ssm_id){if(s.name==e.mds.queries.ld.mOverlay.ldtkname){a.property("disabled",true);continue}}a.on("click",(()=>{e.itemtip.hide();e.mds.queries.ld.mOverlay={ldtkname:s.name,m:{chr:t.chr,pos:t.pos,ref:t.ref,alt:t.alt,ssm_id:t.ssm_id}};e.load()}))}}async function Lt(t){const e=t.div.append("div").text("Loading...").style("padding","10px").style("color","#8AB1D4").style("font-size","1.25em").style("font-weight","bold");t.tid2value_orig=new Set;if(t.tid2value)Object.keys(t.tid2value).forEach(t.tid2value_orig.add,t.tid2value_orig);try{t.querytype=t.tk.mds.variant2samples.type_samples;const s=await t.tk.mds.variant2samples.get(t);await zt(s.samples,t);e.remove()}catch(t){e.text("Error: "+(t.message||t));if(t.stack)console.log(t.stack)}}async function zt(t,e){if(t.length==1){return await $t(t[0],e)}const[s,a]=await Tt(t,e.tk);const n={rows:a,columns:s,div:e.div,resize:a.length>10,dataTestId:"sjpp_mds3tk_sampletable"};n.columnButtons=[];if(e.tk.mds.queries?.singleSampleMutation){const s={text:"Disco",dataTestId:"sja_sample_table_disco_button",callback:async(s,a)=>{e.tk.itemtip.hide();e.tk.menutip.hide();let n;if(t[a].ssm_id_lst?.[0]){n=(e.tk.skewer.rawmlst||e.tk.custom_variants).find((e=>e.ssm_id==t[a].ssm_id_lst[0]))}await It(e.tk,e.block,t[a],n)}};n.columnButtons.push(s)}if(e.tk.mds.queries?.singleSampleGenomeQuantification){for(const s in e.tk.mds.queries.singleSampleGenomeQuantification){const a={text:s,dataTestId:`${s}_button`,callback:async(a,n)=>{const i=h(e.tk.newChartHolder||e.block.holder0);i.header.text(t[n].sample_id);await(await import("./plot.ssgq-1949c207.js")).plotSingleSampleGenomeQuantification(e.tk.mds,e.tk.mds.label,s,t[n],i.body.append("div").style("margin","20px"),e.block.genome,e.block.usegm?.name)}};n.columnButtons.push(a)}}if(e.tk.allow2selectSamples){n.buttons=[{text:e.tk.allow2selectSamples.buttonText,class:e.tk.allow2selectSamples.class,callback:s=>{Nt(e.tk,e.block,t,s);e.tk.itemtip.hide();e.tk.menutip.hide()}}]}return R(n)}async function Nt(t,e,s,a){const n=[...s];const i=a.map((t=>n[t]));t.allow2selectSamples.callback({samples:await t.mds.termdb.vocabApi.convertSampleId(i,t.allow2selectSamples.attributes),source:"Samples with "+Dt(e)})}async function $t(t,e){const s=e.singleSampleDiv||m({holder:e.div});if(t.sample_id){const[a,n]=s.addRow();a.text(e.tk.mds.termdbConfig?.lollipop?.sample||"Sample");let i;if(t.ssm_id_lst?.[0]){i=e.tk.skewer.rawmlst.find((e=>e.ssm_id==t.ssm_id_lst[0]))}Rt(t,e.tk,n,e.block,i)}if("caseIsOpenAccess"in t){const[e,a]=s.addRow();e.text("Access");a.text(t.caseIsOpenAccess?"Open":"Controlled")}if(e.tk.mds.variant2samples.twLst){for(const a of e.tk.mds.variant2samples.twLst){const[e,n]=s.addRow();e.text(a.term.name).style("text-overflow","ellipsis");n.style("text-overflow","ellipsis");if(a.term.id in t){if(Array.isArray(t[a.term.id])){if(a.baseURL){n.html(t[a.term.id].map((t=>`<a href=${a.baseURL+t} target=_blank>${t}</a>`)).join("<br>"))}else{n.html(t[a.term.id].join("<br>"))}}else{const e=Ot(t,a);if(a.baseURL){n.html(`<a href=${a.baseURL+e} target=_blank>${e}</a>`)}else{n.text(e)}}}}}if(t.ssmid2format){for(const a of t.ssm_id_lst){if(t.ssm_id_lst.length>1){const[t,n]=s.addRow();n.style("padding-top","20px");const i=e.tk.skewer.rawmlst.find((t=>t.ssm_id==a));if(i){if(i.dt==f){_t(n,i,e.tk,e.block)}else if(i.dt==r||i.dt==l){Mt(i.pairlst[0],n)}else{n.text(a)}}else{n.text(a)}}for(const n in t.ssmid2format[a]){const i=t.ssmid2format[a][n];const[o,r]=s.addRow();const l=e.tk.mds?.bcf?.format?.[n];o.text(l&&l.Description||n);r.html(Ft(l,i))}}}}function Ot(t,e){if(!(e.term.id in t))return"";const s=t[e.term.id];if(e.term.values?.[s]?.label)return e.term.values[s].label;const a=e.term.valueConversion;if(a)return p(s,a.fromUnit,a.toUnit,a.scaleFactor);return s}function Rt(t,e,s,a,n){const i=e.mds.termdbConfig?.urlTemplates?.sample;if(i){const e=s.append("a");e.attr("href",i.base+(t[i.namekey]||t.sample_id));e.attr("target","_blank");e.text(t.sample_id);e.style("word-break","break-word")}else{s.append("span").attr("class","pp_mds3_singleSampleNameSpan").text(t.sample_id)}const o=s.append("div");if(e.allow2selectSamples){const s=e.allow2selectSamples.buttonText;const n=o.append("button").style("margin-right","10px").text(s.endsWith("s")?s.substring(0,s.length-1):s).on("click",(()=>{Nt(e,a,[t],[0]);e.itemtip.hide();e.menutip.hide()}));if(e.allow2selectSamples.class)n.attr("class",e.allow2selectSamples.class)}if(e.mds.queries?.singleSampleMutation){o.append("button").style("margin-right","10px").text("Disco plot").attr("data-testid","proteinpaint_disc_table_disco_button").on("click",(async()=>{e.itemtip.hide();await It(e,a,t,n)}))}if(e.mds.queries?.singleSampleGenomeQuantification){for(const s in e.mds.queries.singleSampleGenomeQuantification){o.append("button").text(s).on("click",(async()=>{const