@sjcrh/proteinpaint-client 2.77.0 → 2.78.0

package/dist/{block.mds.svcnv-462d762d.js → block.mds.svcnv-a532eca7.js}

@@ -1 +1 @@
-import{p as t,bY as e,ac as n,Z as a,am as s,bZ as o,b_ as l,c as i,x as r,aa as c,a as p,q as d,a9 as f,b$ as m,j as u,ap as h,aq as g,ar as b,as as k,at as v,ak as x,z as y,ae as _,aN as w,aA as A,c0 as j,v as M,b as z,b6 as L,b7 as S,I as N,ah as U,ag as q,d as B,a8 as C,B as E,an as R,r as V,aW as I,bw as O,f as F,a7 as H,ao as P,ad as T,M as D,be as Y,bb as G}from"./app-3d14cbe4.js";import{a as X,s as J,u as Z,m as W,i as $}from"./block.mds.expressionstat-2c396bb9.js";import{s as K}from"./legacy-d3-polyfill-bdb2d792.js";import{l as Q}from"./block.legend-3dbc41a8.js";import{c as tt,d as et}from"./axis-747c801e.js";import{l as nt}from"./log-0ea548ec.js";import{v as at}from"./vcf-e43b533a.js";import{r as st,c as ot}from"./block.mds.svcnv.share-766e4b22.js";import"./partition-db811f6b.js";import"./arc-3d6751aa.js";import"./constant-426a1483.js";import"./math-2fb199c6.js";const lt="svcnv";const it="vcf";const rt="expression";async function ct(t){const{feature:n,tk:p,block:d,limitsamplebyeitherannotation:f,limitbysamplesetgroup:m}=t;const u=a({x:100,y:100,close:()=>{e(u.pane,p.config_handle);u.pane.style("display","none")}});if(f){const t=f[0];if(t){u.header.html('<span style="font-size:.8em;opacity:.5">'+p.name+"</span> "+t.value)}}else if(m){u.header.html('<span style="font-size:.8em;opacity:.5">'+p.name+"</span> "+m.name)}else{u.header.text(p.name)}const h={debugmode:d.debugmode,genome:d.genome,features:[n],hostURL:d.hostURL,limitsamplebyeitherannotation:f,limitbysamplesetgroup:m,jwt:d.jwt,holder:u.body.append("div").style("margin","20px")};if(p.iscustom){h.iscustom=1;h.querykey2tracks={};h.querykey2tracks[lt]={type:s.mdssvcnv,file:p.file,url:p.url,indexURL:p.indexURL};if(p.checkexpressionrank){h.querykey2tracks[rt]={type:s.mdsexpressionrank};for(const t in p.checkexpressionrank){h.querykey2tracks[rt][t]=p.checkexpressionrank[t]}}if(p.checkvcf){h.querykey2tracks[it]={type:s.mdsvcf};for(const t in p.checkvcf){if(t=="stringifiedObj")continue;h.querykey2tracks[it][t]=p.checkvcf[t]}}}else{h.dslabel=p.mds.label}if(window.location.search.includes("smx=3")){h.client=o;h.common=l;h.string2pos=i;h.invalidcoord=r;h.block=import("./block-944afb9f.js").then((function(t){return t.c}));const t=await c();t.dthm(h).then((t=>{t._pane=u;p.samplematrices.push(t)}))}else{import("./samplematrix-3556e5c0.js").then((t=>{const e=new t.Samplematrix(h);e._pane=u;p.samplematrices.push(e)}))}}function pt(a,s){if(!a.samplematrices||a.samplematrices.length==0)return;const o=a.tkconfigtip.d.append("table").style("margin-bottom","5px");for(const s of a.samplematrices){const l=o.append("tr");{const a=[];if(s.limitsamplebyeitherannotation){const t=s.limitsamplebyeitherannotation[0];a.push(t.value)}else if(s.limitbysamplesetgroup){a.push(s.limitbysamplesetgroup.name)}else{a.push("Any sample")}const o=s.features.length;a.push(o+" feature"+(o>1?"s":""));a.push(s.samples.length+" samples");const i=l.append("td").append("div").attr("class","sja_menuoption").style("border","solid 1px #ededed").text(a.join(", "));if(s._pane.pane.style("display")=="none"){i.style("border-color","black")}i.on("click",(()=>{if(s._pane.pane.style("display")=="none"){t(s._pane.pane);e(i,s._pane.pane);i.style("border-color","#ededed")}else{e(s._pane.pane,i);n(s._pane.pane);i.style("border-color","black")}}))}{l.append("td").attr("class","sja_menuoption").html("&times;").on("click",(()=>{l.remove();s._pane.pane.remove();for(const[t,e]of a.samplematrices.entries()){if(s.limitsamplebyeitherannotation){if(e.limitsamplebyeitherannotation){const n=s.limitsamplebyeitherannotation[0];const o=e.limitsamplebyeitherannotation[0];if(n.key==o.key&&n.value==o.value){a.samplematrices.splice(t,1);return}}}else{if(!e.limitsamplebyeitherannotation){a.samplematrices.splice(t,1);return}}}}))}}}async function dt(t,e){if(t.iscustom)return;if(t.singlesample)return;const n=t.tkconfigtip.d.append("div").style("margin-bottom","15px");const s=n.append("input").attr("size",20).attr("placeholder","Find sample");const o=n.append("div").style("margin-top","10px");s.on("keyup",p.debounce(l,300));async function l(){o.selectAll("*").remove();const n=s.property("value").trim();if(!n)return;const l={genome:e.genome.name,dslabel:t.mds.label,querykey:t.querykey,findsamplename:n};try{const n=await d("mdssvcnv",l);if(n.error)throw n.error;if(!n.result)return;for(const