n=h(e.newChartHolder||a.holder0);n.header.text(t.sample_id);await(await import("./plot.ssgq-1949c207.js")).plotSingleSampleGenomeQuantification(e.mds,e.mds.label,s,t,n.body.append("div").style("margin","20px"),a.genome,a.usegm?.name)}))}}}async function It(t,e,s,a){const n=h(t.newChartHolder||e.holder0);const i=[s.sample_id];if(a){i.push(", with ");if(e.usegm){i.push(e.usegm.name)}else{i.push(a.isoform)}i.push(" "+a.mname)}n.header.text(i.join(""));try{(await import("./plot.disco-621d1b8e.js")).default(t.mds,t.mds.label,s,n.body,e.genome,{downloadImgName:i.join("")+" Disco",Disco:{prioritizeGeneLabelsByGeneSets:true}})}catch(t){n.body.append("div").text("Error: "+(t.message||t));if(t.stack)console.log(t.stack)}}async function Tt(t,e){const s=t.some((t=>"caseIsOpenAccess"in t)),a=t.some((t=>t.ssm_id))||t.some((t=>t.ssm_id_lst)),n=t.some((t=>t.ssmid2format))&&e.mds?.bcf?.format;const o=new Set;const c=[{label:e.mds.termdbConfig?.lollipop?.sample||"Sample"}],d=[];if(s){c.push({label:"Access"})}if(e.mds.variant2samples.twLst){for(const t of e.mds.variant2samples.twLst){const e={label:t.term.name};c.push(e)}}if(a){c.push({label:"Mutations",isSsm:true})}if(n){for(const e of t){if(!e.ssmid2format)continue;for(const t in e.ssmid2format){for(const s in e.ssmid2format[t])o.add(s)}}for(const t in e.mds.bcf.format){if(!o.has(t))continue;const s=e.mds.bcf.format[t];c.push({label:s.Description||t})}}for(const c of t){const t=[{value:c.sample_id}];let m=c.ssm_id_lst;if(!m&&c.ssm_id)m=[c.ssm_id];{const s=e.mds.termdbConfig?.urlTemplates?.sample;if(s){t[0].url=s.base+(c[s.namekey]||c.sample_id)}}if(s){t.push({value:c.caseIsOpenAccess?"Open":"Controlled"})}if(e.mds.variant2samples.twLst){for(const s of e.mds.variant2samples.twLst){const e=Ot(c,s);if(s.baseURL){t.push({html:`<a href=${s.baseURL+e} target=_blank>${e}</a>`})}else{t.push({value:e})}}}if(a){if(m){const s=[];for(const t of m){const a=[];const n=(e.skewer.rawmlst||e.custom_variants).find((e=>e.ssm_id==t));if(n){if(n.dt==f){if(e.mds.queries&&e.mds.queries.snvindel&&e.mds.queries.snvindel.url){a.push(`<a href=${e.mds.queries.snvindel.url.base+n.ssm_id} target=_blank>${n.mname}</a>`)}else{a.push(n.mname)}}else if(n.dt==r||n.dt==l){const t=n.pairlst[0];a.push(`${t.a.name||""} ${t.a.chr}:${t.a.pos} ${t.a.strand=="+"?"forward":"reverse"} > ${t.b.name||""} ${t.b.chr}:${t.b.pos} ${t.b.strand=="+"?"forward":"reverse"}`)}else{throw"unknown dt"}a.push(`<span style="color:${g(i[n.class].color).darker()};font-size:0.8em;">${i[n.class].label}</span>`);s.push(a.join(" "))}else{s.push(t)}}t.push({html:s.join("<br>")})}else{t.push({value:""})}}if(n){if(!m)throw"ssm_id_lst missing, cannot show format";for(const s in e.mds.bcf.format){if(!o.has(s))continue;if(!c.ssmid2format){t.push({value:""});continue}const a=e.mds.bcf.format[s];const n=[];for(const t of m){const e=c.ssmid2format?.[t]?.[s];n.push(Ft(a,e))}t.push({html:n.join("<br>")})}}d.push(t)}return[c,d]}function Ft(t,e){if(t&&e&&t.Number=="R"&&t.Type=="Integer"){const t=e.split(",").map(Number);if(t.length==2){const[e,s]=t;if(e>=0&&s>=0&&e+s>0){return`${b(null,{f:s/(s+e)})} <span style="font-size:.8em">${s}/${s+e}</span>`}}}return e}function Dt(t){if(t.gmmode=="genomic"){const e=t.rglst[0];return"mutations from "+e.chr+":"+e.start+"-"+e.stop}if(t.usegm)return"mutations in "+t.usegm.name;return"mutations"}const Bt=10;async function Gt(t,e,s,a,n){try{if(e.click_snvindel){e.skewer.hlssmid=new Set(t.mlst.map((t=>t.ssm_id)));ie(e);e.click_snvindel(t.mlst[0]);return}if("occurrence"in t&&t.occurrence>=Bt&&e.mds.variant2samples&&e.mds.variant2samples.sunburst_twLst){await Ht(t,e,s,a);return}await Ut({mlst:t.mlst,tk:e,block:s,tippos:a})}catch(t){s.error(t.message||t);if(t.stack)console.log(t.stack)}}async function Ht(t,e,s,a){e.glider.style("cursor","wait");const n=await e.mds.variant2samples.get({mlst:t.mlst,querytype:e.mds.variant2samples.type_sunburst});e.glider.style("cursor","auto");const i={nodes:n.nodes,occurrence:t.occurrence,boxyoff:e.yoff,boxheight:Math.min(800,e.height),boxwidth:s.width,svgheight:Number.parseFloat(s.svg.attr("height")),g:e.skewer.g.append("g"),pica:e.pica,click_listbutton:(n,i)=>{Ut({mlst:t.mlst,tk:e,block:s,tippos:a})},click_ring:async(a,n)=>{e.itemtip.clear();const i={mlst:t.mlst,tk:e,block:s,div:e.itemtip.d,tid2value:{}};i.tid2value[n.data.id0]=n.data.v0;if(n.data.id1)i.tid2value[n.data.id1]=n.data.v1;if(n.data.id2)i.tid2value[n.data.id2]=n.data.v2;i.mlst=t.mlst.map((t=>{if(e.mds.variant2samples.variantkey=="ssm_id"){return{ssm_id:t.ssm_id,occurrence:0}}throw"unknown variant2samples.variantkey"}));i.mlst[0].occurrence=n.value;const o=a.clientX;const r=a.clientY;await Lt(i);e.itemtip.show2(o,r)}};if(t.aa){i.cx=t.aa.x;i.cy=Jt(t,e)+t.yoffset*(e.skewer.pointup?-1:1)}else{i.cx=t.x;i.cy=t.y+(e.skewer.pointup?1:-1)*e.skewer.stem1/2}if(t.mlst.length==1){i.chartlabel=t.mlst[0].mname}else{const e=new Set(t.mlst.map((t=>t.mname)));if(e.size==1){i.chartlabel=[...e][0]}else{i.chartlabel=t.mlst.reduce(((t,e)=>e.occurrence>t.occurrence?e:t)).mname+" etc"}}const o=await import("./sunburst-bbff8818.js");o.default(i)}async function Ut(t){t.tk.itemtip.clear().show(t.tippos.left-10,t.tippos.top-10);t.div=t.tk.itemtip.d;t.tipDiv=t.tk.itemtip.d;await pt(t)}const Pt=0;const Et=1;const Vt=.3;const Kt=1;const Wt=.6;const Xt="Arial";function Qt(t,e){const s=t.skewer;for(const t of s.data){t.x0=t.x;if(t.xoffset!=undefined){t.x=t.x0+t.xoffset}for(const e of t.groups){e.aa=t}}const a=Math.max(14,e.width/110);let n=0;for(const t of s.data){for(const e of t.groups){n=Math.max(n,e.occurrence)}}let i=0;const o=Math.pow(a/2,2)*Math.PI;if(n<=10)i=o*n*.9;else if(n<=100)i=o*10;else if(n<=1e3)i=o*14;else i=o*20;const c=d().domain([1,n*.5,n*.6,n*.7,n*.8,n]).range([o,o+(i-o)*.8,o+(i-o)*.85,o+(i-o)*.9,o+(i-o)*.95,i]);let m=a/2;s.maxheight=0;for(const t of s.data){if(t.showmode==undefined)t.showmode=Pt;if(t.slabelrotate==undefined)t.slabelrotate=false;t.maxradius=0;t.maxrimwidth=0;t.width=0;t.slabelwidth=0;for(const e of t.groups){if(e.occurrence<=1){e.radius=a/2}else{const t=e.occurrence.toString().length;e.radius=Math.max(Math.sqrt(c(e.occurrence)/Math.PI),t*5)}t.maxradius=Math.max(t.maxradius,e.radius);m=Math.max(m,e.radius);e.rimwidth=e.rim1count+e.rim2count==0?0:Math.max(2,e.radius/6);t.maxrimwidth=Math.max(t.maxrimwidth,e.rimwidth)}let e=0;for(const s of t.groups){s.yoffset=e+s.radius+s.rimwidth;e+=(s.radius+s.rimwidth)*2}s.maxheight=Math.max(s.maxheight,e)}s.selection=s.g.selectAll().data(s.data).enter().append("g").attr("class","sja_skg").each((function(t){t.skewer=this}));const u=s.selection.selectAll().data((t=>t.groups)).enter().append("g").attr("transform",(e=>"translate(0,"+(e.aa.showmode==Pt?0:e.yoffset*(t.skewer.pointup?-1:1))+")")).attr("class","sja_aa_discg").each((function(t){t.g=this}));const p=u.append("circle");p.filter((t=>t.dt==f||t.dt==r||t.dt==l)).attr("fill",(e=>t.color4disc(e.mlst[0]))).attr("stroke","white").attr("r",(t=>t.radius-.5));u.filter((t=>t.dt==l||t.dt==r)).append("path").attr("fill","white").attr("stroke","none").attr("d",(t=>I()({innerRadius:0,outerRadius:t.radius-2,startAngle:t.useNterm?0:Math.PI,endAngle:t.useNterm?Math.PI:Math.PI*2})));const h=u.filter((t=>t.occurrence>1)).append("text").text((t=>t.occurrence)).attr("font-family",Xt).attr("class","sja_aa_discnum").attr("fill-opacity",(t=>t.aa.showmode==Pt?0:1)).attr("stroke-opacity",(t=>t.aa.showmode==Pt?0:1)).attr("text-anchor","middle").each((t=>{const e=t.radius*1.5;t.discnumfontsize=Math.min(e/(t.occurrence.toString().length*Wt),e)})).attr("font-size",(t=>t.discnumfontsize)).attr("y",(t=>t.discnumfontsize*Vt));h.filter((t=>t.dt==f)).attr("fill","white");h.filter((t=>t.dt==r||t.dt==l)).attr("stroke",(e=>t.color4disc(e.mlst[0]))).attr("stroke-width",.8).attr("font-weight","bold").attr("fill","white");u.append("text").text((e=>e.mnameCompact||t.mnamegetter(e.mlst[0]))).attr("font-size",(t=>{t._labfontsize=Math.max(12,t.radius*1.2);return t._labfontsize})).each((function(t){const e=this.getBBox().width;t._label_width=e;if(t.aa.groups.length==1){t.aa.slabelrotate=true;t.aa.slabelwidth=e;s.maxheight=Math.max(s.maxheight,(t.radius+t.rimwidth)*2+2+e)}})).attr("fill",(e=>t.color4disc(e.mlst[0]))).attr("x",(t=>t.radius+t.rimwidth+1)).attr("y",(t=>t._labfontsize*Vt)).attr("font-family",Xt).classed("sja_aa_disclabel",true).attr("fill-opacity",(t=>t.aa.showmode==Pt?0:1)).attr("transform","scale(1) 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t.rim1_startangle}));u.filter((t=>t.rim1count>0)).append("path").attr("d",g).attr("fill",(e=>t.color4disc(e.mlst[0]))).attr("class","sja_aa_discrim").attr("fill-opacity",0);const b=I().innerRadius((t=>t.radius+.5)).outerRadius((t=>t.radius+.5+t.rimwidth)).startAngle((t=>t.rim1_startangle)).endAngle((t=>t.rim1_startangle+Math.PI*2*t.rim2count/t.occurrence));u.filter((t=>t.rim2count>0)).append("path").attr("d",b).attr("stroke",(e=>t.color4disc(e.mlst[0]))).attr("fill","none").attr("class","sja_aa_discrim").attr("stroke-opacity",0);{let t=0;let e=0;for(const a of s.data){if(a.x-a.maxradius-a.maxrimwidth<e){t++}e=Math.max(e,a.x+a.width-a.maxradius-a.maxrimwidth)}s.stem1=t==0?0:a;s.stem2=d().domain([0,1,s.data.length]).range([0,a,a*3])(t)}const v=a*.7;let y=0;for(const t of s.data){for(const e of t.groups){y=Math.max(y,e.occurrence)}}s.stem3=Math.max(2,v+a*Math.min(5,y));s.selection.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.skewer.pointup?