s of n.result){const n=o.append("div");n.append("span").text(s.name);if(s.grouplabel){n.append("span").style("margin-left","10px").style("font-size",".7em").text(s.grouplabel)}if(s.num_assay_tracks){n.append("span").style("font-size",".7em").style("padding","1px 5px").style("margin-left","10px").style("background","#bbb").style("color","white").style("border-radius","3px").text(s.num_assay_tracks+" track"+(s.num_assay_tracks>1?"s":""))}if(s.disco){n.append("span").style("font-size",".7em").style("padding","1px 5px").style("margin-left","10px").style("background","#bbb").style("color","white").style("border-radius","3px").text("Genome view")}if(s.mutation_signature){n.append("span").style("font-size",".7em").style("padding","1px 5px").style("margin-left","10px").style("background","#bbb").style("color","white").style("border-radius","3px").text("Mutation signature")}n.attr("class","sja_menuoption").on("click",(()=>{t.tkconfigtip.hide();const n=[];Ft(n,{tk:t,block:e,sample:{samplename:s.name},samplegroup:{attributes:s.attributes}});Pt(n,{tk:t,block:e,sample:{samplename:s.name}});Ht(n,{tk:t,block:e,sample:{samplename:s.name}});Tt(n,s.name,t,e);if(s.attr&&t.sampleAttribute&&t.sampleAttribute.attributes){n.push({label:"Attributes",callback:e=>{for(const e of s.attr){const n=t.sampleAttribute.attributes[e.k];if(n)e.k=n.label}f(e,s.attr)}})}const o=a({x:100,y:100});o.header.text(s.name);m(o.body.style("padding-top","10px"),n)}))}}catch(t){u(o,err.message||err);if(err.stack)console.log(err.stack)}}}function ft(t,e,n){if(e.sampleset)return mt(t,e,n);if(e.iscustom)return;if(!t.attributes){return}const a=t=>u(e.tip2.d,t);if(!e.sampleAttribute)return a("tk.sampleAttribute missing");if(!e.sampleAttribute.attributes)return a("tk.sampleAttribute.attributes{} missing");e.tip2.d.append("div").style("margin","4px 10px").style("font-size",".7em").text(t.name);e.tip2.d.append("div").attr("class","sja_menuoption").text("Hide").on("click",(()=>{e.tip2.clear();gt(t,e,true);e.tip2.hide();an(e,n)}));e.tip2.d.append("div").attr("class","sja_menuoption").text("Show only").on("click",(()=>{e.tip2.clear();for(const t of e._data){gt(t,e,true)}gt(t,e,false);e.tip2.hide();an(e,n)}));{const[a,s,o]=ht(t,e);if(a);else if(o.hiddenvalues.size>0){e.tip2.d.append("div").attr("class","sja_menuoption").text("Show all").on("click",(()=>{e.tip2.hide();o.hiddenvalues.clear();an(e,n)}))}}e.tip2.d.append("div").attr("class","sja_menuoption").text("Table view").on("click",(()=>{e.tip2.hide();kt(t,e,n)}));e.tip2.d.append("div").attr("class","sja_menuoption").text("Matrix view").on("click",(()=>{e.tip2.hide();ut(e,n,t)}));Ct(t,e,n);Gt({tk:e,block:n,samplegroup:t,holder:e.tip2.d});Xt(e,n,e.tip2.d,t)}function mt(t,e,n){e.tip2.d.append("div").style("margin","4px 10px").style("font-size",".7em").text(t.name);e.tip2.d.append("div").attr("class","sja_menuoption").text("Table view").on("click",(()=>{e.tip2.hide();kt(t,e,n)}));e.tip2.d.append("div").attr("class","sja_menuoption").text("Matrix view").on("click",(()=>{e.tip2.hide();ut(e,n,t)}))}function ut(e,n,a){const s=n.rglst[n.startidx];const o={ismutation:1,width:60,chr:s.chr,start:s.start,stop:s.stop,cnv:{valuecutoff:e.valueCutoff,focalsizelimit:e.bplengthUpperLimit},loh:{valuecutoff:e.segmeanValueCutoff,focalsizelimit:e.lohLengthUpperLimit},itd:{},sv:{},fusion:{},snvindel:{excludeclasses:{}}};if(e.legend_mclass&&e.legend_mclass.hiddenvalues){for(const t of e.legend_mclass.hiddenvalues){if(typeof t=="string"){o.snvindel.excludeclasses[t]=1}else{if(t==h){o.cnv.hidden=1}else if(t==g){o.loh.hidden=1}else if(t==b){o.itd.hidden=1}else if(t==k){o.sv.hidden=1}else if(t==v){o.fusion.hidden=1}else{console.error("unknown hidden dt?? "+t)}}}}if(e.showinggene){o.label=e.showinggene}else{o.label=s.chr+":"+s.start+"-"+s.stop}const l={tk:e,block:n,feature:o};o.querykeylst=[];if(e.iscustom){if(e.file||e.url)o.querykeylst.push(lt);if(e.checkvcf)o.querykeylst.push(it)}else if(e.querykey){o.querykeylst.push(e.querykey);if(e.checkvcf)o.querykeylst.push(e.checkvcf.querykey)}if(e.sampleset){for(const n of e.samplematrices){if(n.limitbysamplesetgroup&&n.limitbysamplesetgroup.name==a.name){t(n._pane.pane);n.addnewfeature_update(o);return}}l.limitbysamplesetgroup={name:a.name,samples:JSON.parse(JSON.stringify(e.sampleset.find((t=>t.name==a.name)).samples))}}else if(a.attributes){const n=a.attributes[a.attributes.length-1];for(const a of e.samplematrices){if(a.limitsamplebyeitherannotation){const