-1:1)*e.maxradius)).attr("transform",(t=>`scale(${t.showmode==Pt?"1,1":"0.01,0.01"})`)).on("mouseover",((e,s)=>{let a=0;let n=0;const i=5;const o=t.skewer.pointup?7:14;for(const e of s.groups){e.pica_fontsize=Math.max(11,e.radius);a+=e.pica_fontsize+1;t.pica.g.append("text").text((e.mnameCompact||e.mlst[0].mname)+(e.occurrence>1?" x"+e.occurrence:"")).attr("font-size",e.pica_fontsize).each((function(){n=Math.max(n,this.getBBox().width)})).remove()}n+=i*2;const r=a+5;t.pica.g.append("rect").attr("y",t.skewer.pointup?-r:0).attr("width",n).attr("height",r).attr("fill","white").attr("fill-opacity",.8).attr("stroke","#ccc").attr("shape-rendering","crispEdges");a=0;const 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d=t.pica.g.append("g").attr("transform","translate("+(i+c/2)+","+(t.skewer.pointup?1:-1)+")");d.append("line").attr("y2",(t.skewer.pointup?1:-1)*o).attr("stroke","#858585").attr("shape-rendering","crispEdges");d.append("line").attr("x1",-1).attr("x2",-1).attr("y2",(t.skewer.pointup?1:-1)*o).attr("stroke","white").attr("shape-rendering","crispEdges");d.append("line").attr("x1",1).attr("x2",1).attr("y2",(t.skewer.pointup?1:-1)*o).attr("stroke","white").attr("shape-rendering","crispEdges")})).on("mouseout",((e,s)=>{t.pica.g.selectAll("*").remove()})).on("click",((s,a)=>{t.pica.g.selectAll("*").remove();te([a],t,e)}));let k=0;for(const t of s.data){k=Math.max(k,t.occurrence)}const x=d().domain([1,k]).range([v,s.stem3-m]);s.selection.attr("transform",(e=>{e.foldyoffset=x(e.occurrence);e.y=Jt(e,t);return"translate("+e.x+","+e.y+")"}));s.selection.append("path").attr("class","sja_aa_stem").attr("d",(e=>Yt(e,t))).attr("stroke",(e=>t.color4disc(e.groups[0].mlst[0]))).attr("fill","none");const 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s=w(t.target.parentNode);s.selectAll(".sja_aa_disckick").transition().attr("stroke-opacity",1);s.select(".sja_aa_ssk_bg").transition().attr("fill-opacity",1).attr("stroke-opacity",1);s.select(".sja_aa_ssk_text").transition().attr("fill-opacity",1)})).on("mouseout",(function(t,e){const s=w(t.target.parentNode);s.selectAll(".sja_aa_disckick").transition().attr("stroke-opacity",0);s.select(".sja_aa_ssk_bg").transition().attr("fill-opacity",0).attr("stroke-opacity",0);s.select(".sja_aa_ssk_text").transition().attr("fill-opacity",0)})).on("click",(async(s,a)=>{Gt(a,t,e,s.target.getBoundingClientRect(),null,s.target)}))}function Jt(t,e){if(e.skewer.pointup){if(t.showmode==Pt){return e.skewer.maxheight+e.skewer.stem1+e.skewer.stem2+e.skewer.stem3-t.foldyoffset}return e.skewer.maxheight}if(t.showmode==Pt)return t.foldyoffset;return e.skewer.stem1+e.skewer.stem2+e.skewer.stem3}function 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t.mlst){if(!o.has(e.dt))o.set(e.dt,[]);o.get(e.dt).push(e)}}if(t.cnv?.cnvLst){o.set(s,t.cnv.cnvLst)}if(o.size==1){const e=t.menutip.d.append("div").style("margin","10px");await pt({div:e,mlst:o.get([...o.keys()][0]),tk:t,block:a,doNotListSample4multim:true});return}const r=[];for(const[t,s]of o){r.push({label:s.length+" "+e[t]})}new A({holder:t.menutip.d.append("div").attr("class","sja_pp_vlb_dttabdiv").style("margin","10px"),tabs:r}).main();let l=0;for(const[e,s]of o){pt({div:r[l++].contentHolder.append("div").style("margin-left","10px"),mlst:s,tk:t,block:a,doNotListSample4multim:true})}}function He(t,e){if(!t.skewer)return;if(t.skewer.viewModes.length<=1){return}const s=[];for(const[e,a]of t.skewer.viewModes.entries()){const t={label:Ue(a),value:e};if(a.inuse)t.checked=true;s.push(t)}D({holder:t.menutip.d.append("div").attr("class","sja_pp_vlb_viewmoderadiodiv").style("margin","10px"),options:s,callback:async s=>{for(const e of t.skewer.viewModes)e.inuse=false;t.skewer.viewModes[s].inuse=true;Ne({skewer:t.skewer.rawmlst},t,e);Xe(t,e);t._finish()}})}function Ue(t){if(!t)return"MISSING!!";if(t.type=="skewer")return"As lollipops";if(t.type=="numeric")return t.label+" as Y axis";return"unknown mode"}async function Pe(t,e){if(!t.mds.variant2samples){console.log("TODO: variant-only");return}const s={querytype:"samples"};Ds(t,e,s);const a=(await t.mds.variant2samples.get(s)).samples;const[n,o]=await Tt(a,t);const c=[];for(const t of n){if(t.isSsm){c.push("AAchange");c.push("Consequence");c.push("Mutation");continue}if(t.isMaf){c.push("Alternative allele depth in tumor");c.push("Total depth in tumor");continue}c.push(t.label)}const d=[];for(const[e,s]of a.entries()){let a;if(Array.isArray(s.ssm_id_lst)){a=s.ssm_id_lst}else if(s.ssm_id){a=[s.ssm_id]}else{console.log("sample obj lacks ssm_id and ssm_id_lst");continue}for(const s of a){const a=t.skewer.rawmlst.find((t=>t.ssm_id==s));if(!a){console.log("ssm not found by 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t;e.menutip=new t({padding:""});e.load=_s(e,s);e.mnamegetter=t=>{if(e.mds.queries?.snvindel?.vcfid4skewerName&&t.vcf_id)return t.vcf_id;const s=t.mname;if(!s)return"";if(s.length>25){return s.substr(0,20)+"..."}return s};await hs(e,s);await bs(e,s);await ys(e,s);ws(e,s);vs(e,s);fs(e);ms(e);await zs(e);e.tklabel.text(e.mds.label||e.name);e.clear=()=>{if(e.skewer)e.skewer.g.selectAll("*").remove()};X(e,s);ps(e);e.color4disc=t=>{if(e.mutationColorBy){if(e.mutationColorBy=="hardcode"){if(t.color)return t.color}}if(e.mds.queries?.ld?.mOverlay?.data){const s=e.mds.queries.ld.mOverlay.m;if(t.chr==s.chr&&t.pos==s.pos&&t.ref==s.ref&&t.alt==s.alt){return e.mds.queries.ld.overlay.color_1}for(const s of e.mds.queries.ld.mOverlay.data){if(s.pos==t.pos&&s.alleles==t.ref+"."+t.alt){return e.mds.queries.ld.colorScale(s.r2)}}return e.mds.queries.ld.overlay.color_0}if(e.vcfinfofilter&&e.vcfinfofilter.setidx4mclass!=undefined){const s=e.vcfinfofilter.lst[e.vcfinfofilter.setidx4mclass];const[a,n]=js(s,t);if(a||n==undefined)return"black";for(const t of n){if(s.categories[t]){return s.categories[t].color}else{return"black"}}}if(i[t.class]){return i[t.class].color}return"black"};ds(e);if(e.hlssmid){e.skewer.hlssmid=new Set(e.hlssmid.split(","));delete e.hlssmid}try{Ls(e)}catch(t){console.error(t)}}function cs(t,e){return s=>{t.legend?.headTd.text(t.name+(t.filterObj?" - "+ts(t.filterObj):""));if(t.cnv){t.cnv.g.transition().attr("transform",`translate(0,${t.subtk2height.skewer||0})`)}if(s){if(s.error){t.subtk2height.skewer=40}else{let a=0;if(s.skewer)a=s.skewer.length;if(s.cnv)a+=s.cnv.length;if(a==0){let s="view range";if(e.usegm&&e.gmmode!="genomic")s=e.usegm.name||e.usegm.isoform;t.skewer.g.append("text").text("No mutation in "+s).attr("y",25).attr("x",e.width/2).attr("text-anchor","middle").attr("dominant-baseline","center");t.subtk2height.skewer=40}}}t.height_main=Math.max(t.subtk2height.leftlabels||0,t.subtk2height.skewer+(t.subtk2height.cnv||0))+t.toppad+t.bottompad;if(s){st(s,t)}t.leftLabelMaxwidth=Math.max(t.leftlabels.maxwidth+t.leftlabels.xoff,t.skewer?t.skewer.maxwidth:0);e.tkcloakoff(t,{error:s?s.error:null});e.block_setheight();e.setllabel();if(typeof t.callbackOnRender=="function"){t.callbackOnRender(t,e)}}}function ds(t){const e=M();if(t.skewer){if(e.has("hlaachange")){t.hlaachange=e.get("hlaachange")}if(e.has("hlssmid")){t.hlssmid=e.get("hlssmid").split(",")}}}function fs(t){if(!t.mds.has_skewer)return;t.skewer={g:t.glider.append("g"),hlBoxColor:t.mds.hlBoxColor||"red",hideDotLabels:false,pointup:true};us(t)}function ms(t){const e=t.mds.termdbConfig?.queries?.cnv;if(!e)return;t.cnv={g:t.glider.append("g"),cnvMaxLength:e.cnvMaxLength,cnvGainCutoff:e.cnvGainCutoff,cnvLossCutoff:e.cnvLossCutoff,absoluteValueRenderMax:e.absoluteValueRenderMax||5,gainColor:e.gainColor||"#D6683C",lossColor:e.lossColor||"#67a9cf"}}function us(t){t.skewer.viewModes=t.skewerModes;delete t.skewerModes;if(!t.skewer.viewModes)t.skewer.viewModes=[];const e=t.skewer.viewModes;if(!Array.isArray(e))throw"skewerModes[] is not array";if(t.mds.skewerModes){for(const s of t.mds.skewerModes)e.push(s)}if(!e.find((t=>t.type=="skewer")))e.push({type:"skewer"});for(const t of e){if(typeof t!="object")throw"one of skewerModes[] is not object";if(t.type=="skewer"){if(!t.label)t.label="lollipops"}else if(t.type=="numeric"){if(t.byAttribute){if(!t.label)t.label=t.byAttribute}else if(t.byInfo);else{throw"unknown data method for a type=numeric mode"}}else{throw"unknown type from a skewerModes[]"}}if(!e.find((t=>t.inuse)))e[0].inuse=true}function ps(t){if(t.mds.hiddenmclass){for(const e of t.mds.hiddenmclass)t.legend.mclass.hiddenvalues.add(e)}}async function hs(t,e){if(t.dslabel){const s=await u("getDataset",{body:{genome:e.genome.name,dsname:t.dslabel}});if(s.error)throw"Error: "+s.error;if(!s.ds)throw"data.ds{} missing";t.mds=s.ds;t.name=s.ds.label;return}if(!t.name)t.name="Custom data";t.mds={};if(t.bcf){if(!t.bcf.file&&!t.bcf.url)throw"file or url missing for tk.bcf{}";t.mds.has_skewer=true;await qs(t,e.genome)}else if(t.custom_variants){t.mds.has_skewer=true;As(t,e);Cs(t)}else{throw"unknown data source for custom track"}gs(t)}function gs(t){if(!t.sampleAnnotation)return;if(!Array.isArray(t.sampleAnnotation.terms))throw"sampleAnnotation.terms is not array";if(!t.mds.termdb)t.mds.termdb={};t.mds.termdb.terms=t.sampleAnnotation.terms;t.mds.termdb.annotations=t.sampleAnnotation.annotations}async function bs(t,e){const s=t.mds.termdb;if(!s)return;{const a={};if(t.mds.label){a.vocab={genome:e.genome.name,dslabel:t.mds.label}}else if(s.terms){a.vocab={terms:s.terms,sampleannotation:s.annotations}}else{throw"do not know how to init vocab"}const n=await import("./FilterRxComp-fc769f34.js").then((function(t){return t.z}));s.vocabApi=n.vocabInit(a)}t.mds.termdbConfig=await s.vocabApi.getTermdbConfig();if(t.mds.termdb.allowCaseDetails){t.mds.termdb.allowCaseDetails.get=async t=>{}}}function ws(t,e){if(!t.mds.queries?.snvindel?.m2csq)return;t.mds.queries.snvindel.m2csq.get=async