e=a.limitsamplebyeitherannotation[0];if(e&&e.key==n.k&&e.value==n.kvalue){t(a._pane.pane);a.addnewfeature_update(o);return}}}l.limitsamplebyeitherannotation=[{key:n.k,value:n.kvalue}]}ct(l)}function ht(t,e){if(!t.attributes)return[".attributes[] missing for group "+t.name];if(t.attributes.length==0)return[".attributes[] zero length for group "+t.name];const n=t.attributes[t.attributes.length-1];const a=e.sampleAttribute.attributes[n.k];if(!a)return['"'+n.k+'" not registered in sampleAttribute for group '+t.name];return[null,n,a]}function gt(t,e,n){const[a,s,o]=ht(t,e);if(a)return a;if(n){o.hiddenvalues.add(s.kvalue)}else{o.hiddenvalues.delete(s.kvalue)}return null}function bt(t,e){const n=e.tktip.clear().d.append("div");if(t.attributes){for(const e of t.attributes){n.append("div").html(e.kvalue+(e.fullvalue?' <span style="opacity:.5;font-size:.8em;">'+e.fullvalue+"</span>":""))}}else if(t.name){n.append("div").text(t.name)}const a=[t.samples.length+" sample"+(t.samples.length>1?"s":"")];if(t.sampletotalnum)a.push(t.sampletotalnum+" samples total, "+Math.ceil(100*t.samples.length/t.sampletotalnum)+"%");if(e.sampleset){const n=e.sampleset.find((e=>e.name==t.name));if(n){a.push(n.samples.length+" samples total, "+Math.ceil(100*t.samples.length/n.samples.length)+"%")}}e.tktip.d.append("div").style("margin-top","10px").style("color","#858585").html(a.join("<br>"));e.tktip.show(event.clientX,event.clientY)}function kt(t,e,n){const s=a({x:event.clientX+100,y:Math.max(100,event.clientY-100)});s.header.html(t.name+' <span style="font-size:.7em">'+e.name+"</span>");if(t.samples.length==1){const a=t.samples[0];const o=s.body.append("table").style("margin","10px").style("border-spacing","4px");{const t=o.append("tr");t.append("td").text("Sample").style("opacity",.5);t.append("td").text(a.samplename)}if(a.sampletype){const t=o.append("tr");t.append("td").text("Sample type").style("opacity",.5);t.append("td").text(a.sampletype)}const[l,i,r,c,p,d,f,m,u,h]=Bt(a.samplename,a.items,e);if(l.length){const s=o.append("tr");s.append("td").text("CNV").style("opacity",.5);const i=s.append("td");for(let s=0;s<l.length;s++){i.append("div").html(l[s]).attr("class","sja_clbtext").on("mouseover",(()=>{At({item:d[s],sample:a,samplegroup:t,tk:e})})).on("mouseout",(()=>{e.tktip.hide();vn(a)})).on("click",(()=>{wt({item:d[s],sample:a,samplegroup:t,tk:e,block:n})}))}}if(i.length){const s=o.append("tr");s.append("td").text("SV").style("opacity",.5);const l=s.append("td");for(let s=0;s<i.length;s++){l.append("div").html(i[s]).attr("class","sja_clbtext").on("mouseover",(()=>{At({item:f[s],sample:a,samplegroup:t,tk:e})})).on("mouseout",(()=>{e.tktip.hide();vn(a)})).on("click",(()=>{wt({item:f[s],sample:a,samplegroup:t,tk:e,block:n})}))}}if(r.length){const s=o.append("tr");s.append("td").text("LOH").style("opacity",.5);const l=s.append("td");for(let s=0;s<r.length;s++){l.append("div").html(r[s]).attr("class","sja_clbtext").on("mouseover",(()=>{At({item:m[s],sample:a,samplegroup:t,tk:e})})).on("mouseout",(()=>{e.tktip.hide();vn(a)})).on("click",(()=>{wt({item:m[s],sample:a,samplegroup:t,tk:e,block:n})}))}}if(c.length){const s=o.append("tr");s.append("td").text("ITD").style("opacity",.5);const l=s.append("td");for(let s=0;s<c.length;s++){l.append("div").html(c[s]).attr("class","sja_clbtext").on("mouseover",(()=>{At({item:u[s],sample:a,samplegroup:t,tk:e})})).on("mouseout",(()=>{e.tktip.hide();vn(a)})).on("click",(()=>{wt({item:u[s],sample:a,samplegroup:t,tk:e,block:n})}))}}if(p.length){const s=o.append("tr");s.append("td").text("SNV/indel").style("opacity",.5);const l=s.append("td");for(let s=0;s<p.length;s++){const o=h[s].sampledata.find((t=>t.sampleobj.name==a.samplename));l.append("div").html(p[s]).attr("class","sja_clbtext").on("mouseover",(()=>{At({item:h[s],m_sample:o,sample:a,samplegroup:t,tk:e})})).on("mouseout",(()=>{e.tktip.hide();vn(a)})).on("click",(()=>{wt({item:h[s],sample:a,m_sample:o,samplegroup:t,tk:e,block:n})}))}}return}const o=s.body.append("table").style("border-spacing","2px").style("margin","20px");const l=t.samples.find((t=>t.sampletype));const i=o.append("tr");i.append("td").text("Sample").style("opacity",.5);if(l){i.append("td").text("Sample type").style("opacity",.5)}i.append("td").text("CNV").style("opacity",.5);i.append("td").text("SV").style("opacity",.5);i.append("td").text("LOH").style("opacity",.5);i.append("td").text("ITD").style("opacity",.5);if(e.data_vcf){i.append("td").text("SNV/indel").style("opacity",.5)}for(const[a,s]of t.samples.entries()){const i=o.append("tr");if(!(a%2)){i.style("background","#f1f1f1")}i.append("td").text(s.samplename);if(l){i.append("td").text(s.sampletype||"")}const[r,c,p,d,f,m,u,h,g,b]=Bt(s.samplename,s.items,e);{const a=i.append("td");for(let o=0;o<r.length;o++){a.append("div").html(r[o]).attr("class","sja_clbtext").on("mouseover",(()=>{At({item:m[o],sample:s,samplegroup:t,tk:e})})).on("mouseout",(()=>{e.tktip.hide();vn(s)})).on("click",(()=>{wt({item:m[o],sample:s,samplegroup:t,tk:e,block:n})}))}}{const a=i.append("td");for(let o=0;o<c.length;o++){a.append("div").html(c[o]).attr("class","sja_clbtext").on("mouseover",(()=>{At({item:u[o],sample:s,samplegroup:t,tk:e})})).on("mouseout",(()=>{e.tktip.hide();vn(s)})).on("click",(()=>{wt({item:u[o],sample:s,samplegroup:t,tk:e,block:n})}))}}{const a=i.append("td");for(let o=0;o<p.length;o++){a.append("div").html(p[o]).attr("class","sja_clbtext").on("mouseover",(()=>{At({item:h[o],sample:s,samplegroup:t,tk:e})})).on("mouseout",(()=>{e.tktip.hide();vn(s)})).on("click",(()=>{wt({item:h[o],sample:s,samplegroup:t,tk:e,block:n})}))}}{const a=i.append("td");for(let o=0;o<d.length;o++){a.append("div").html(d[o]).attr("class","sja_clbtext").on("mouseover",(()=>{At({item:g[o],sample:s,samplegroup:t,tk:e})})).on("mouseout",(()=>{e.tktip.hide();vn(s)})).on("click",(()=>{wt({item:g[o],sample:s,samplegroup:t,tk:e,block:n})}))}}if(e.data_vcf){const a=i.append("td");for(let o=0;o<f.length;o++){const l=b[o].sampledata.find((t=>t.sampleobj.name==s.samplename));a.append("div").html(f[o]).attr("class","sja_clbtext").on("mouseover",(()=>{At({item:b[o],m_sample:l,sample:s,samplegroup:t,tk:e})})).on("mouseout",(()=>{e.tktip.hide();vn(s)})).on("click",(()=>{wt({item:b[o],m_sample:l,sample:s,samplegroup:t,tk:e,block:n})}))}}}}function vt(t,e,n){if(t.items.length==1){const a=t.items[0];At({item:a,sample:a._sample,samplegroup:a._samplegroup,tk:e,block:n});return}e.tktip.clear();let a="Group";if(e.groupsamplebyattr&&e.groupsamplebyattr.attrlst){a=e.groupsamplebyattr.attrlst[e.groupsamplebyattr.attrlst.length-1].label}const s=[{k:a,v:t.name}];let o=0,l=0;for(const e of t.items){if(e.dt==k)o++;else if(e.dt==v)l++}if(o)s.push({k:"# of SV",v:o});if(l)s.push({k:"# of fusion",v:l});f(e.tktip.d,s);e.tktip.show(event.clientX,event.clientY)}function xt(t,e,n){if(t.items.length==1){const a=t.items[0];wt({item:a,sample:a._sample,samplegroup:a._samplegroup,tk:e,block:n});return}const s=a({x:event.clientX,y:event.clientY});s.header.html(t.name+' <span style="font-size:.8em">'+e.name+"</span>");const o=new Map;for(const e of t.items){if(!o.has(e.sample)){o.set(e.sample,{sv:[],fusion:[]})}if(e.dt==k){o.get(e.sample).sv.push(e)}else if(e.dt==v){o.get(e.sample).fusion.push(e)}}const l=s.body.append("table").style("border-spacing","2px").style("margin","10px");const i=l.append("tr");i.append("td").text("Sample").style("font-size",".8em").style("opacity",.5);i.append("td").text("SV").style("font-size",".8em").style("opacity",.5);i.append("td").text("RNA fusion").style("font-size",".8em").style("opacity",.5);let r=0;for(const[t,a]of o){const s=l.append("tr");if(!(r++%2)){s.style("background","#f1f1f1")}s.append("td").text(t);const o=s.append("td");for(const t of a.sv){const a=qt(t,e);o.append("div").attr("class","sja_clbtext").html(t.cytogeneticname?t.cytogeneticname+' <span style="font-size:.7em">'+a+"</span>":a).on("mouseover",(()=>{At({item:t,sample:t._sample,samplegroup:t._samplegroup,tk:e})})).on("mouseout",(()=>{e.tktip.hide();vn(t._sample)})).on("click",(()=>{wt({item:t,sample:t._sample,samplegroup:t._samplegroup,tk:e,block:n})}))}const i=s.append("td");for(const t of a.fusion){i.append("div").attr("class","sja_clbtext").html(yn(t)+' <span 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a.sampledata){const[s,o]=Nt({m:a,m_sample:t,tk:e});i.append("div").text(t.sampleobj.name).attr("class","sja_clbtext").on("mouseover",(()=>{At({item:a,m_sample:t,sample:s,samplegroup:o,tk:e,block:n})})).on("mouseout",(()=>{e.tktip.hide();vn(s)})).on("click",(()=>{wt({item:a,m_sample:t,sample:s,samplegroup:o,tk:e,block:n})}))}Ot(a,n,o)}else{throw"Unknown dt: "+a.dt}return}const o=s.body.append("table").style("margin-top","10px").style("border-spacing","4px");for(const a of t.items){const t=o.append("tr");t.append("td").text(a.mname).style("color",y[a.class].color).style("font-weight","bold").style("vertical-align","top");{const e=t.append("td");if(a.dt==x){e.style("opacity",".5").text(a.ref+" > "+a.alt).style("vertical-align","top")}}{const