s=>{const a={genome:e.genome.name,dslabel:t.mds.label,m2csq:1};if(t.mds.queries.snvindel.m2csq.by=="ssm_id"){a.ssm_id=s.ssm_id}else{return{error:"unknown query method"}}const n={"Content-Type":"application/json",Accept:"application/json"};if(t.token)n["X-Auth-Token"]=t.token;return await u("mds3",{body:a,headers:n},{serverData:t.cache})}}function vs(t,e){if(!t.mds.queries?.singleSampleMutation)return;t.mds.queries.singleSampleMutation.get=async s=>{const a={genome:e.genome.name,dslabel:t.mds.label,sample:s};const n={"Content-Type":"application/json",Accept:"application/json"};if(t.token)n["X-Auth-Token"]=t.token;const i=await u("termdb/singleSampleMutation",{body:a,headers:n});if(i.error)throw i.error;if(!Array.isArray(i.mlst))throw"data.mlst is not array";return i.mlst}}async function ys(t,e){if(!t.mds.variant2samples)return;if(t.custom_variants){ks(t)}else{xs(t,e)}if(t.mds.variant2samples.twLst){if(!Array.isArray(t.mds.variant2samples.twLst))throw"v2s.twLst[] not array";if(!t.mds.termdb?.vocabApi)throw"mds.termdb.vocabApi should be present for initiating v2s.twLst";for(const e of t.mds.variant2samples.twLst)await E(e,t.mds.termdb.vocabApi)}}function ks(t,e){t.mds.variant2samples.get=e=>{if(e.querytype==t.mds.variant2samples.type_samples){const t=[];for(const s of e.mlst){if(!s.samples)continue;for(const e of s.samples){const a=JSON.parse(JSON.stringify(e));a.ssm_id=s.ssm_id;t.push(a)}}return{samples:t}}if(e.querytype==t.mds.variant2samples.type_summary){throw"todo: summary"}if(e.querytype==t.mds.variant2samples.type_sunburst){throw"todo: sunburst"}throw"unknown querytype"};t.mds.getSamples=()=>{const e=new Map;for(const s of t.custom_variants){if(!s.samples)continue;for(const t of s.samples){if(e.has(t.sample_id)){e.get(t.sample_id).ssm_id_lst.push(s.ssm_id)}else{const a=JSON.parse(JSON.stringify(t));a.ssm_id_lst=[s.ssm_id];e.set(t.sample_id,a)}}}return{samples:[...e.values()]}}}function xs(t,e){t.mds.variant2samples.get=async s=>{const a={genome:e.genome.name,variant2samples:1,get:s.querytype};if(t.mds.label){a.dslabel=t.mds.label}else if(t.bcf){if(t.bcf.file)a.bcffile=t.bcf.file;else if(t.bcf.url)a.bcfurl=t.bcf.url;else throw"tk.bcf{}: file/url missing"}else{throw"no dslabel or tk.bcf"}if(s.groupSsmBySample){a.groupSsmBySample=1}if(s.mlst){if(t.mds.variant2samples.variantkey=="ssm_id"){a.ssm_id_lst=s.mlst.map((t=>t.ssm_id)).join(",")}else{throw"unknown variantkey for variant2samples"}}if(s.isoform){a.isoform=s.isoform}if(s.rglst){a.rglst=s.rglst}const n={"Content-Type":"application/json",Accept:"application/json"};if(t.set_id)a.set_id=t.set_id;if(t.token)n["X-Auth-Token"]=t.token;if(t.filter0)a.filter0=t.filter0;if(t.filterObj)a.filterObj=t.filterObj;if(s.tid2value)a.tid2value=s.tid2value;if(s.querytype==t.mds.variant2samples.type_sunburst){if(t.mds.variant2samples.sunburst_twLst){a.twLst=t.mds.variant2samples.sunburst_twLst}}else if(s.querytype==t.mds.variant2samples.type_samples){if(t.mds.variant2samples.twLst)a.twLst=t.mds.variant2samples.twLst}else if(s.querytype==t.mds.variant2samples.type_summary){if(t.mds.variant2samples.twLst)a.twLst=t.mds.variant2samples.twLst}else{throw"unknown querytype"}a.skewerRim=t.mds.queries.snvindel?.skewerRim;if(t.legend.formatFilter){const e={};for(const s in t.legend.formatFilter){if(t.legend.formatFilter[s].hiddenvalues.size){e[s]=[...t.legend.formatFilter[s].hiddenvalues]}}if(Object.keys(e).length){a.formatFilter=e}}if(t.legend.mclass?.hiddenvalues?.size){a.hiddenmclasslst=[...t.legend.mclass.hiddenvalues].join(",")}const i=await u("mds3",{body:a,headers:n},{serverData:t.cache});if(i.error)throw i.error;const o=i.variant2samples;if(!o)throw"result error";if(s.querytype==t.mds.variant2samples.type_sunburst){if(!Array.isArray(o.nodes))throw"nodes[] not array from return"}else if(s.querytype==t.mds.variant2samples.type_samples){if(!Array.isArray(o.samples))throw"samples[] not array from return"}else if(s.querytype==t.mds.variant2samples.type_summary){if(!Array.isArray(o.summary))throw"summary[] not array from return"}else{throw"unknown querytype"}return o};t.mds.getSamples=async(s={})=>{if(s.isSummary){s.querytype=t.mds.variant2samples.type_summary}else{s.querytype=t.mds.variant2samples.type_samples;s.groupSsmBySample=1}Ds(t,e,s);return await t.mds.variant2samples.get(s)}}function _s(t,e){return async()=>await Is(t,e)}function js(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 a=Array.isArray(s)?s:[s];if(t.altalleleinfo.separator){a=a[0].split(t.altalleleinfo.separator)}return[null,a]}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 a=Array.isArray(s)?s:[s];if(t.locusinfo.separator){a=a[0].split(t.locusinfo.separator)}return[null,a]}return["no trigger"]}function As(t,e){for(const s of t.custom_variants){if(s.dt==f){Ms(s);continue}if(s.dt==l||s.dt==r){Ss(s,e);continue}throw"unknown dt for a custom variant"}}function Ms(t){if(!t.chr)throw".chr missing for custom snvindel";if(!Number.isInteger(t.pos))throw".pos not integer for custom snvindel";if(!t.ssm_id){t.ssm_id=t.chr+"."