s=t.append("td");if(a.dt==x){for(const t of a.sampledata){const[o,l]=Nt({m:a,m_sample:t,tk:e});s.append("div").text(t.sampleobj.name).attr("class","sja_clbtext").on("mouseover",(()=>{At({item:a,m_sample:t,sample:o,samplegroup:l,tk:e,block:n})})).on("mouseout",(()=>{e.tktip.hide();vn(o)})).on("click",(()=>{wt({item:a,m_sample:t,sample:o,samplegroup:l,tk:e,block:n})}))}}else{console.error("unknown dt: "+a.dt)}}}}function _t(t,e,n){e.tktip.clear();if(t.items.length==1){const a=t.items[0];if(a.dt==x){if(a.sampledata.length==1){const[t,s]=Nt({m:a,m_sample:a.sampledata[0],tk:e});At({item:a,m_sample:a.sampledata[0],sample:t,samplegroup:s,tk:e,block:n});return}const t=St(a,e);t.push({k:"Samples",v:a.sampledata.length>10?a.sampledata.slice(0,6).map((t=>t.sampleobj.name)).join("<br>")+"<br><i>... and "+(a.sampledata.length-6)+" more samples</i>":a.sampledata.map((t=>t.sampleobj.name)).join("<br>")});const s=f(e.tktip.d,t);Ot(a,n,s);e.tktip.show(event.clientX,event.clientY)}else{throw"unknown dt: 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n=[];n.push({label:"Details",callback:e=>{t.holder=e;jt(t)}});Ft(n,t);Rt(n,t);Pt(n,t);Ht(n,t);Tt(n,t.sample.samplename,t.tk,t.block);Yt(n,{tk:t.tk,block:t.block,m:t.item,sample:t.sample});Dt(n,{tk:t.tk,block:t.block,m:t.item,sample:t.sample,samplegroup:t.samplegroup});m(e.body.style("padding-top","10px"),n)}function At(t){kn(t.sample);t.holder=t.tk.tktip.clear().d;jt(t);t.tk.tktip.show(event.clientX,event.clientY)}function jt(t){const e=[];if(t.sample){e.push({k:"Sample",v:t.sample.samplename});Et(t.sample.samplename,t.tk,e)}const n=t.item;let a;if(n.dt==b){e.push({k:"ITD",v:n.chr+":"+(n.start+1)+"-"+(n.stop+1)});if(n.gene||n.isoform){const t=[];if(n.gene)t.push(n.gene);if(n.isoform)t.push(n.isoform);e.push({k:"Gene",v:t.join(", ")})}if(n.rnaduplength){e.push({k:"RNA duplicated",v:n.rnaduplength+" bp"})}if(n.aaduplength){e.push({k:"AA duplicated",v:n.aaduplength+" aa"})}a=n.mattr}else if(n.dt==h||n.dt==g){if(n.dt==g){e.push({k:"LOH seg.mean",v:n.segmean.toFixed(2)})}else{e.push({k:"CNV 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Ut(t,e){if(e.legend_svchrcolor.interchrs.has(t)){return'<span style="background:'+e.legend_svchrcolor.colorfunc(t)+';font-weight:bold;padding:0px 5px;color:white">'+t+"</span>"}return t}function qt(t,e){return Ut(t.chrA,e)+":"+t.posA+(t.strandA?":"+t.strandA:"")+" &raquo; "+Ut(t.chrB,e)+":"+t.posB+(t.strandB?":"+t.strandB:"")}function Bt(t,e,n){const a=[],s=[],o=[],l=[],i=[],r=[],c=[],p=[],d=[],f=[];{const t=e.filter((t=>t.dt==k||t.dt==v));const a=Gn(t);for(const t of a){s.push('<div style="white-space:nowrap">'+yn(t)+' <span style="font-size:.7em">'+qt(t,n)+"</span>"+(t.dt==v?' <span style="font-size:.7em">(RNA fusion)</span>':"")+"</div>");c.push(t)}}for(const t of e){if(t.dt==k||t.dt==v)continue;if(t.dt==g){o.push('<div style="white-space:nowrap">'+t.chr+":"+(t.start+1)+"-"+(t.stop+1)+' <span style="font-size:.8em">'+_(t.stop-t.start)+" seg.mean: "+t.segmean+"</span>");p.push(t)}else if(t.dt==h){a.push('<div style="white-space:nowrap">'+t.chr+":"+(t.start+1)+"-"+(t.stop+1)+' <span style="font-size:.8em">'+_(t.stop-t.start)+"</span>"+' <span style="background:'+(t.value>0?n.cnvcolor.gain.str:n.cnvcolor.loss.str)+';font-size:.8em;color:white">&nbsp;'+t.value+"&nbsp;</span>"+"</div>");r.push(t)}else if(t.dt==b){l.push('<div style="white-space:nowrap">'+t.chr+":"+(t.start+1)+"-"+(t.stop+1)+(t.rnaduplength?", "+t.rnaduplength+" bp duplicated in RNA":"")+(t.aaduplength?", "+t.aaduplength+" AA duplicated":"")+"</div>");d.push(t)}else{throw"unknown dt: "+t.dt}}if(n.data_vcf){for(const e of n.data_vcf){if(e.dt==x){if(e.sampledata.find((e=>e.sampleobj.name==t))){const t=y[e.class];i.push('<div style="white-space:nowrap">'+'<span style="color:'+t.color+';font-weight:bold">'+e.mname+"</span> "+'<span style="font-size:.7em">'+t.label+"</span></div>");f.push(e)}}else{throw"unknown dt: "+e.dt}}}return[a,s,o,l,i,r,c,p,d,f]}function Ct(t,e,n){if(!e.mds||!e.mds.annotationsampleset2matrix)return;if(!t.attributes)return;const s=t.attributes.find((t=>t.k==e.mds.annotationsampleset2matrix.key));if(!s)return;const o=e.mds.annotationsampleset2matrix.groups[s.kvalue];if(!o)return;if(!o.groups)return;for(const t of o.groups){if(!t.name||!t.matrixconfig)continue;e.tip2.d.append("div").html(t.name+' <span style="font-size:.8em;opacity:.5">SUMMARY</span>').attr("class","sja_menuoption").on("click",(()=>{e.tip2.hide();const s=a({x:100,y:100});s.header.text(t.name+" summary");const o={dslabel:e.mds.label,debugmode:n.debugmode,genome:n.genome,hostURL:n.hostURL,jwt:n.jwt,holder:s.body.append("div").style("margin","20px")};for(const e in t.matrixconfig){o[e]=t.matrixconfig[e]}import("./samplematrix-3556e5c0.js").then((t=>{new t.Samplematrix(o)}))}))}}function Et(t,e,n){if(!e.sampleAttribute)return;if(!e.sampleAttribute.attributes||!e.sampleAttribute.samples)return;const a=e.sampleAttribute.samples[t];if(!a)return;for(const t in a){const s=e.sampleAttribute.attributes[t]||{};const o=a[t];if(o==undefined)continue;let l=o;if(s.values){const t=s.values[o];if(t&&t.name){l=t.name}}n.push({k:s.label||t,v:l})}}function Rt(t,e){if(!e.item)return;if(e.item.dt!=k&&e.item.dt!=v)return;t.push({label:"Fusion graph",callback:async t=>{const n=M(t);await Vt(e,t);n.remove()}})}async function Vt(t,e){const n={a:{chr:t.item.chrA,position:t.item.posA,strand:t.item.strandA},b:{chr:t.item.chrB,position:t.item.posB,strand:t.item.strandB}};const a=e.append("div");try{{a.text("Loading gene at "+n.a.chr+":"+n.a.position+" ...");const e=await It(t,n.a.chr,n.a.position);const s=e.find((t=>t.isdefault))||e[0];if(s){n.a.name=s.name;n.a.gm={isoform:s.isoform}}}{a.text("Loading gene at "+n.b.chr+":"+n.b.position+" ...");const e=await It(t,n.b.chr,n.b.position);const s=e.find((t=>t.isdefault))||e[0];if(s){n.b.name=s.name;n.b.gm={isoform:s.isoform}}}a.remove();const s={pairlst:[n],genome:t.block.genome,holder:e};import("./svgraph-037fd7b6.js").then((t=>{t.default(s)}))}catch(t){if(t.stack)console.log(t.stack);a.text("Error: 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de(t,e){if(!t.mds||!t.mds.mutation_signature)return;for(const e in t.mutation_signature_legend.sets){t.mutation_signature_legend.sets[e].tr.style("display","none")}if(!t.data_vcf){return}const n=new Map;for(const e of t.data_vcf){if(e.x==undefined)continue;if(!e.sampledata||!e.sampledata[0])continue;for(const a in t.mds.mutation_signature.sets){const s=e.sampledata[0][a];if(s==undefined)continue;const o=t.mds.mutation_signature.sets[a].signatures[s];if(o){if(o.nodata)continue;if(!n.has(a))n.set(a,new Map);n.get(a).set(s,1+(n.get(a).get(s)||0))}}}for(const[e,a]of n){const n=t.mutation_signature_legend.sets[e];n.tr.style("display","table-row");n.table.selectAll("*").remove();const s=[...a].sort(((t,e)=>e[1]-t[1]));for(const[a,o]of s){const s=t.mds.mutation_signature.sets[e].signatures[a];const l=n.table.append("tr");l.append("td").style("background",s.color).style("padding","0px 4px").style("color","white").style("text-align","right").html(o>1?o:"");const 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t.legend_hideable){a.row.select("td").classed("sja_hideable_legend",true).on("click",(()=>{t.tip2.hide();a.hidden=1;t.legend_more_row.style("display","table-row");e(a.row.select("td"),t.legend_more_label);a.row.transition().delay(500).style("display","none");setTimeout((()=>{fe(t,n)}),500)}));a.row.style("display",a.hidden?"none":"table-row");if(a.hidden){s++}}if(!a.length&&!s){t.legend_more_row.style("display","none")}else{t.legend_more_row.style("display","table-row");t.legend_more_label.selectAll("*").remove();const e=t.legend_more_label.attr("class","sja_legend_more_btn").html("MORE...").on("click",(()=>{t.tip2.clear();for(const e of t.legend_hideable){if(!e.hidden)continue;const a=t.tip2.d.append("div").attr("class","sja_menuoption").on("click",(()=>{t.tip2.hide();e.hidden=0;fe(t,n)}));if(e.hidden&&e.total_count){a.append("div").style("display","inline-block").attr("class","sja_mcdot").style("background","#858585").text(e.total_count)}a.append("span").html("&nbsp;"+e.row.node().firstChild.innerHTML)}for(const e of a){if(!e.hidden)continue;const a=[...e.value2count.values()].reduce(((t,e)=>t+e.totalitems),0);const s=t.tip2.d.append("div").attr("class","sja_menuoption").on("click",(()=>{t.tip2.hide();e.hidden=0;fe(t,n)}));s.append("div").style("display","inline-block").attr("class","sja_mcdot").style("background","#858585").text(a);s.append("span").html("&nbsp;"+e.label)}t.tip2.showunder(e.node())}))}}function ue(t,e,n){if(!