+t.pos+"."+(t.ref&&t.alt?t.ref+"."+t.alt:t.mname)}}function Ss(t,e){if(t.pairlst);else{if(!t.chr1)throw".chr1 missing for custom sv/fusion";if(!Number.isInteger(t.pos1))throw".pos1 not integer for custom svfusion";if(t.strand1!="+"&&t.strand1!="-")throw".strand1 not +/- for custom svfusion";if(!t.chr2)throw".chr1 missing for custom sv/fusion";if(!Number.isInteger(t.pos2))throw".pos1 not integer for custom svfusion";if(t.strand2!="+"&&t.strand2!="-")throw".strand1 not +/- for custom svfusion";t.pairlst=[{a:{chr:t.chr1,pos:t.pos1,strand:t.strand1,name:t.gene1||""},b:{chr:t.chr2,pos:t.pos2,strand:t.strand2,name:t.gene2||""}}];delete t.chr1;delete t.pos1;delete t.strand1;delete t.gene1;delete t.chr2;delete t.pos2;delete t.strand2;delete t.gene2}const s=[t.dt];const a=e.seekcoord(t.pairlst[0].a.chr,t.pairlst[0].a.pos);if(a.length&&a[0].x>0&&a[0].x<e.width){s.push(...[t.pairlst[0].a.chr,t.pairlst[0].a.pos,t.pairlst[0].a.strand,0,t.pairlst[0].a.name]);t.mname=t.pairlst[0].b.name||"";t.chr=t.pairlst[0].a.chr;t.pos=t.pairlst[0].a.pos;t.pairlstIdx=0}else{const a=e.seekcoord(t.pairlst[0].b.chr,t.pairlst[0].b.pos);if(a.length&&a[0].x>0&&a[0].x<e.width){s.push(...[t.pairlst[0].b.chr,t.pairlst[0].b.pos,t.pairlst[0].b.strand,1,t.pairlst[0].b.name]);t.mname=t.pairlst[0].a.name||"";t.chr=t.pairlst[0].b.chr;t.pos=t.pairlst[0].b.pos;t.pairlstIdx=1}}t.ssm_id=s.join(".")}function Cs(t){if(t.custom_variants.find((t=>t.occurrence!=undefined))){return}for(const e of t.custom_variants){if(e.sample){e.sample_id=e.sample;delete e.sample}}if(!t.custom_variants.find((t=>t.sample_id))){return}const e=new Map;for(const s of t.custom_variants){const t=s.mname+"."+s.chr+"."+s.pos+"."+s.ref+"."+s.alt;const a=e.get(t);if(a){a.occurrence++;a.samples.push({sample_id:s.sample_id})}else{s.occurrence=1;s.samples=[{sample_id:s.sample_id}];delete s.sample_id;e.set(t,s)}}t.custom_variants=[];for(const s of e.values())t.custom_variants.push(s);if(!t.mds.variant2samples)t.mds.variant2samples={};const s=t.mds.variant2samples;s.type_samples="samples";s.type_summary="summary";s.type_sunburst="sunburst"}async function qs(t,e){const s={genome:e.name};if(t.bcf.file){s.file=t.bcf.file}else{s.url=t.bcf.url;if(t.bcf.indexURL)s.indexURL=t.bcf.indexURL}const a=await u("vcfheader",{body:s});if(a.error)throw a.error;const[n,i,o,r]=B(a.metastr.split("\n"));if(r)throw"Error parsing VCF meta lines: "+r.join("; ");t.mds.bcf={info:n,format:i};if(o?.length){t.mds.bcf.samples=o;t.mds.variant2samples={type_samples:"samples",variantkey:"ssm_id"}}if(!t.mds.queries)t.mds.queries={};t.mds.queries.snvindel={forTrack:true}}function Ls(t){const e=t.allow2selectSamples;if(!e)return;if(!e.buttonText)e.buttonText="Select samples";if(typeof e.buttonText!="string")throw"allow2selectSamples.buttonText value is not string";if(!e.attributes)e.attributes=[{from:"sample_id",to:"sample_id"}];if(!Array.isArray(e.attributes))throw"allow2selectSamples.attributes[] is not array";if(e.attributes.length==0)throw"allow2selectSamples.attributes[] blank array";for(const t of e.attributes){if(typeof t.from!="string"||!t.from)throw"allow2selectSamples.attributes.from is not string";if(typeof t.to!="string"||!t.to)throw"allow2selectSamples.attributes.to is not string"}if(typeof e.callback!="function")throw"allow2selectSamples.callback() is not function";e._cart=[]}async function zs(t){if(!t.filterObj)return;if(typeof t.filterObj!="object")throw"tk.filterObj{} is set but is not object";await e(t.filterObj);async function e(s){if(s.type=="tvs"){if(!s.tvs?.term)throw"tvs.tvs.term missing";if(!s.tvs.term.id)throw"tvs.tvs.term.id missing";s.tvs.term=await t.mds.termdb.vocabApi.getterm(s.tvs.term.id);return}if(s.type=="tvslst"){if(!Array.isArray(s.lst))throw"tvslst.lst[] not array";for(const t of s.lst)await e(t);return}throw"type not tvs or tvslst"}}function Ns(t,e,s){e.cnv?.g.selectAll("*").remove();if(!t.cnv){delete e.subtk2height.cnv;return}const[a,n,i]=$s(t,e,s);e.cnv.cnvLst=n;e.cnv.absoluteMax=i;e.cnv.colorScale=d([-i,0,i],[e.cnv.lossColor,"white",e.cnv.gainColor]).clamp(true);const[o,r]=Rs(a);let l=0;for(const t of a){for(const a of t.cnvs){const n=Math.max(0,a.x1),i=Math.min(a.x2,s.width);e.cnv.g.append("rect").attr("x",n).attr("y",l).attr("width",i-n).attr("height",o).attr("fill",e.cnv.colorScale(a.value)).on("mouseover",(s=>{s.target.setAttribute("stroke","black");e.itemtip.clear().show(s.clientX,s.clientY);const n=m({holder:e.itemtip.d});const i=structuredClone(a);i.samples=[{sample_id:t.sample_id}];At({mlst:[i],tk:e},n)})).on("mouseout",(t=>{t.target.setAttribute("stroke","");e.itemtip.hide()}))}l+=o+r}e.subtk2height.cnv=l}function $s(t,e,s){let a=0;const n=new Map;const i=[];for(const e of t.cnv){if(!e.chr)continue;if(!Number.isFinite(e.value)){if(typeof e.class=="string"){if(e.class==S){e.value=1}else if(e.class==C){e.value=-1}else{continue}}else{continue}}if(!Number.isInteger(e.start)||!Number.isInteger(e.stop))continue;const t=s.seekcoord(e.chr,e.start)[0];if(!t)continue;const o=s.seekcoord(e.chr,e.stop)[0];if(!o)continue;const r={chr:e.chr,start:e.start,stop:e.stop,value:e.value,dt:e.dt};if(t.x>o.x){r.x1=o.x;r.x2=t.x}else{r.x1=t.x;r.x2=o.x}if(!Array.isArray(e.samples))continue;i.push(e);for(const t of e.samples){if(!n.has(t.sample_id))n.set(t.sample_id,[]);n.get(t.sample_id).push(structuredClone(r))}a=Math.max(a,Math.abs(e.value))}const o=[];for(const[t,e]of n){o.push({sample_id:t,cnvs:e,x1:Math.min(...e.map((t=>t.x1))),x2:Math.max(...e.map((t=>t.x2)))})}o.sort(((t,e)=>t.x1-e.x1));return[o,i,Math.min(e.cnv.absoluteValueRenderMax,a)]}const Os=d([40,120],[10,1]);function Rs(t,e){if(t.length>120)return[1,0];if(t.length<40)return[10,1];return[Math.ceil(Os(t.length)),1]}async function Is(t,e){e.tkcloakon(t);e.block_setheight();try{if(!t.mds||t.uninitialized){await ls(t,e)}const s=await Fs(t,e);if(t.uninitialized){t.clear();delete t.uninitialized}Ne(s,t,e);Ns(s,t,e);await Ke(s,t,e);t._finish(s)}catch(e){if(t.clear)t.clear();if(t.subtk2height)t.subtk2height.skewer=50;if(t._finish)t._finish({error:e.message||e});if(e.stack)console.log(e.stack);return}}function Ts(t,e){const s={genome:e.genome.name,forTrack:1,skewerRim:t.mds.queries?.snvindel?.skewerRim};const a={"Content-Type":"application/json",Accept:"application/json"};if(t.mds.has_skewer){s.skewer=1}if(t.set_id){s.set_id=t.set_id}if(t.filter0){s.filter0=t.filter0}if(t.filterObj){if(t.filterObj?.lst.length){s.filterObj=t.filterObj}}if(t.token){a["X-Auth-Token"]=t.token}if(t.mds.label){s.dslabel=t.mds.label}else{if(t.bcf){if(t.bcf.file){s.bcffile=t.bcf.file}else if(t.bcf.url){s.bcfurl=t.bcf.url;if(t.bcf.indexURL)s.bcfindexURL=t.bcf.indexURL}else{throw".file and .url missing for tk.bcf{}"}}}Ds(t,e,s);if(t.legend.mclass.hiddenvalues.size){s.hiddenmclasslst=[...t.legend.mclass.hiddenvalues].join(",")}if(t.legend.bcfInfo){const e={};for(const s in t.legend.bcfInfo){if(t.legend.bcfInfo[s].hiddenvalues.size){e[s]=[...t.legend.bcfInfo[s].hiddenvalues]}}if(Object.keys(e).length){s.infoFilter=e}}if(t.legend.formatFilter){const e={};for(const s in t.legend.formatFilter){if(t.legend.formatFilter[s].hiddenvalues.size){e[s]=[...t.legend.formatFilter[s].hiddenvalues]}}if(Object.keys(e).length){s.formatFilter=e}}if(t.cnv){if(t.cnv.cnvMaxLength)s.cnvMaxLength=t.cnv.cnvMaxLength;if(t.cnv.cnvGainCutoff)s.cnvGainCutoff=t.cnv.cnvGainCutoff;if(t.cnv.cnvLossCutoff)s.cnvLossCutoff=t.cnv.cnvLossCutoff}return[s,a]}async function Fs(t,e){let s;if(t.custom_variants){s=await Bs(t,e)}else{const[a,n]=Ts(t,e);s=await u("mds3",{body:a,headers:n})}if(s.error)throw s.error;return s}function Ds(t,e,s){if(typeof s!="object")throw"par{} is not object";let a=[];if(e.usegm){const t={chr:e.rglst[0].chr,reverse:e.rglst[0].reverse,width:0,start:null,stop:null};for(let s=e.startidx;s<=e.stopidx;s++){const a=e.rglst[s];t.width+=a.width+e.regionspace;t.start=t.start==null?a.start:Math.min(t.start,a.start);t.stop=t.stop==null?a.stop:Math.max(t.stop,a.stop)}a.push(t);if(e.gmmode=="genomic");else{s.isoform=e.usegm.isoform;s.gene=e.usegm.name}}else{a=e.tkarg_rglst(t)}let n=0;for(const t of a){t.xoff=0;n+=t.width+e.regionspace}if(e.subpanels.length==t.subpanels.length){for(const t of e.subpanels){a.push({chr:t.chr,start:t.start,stop:t.stop,width:t.width,exonsf:t.exonsf,xoff:n});n+=t.width+t.leftpad}}s.rglst=a}async function Bs(t,e){const s={skewer:[]};let a=null,n;for(let t=e.startidx;t<=e.stopidx;t++){if(a==null){a=e.rglst[t].start;n=e.rglst[t].stop}else{a=Math.min(a,e.rglst[t].start);n=Math.max(n,e.rglst[t].stop)}}const o=new Map;for(const r of t.custom_variants){if(r.chr!=e.rglst[0].chr)continue;if(r.pos<=a||r.pos>=n)continue;if(!r.class)r.class="X";if(!i[r.class])r.class="X";o.set(r.class,1+(o.get(r.class)||0));if(t.legend.mclass.hiddenvalues.has(r.class))continue;s.skewer.push(r)}if(s.skewer.some((t=>t.samples))){const t=new Set;for(const e of s.skewer){if(e.samples){for(const s of e.samples)t.add(s.sample_id)}}s.sampleTotalNumber=t.size}s.mclass2variantcount=[...o];await Gs(t,s.skewer);return s}async function Gs(t){if(!t.mds.queries?.ld?.mOverlay)return;if(!t.mds.termdb?.vocabApi)return;delete t.mds.queries.ld.mOverlay.data;const e=await t.mds.termdb.vocabApi.getLDdata(t.mds.queries.ld.mOverlay.ldtkname,t.mds.queries.ld.mOverlay.m);if(e.error||!Array.isArray(e.lst))return;t.mds.queries.ld.mOverlay.data=e.lst}export{Is as loadTk,Ds as rangequery_rglst};