(t in n))return;if(!e.filter)return;const a=n[t];if(!e.value2count.has(a)){e.value2count.set(a,{totalitems:0})}e.value2count.get(a).totalitems++;if(!e.values){e.values={}}if(!e.values[a]){e.values[a]={name:a,label:a}}}function he(t,e,n){if(!t){return}if(!e.mutationAttribute)return;for(const a in e.mutationAttribute.attributes){const s=e.mutationAttribute.attributes[a];if(!s.filter)continue;const o=t[a];if(o==undefined){continue}if(!s.value2count.has(o)){s.value2count.set(o,{totalitems:0,dt2count:new Map})}s.value2count.get(o).totalitems++;if(!s.value2count.get(o).dt2count.has(n)){s.value2count.get(o).dt2count.set(n,0)}s.value2count.get(o).dt2count.set(n,s.value2count.get(o).dt2count.get(n)+1)}}function ge(t,e){if(!t.locusAttribute)return;for(const n in t.locusAttribute.attributes){const a=t.locusAttribute.attributes[n];if(!a.filter)continue;const s=e.info[n];if(s==undefined)continue;let o;if(Array.isArray(s)){o=s[0];if(o==".")continue}else{o=s}if(a.hiddenvalues.has(o))continue;if(!a.value2count.has(o)){a.value2count.set(o,{totalitems:0,dt2count:new Map})}a.value2count.get(o).totalitems++;if(!a.value2count.get(o).dt2count.has(e.dt)){a.value2count.get(o).dt2count.set(e.dt,0)}a.value2count.get(o).dt2count.set(e.dt,a.value2count.get(o).dt2count.get(e.dt)+1)}}function be(t,e){cn(t);const n=[];const a=[];const s=[];const o=[];const l={};let i=0,r=0,c=0;if(t.data){for(const p of t.data){if(p.dt==v||p.dt==k){const a=p.chrA+"."+p.posA+"."+p.chrB+"."+p.posB+"."+p.dt;if(!l[a]){je(p,e);if(p.x0||p.x1){l[a]=1;n.push(p);if(p.chrA!=p._chr){t.legend_svchrcolor.interchrs.add(p.chrA);t.legend_svchrcolor.colorfunc(p.chrA)}if(p.chrB!=p._chr){t.legend_svchrcolor.interchrs.add(p.chrB);t.legend_svchrcolor.colorfunc(p.chrB)}}}continue}Pn(p,t,e);if(p.x1==undefined||p.x2==undefined){console.log("unmappable: "+p.chr+" "+p.start+" "+p.stop);continue}if(p.dt==g){c=Math.max(c,p.segmean);s.push(p)}else if(p.dt==h){{if(p.value>0){i=Math.max(i,p.value)}else{r=Math.min(r,p.value)}}a.push(p)}else if(p.dt==b){o.push(p)}}if(a.length){t.cnvcolor.cnvmax=Math.max(i,-r);jn(t)}if(s.length){t.cnvcolor.segmeanmax=c;Mn(t)}}const p=_e(ke(n),t,e);t.cnv_g.attr("transform","translate(0,"+p+")");t.waterfall.axisgg.attr("transform","translate(0,"+p+")");const d=[...a,...s,...o];if(t.data_vcf){for(const e of t.data_vcf){if(e.x!=undefined){d.push(e)}}}const f=xe(d,t,e);t.height_main=t.toppad+p+f+t.bottompad;Qt(t,e)}function ke(t){const e=[];const n=8;for(let a=0;a<t.length;a++){const s=t[a];if(s.__claimed)continue;const o={x0:s.x0,x1:s.x1,_chr:s._chr,chrA:s.chrA,chrB:s.chrB,posA:s.posA,posB:s.posB,lst:[s]};for(let e=a+1;e<t.length;e++){const a=t[e];if(a.__claimed)continue;const l=a.x0==undefined||a.x1==undefined;if(s.x0!=undefined&&s.x1!=undefined){if(l)continue;if(Math.abs(a.x0-s.x0)<=n&&Math.abs(a.x1-s.x1)<=n){o.lst.push(a);a.__claimed=true}}else{if(!l)continue;const t=s.x0==undefined?s.x1:s.x0;const 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Ve(t,e,n,s){if(!n.mds||!n.mds.survivalplot)return;t.append("div").text("Survival plot by "+e.gene+" "+n.gecfg.datatype).attr("class","sja_menuoption").on("click",(()=>{n.tkconfigtip.hide();const t=a({x:100,y:100});t.header.text("Survival plot by "+e.gene+" "+n.gecfg.datatype);const o={genome:s.genome,mds:n.mds,plotlist:[{renderplot:1,samplerule:{set:{geneexpression:1,bymedian:1,gene:e.gene,chr:e.chr,start:e.start,stop:e.stop}}}]};import("./mds.survivalplot-f440db10.js").then((e=>{e.init(o,t.body,s.debugmode)}))}))}function Ie(t,e,n){O({div:t,genome:n.genome.name,tip:e.tip2,callback:t=>{Oe(t,e,n)}})}async function Oe(t,e,n,a){e.tkconfigtip.clear();const s=e.tkconfigtip.d.append("div").text("Searching for "+t+" ...");try{const o=await z("genelookup",{body:{genome:n.genome.name,input:t,deep:1}});if(o.error)throw o.error;if(!o.gmlst)throw".gmlst[] missing";const l=o.gmlst[0];s.text("Loading "+e.gecfg.datatype+" for "+l.name+" ...");const i=await Fe(l,e,n);if(i.error)throw i.error;const r={gene:t,chr:l.chr,start:l.start,stop:l.stop};if(i.sample2rnabam){for(const t in i.sample2rnabam){W(i.sample2rnabam[t],e.gecfg)}r.sample2rnabam=i.sample2rnabam}else{if(!i.sample2rank)throw".sample2rank{} missing";for(const t in i.sample2rank){W(i.sample2rank[t],e.gecfg)}r.sample2rank=i.sample2rank}e.gecfg.fixed.push(r);e.tkconfigtip.hide();if(a){}else{Se(e,n)}}catch(t){if(t.stack)console.log(t.stack);s.text("Error: "+(t.message?t.message:t))}}function Fe(t,e,n){const a={genome:n.genome.name,getexpression4gene:{chr:t.chr,start:t.start,stop:t.stop,name:t.name}};if(e.iscustom){a.iscustom=1;const t=e.checkexpressionrank;if(t){a.checkexpressionrank={file:t.file,url:t.url,indexURL:t.indexURL}}if(e.checkvcf){a.checkvcf=e.checkvcf.stringifiedObj}if(e.checkrnabam){Ln(e,a,true)}}else{a.dslabel=e.mds.label;a.querykey=e.querykey}return d("mdssvcnv",a)}function He(t,e,n,a,s){const o=[{k:"Sample",v:n.samplename}];Et(n.samplename,s,o);if(s.checkrnabam){o.push({k:t+" 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e.checkexpressionrank){t.checkexpressionrank[n]=e.checkexpressionrank[n]}}if(e.checkvcf){t.checkvcf=e.checkvcf.stringifiedObj}if(e.checkrnabam){Ln(e,t,true)}}else{t.dslabel=e.mds.label;t.querykey=e.querykey}if(e.getallsamples){t.getallsamples=true}if(e.sampleset)t.sampleset=e.sampleset;if(e.valueCutoff)t.valueCutoff=e.valueCutoff;if(Number.isInteger(e.bplengthUpperLimit))t.bplengthUpperLimit=e.bplengthUpperLimit;if(e.showonlycnvwithsv)t.showonlycnvwithsv=1;t.hide_cnvgain=e.hide_cnvgain;t.hide_cnvloss=e.hide_cnvloss;if(e.segmeanValueCutoff)t.segmeanValueCutoff=e.segmeanValueCutoff;if(Number.isInteger(e.lohLengthUpperLimit))t.lohLengthUpperLimit=e.lohLengthUpperLimit;if(e.singlesample){t.singlesample=e.singlesample.name}else{if(e.sampleAttribute){const n={};let a=false;for(const t in e.sampleAttribute.attributes){const s=e.sampleAttribute.attributes[t];if(s.hiddenvalues&&s.hiddenvalues.size){n[t]=[...s.hiddenvalues];a=true}}if(a){t.hiddensampleattr=n}}}if(e.mutationAttribute){const 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e.legend_mclass.hiddenvalues){if(Number.isInteger(t))n.push(t)}if(n.length){t.hiddendt=n}}}function dn(t,e){cn(t);let n=e.labelfontsize;if(t.versionlabel)n+=e.labelfontsize;const[a,s]=Sn(t,e);t.samplegroups=a;const o=fn(t,e);const l=un(s,t,e);const i=gn(t,e);An(t);wn(t);const r=Se(t,e);const c=o&&l?3:0;let p=Math.max(n,o+l+c,r);if(o){p+=Math.max(0,n+8-(p-l-c-o/2))}else if(l){p+=Math.max(0,n+8-(p-l/2))}if(r==0||p>r+3+e.labelfontsize){t.config_handle.transition().attr("text-anchor","start").attr("x",0)}else{t.config_handle.transition().attr("text-anchor","end").attr("x",-e.rpad)}t.cnvleftg.transition().attr("transform","translate(0,"+p+")");t.cnvmidg.transition().attr("transform","translate(0,"+p+")");t.vcfdensityg.transition().attr("transform","translate(0,"+(p-l-c)+")");t.svdensityg.transition().attr("transform","translate(0,"+p+")");t.cnvrightg.transition().attr("transform","translate(0,"+p+")");{const n="#858585";if(o&&t.data_vcf){let a=0;for(const e of 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wn(t){if(!t.checkrnabam)return;for(const e in t.checkrnabam.samples){const n=t.checkrnabam.samples[e];if(n.genes){for(const e of n.genes){W(e,t.gecfg)}}}}function An(t){if(!t._data)return;if(!t.gecfg)return;if(t.gecfg.no_ase)return;for(const e of t._data){if(!e.samples)continue;for(const n of e.samples){if(!n.expressionrank)continue;for(const e in n.expressionrank){const a=n.expressionrank[e];W(a,t.gecfg)}}}}function jn(t){t.cnvcolor.cnvlegend.row.style("display","table-row");q({axis:t.cnvcolor.cnvlegend.axisg.call(tt().scale(N().domain([-t.cnvcolor.cnvmax,0,t.cnvcolor.cnvmax]).range([0,t.cnvcolor.cnvlegend.barw,t.cnvcolor.cnvlegend.barw*2])).tickValues([-t.cnvcolor.cnvmax,0,t.cnvcolor.cnvmax]).tickSize(t.cnvcolor.cnvlegend.axistickh))})}function Mn(t){if(!t.cnvcolor.lohlegend)return;t.cnvcolor.lohlegend.row.style("display","table-row");q({axis:t.cnvcolor.lohlegend.axisg.call(tt().scale(N().domain([0,t.cnvcolor.segmeanmax]).range([0,t.cnvcolor.lohlegend.barw])).tickValues([0,t.cnvcolor.segmeanmax]).tickSize(t.cnvcolor.lohlegend.axistickh))})}async function zn(t){const{m:e,sample:n,samplegroup:o,tk:l,block:i}=t;let r;if(t.holder){r=t.holder}else{const t=a({x:100,y:100});r=t.body}const c=r.append("div");const p={style:{margin:"0px"},tklst:[],holder:r,subpanels:[]};F(i.genome,p.tklst);if(l.checkrnabam&&l.checkvcf){const t=l.checkrnabam.samples[n.samplename];if(t){p.chr=i.rglst[0].chr;p.start=i.rglst[0].start;p.stop=i.rglst[0].stop;const e={type:s.ase,name:n.samplename+" ASE",samplename:n.samplename,rnabamfile:t.file,rnabamurl:t.url,rnabamindexURL:t.indexURL,rnabamtotalreads:t.totalreads,vcffile:l.checkvcf.file,vcfurl:l.checkvcf.url,vcfindexURL:l.checkvcf.indexURL};Ln(l,e,false);p.tklst.push(e);const a=i.newblock(p);if(i.debugmode){window.bbb=a}return}}if(l.iscustom){if(l.checkexpressionrank){const t={type:T.mdsexpressionrank,name:n.samplename+" expression rank",sample:n.samplename,iscustom:1};for(const e in l.checkexpressionrank){t[e]=l.checkexpressionrank[e]}p.tklst.push(t)}if(l.sample2assaytrack&&l.sample2assaytrack[n.samplename]){for(const t of l.sample2assaytrack[n.samplename]){p.tklst.push(t)}}}else if(l.mds&&l.mds.queries[l.querykey].checkexpressionrank){if(o){const t={type:T.mdsexpressionrank,name:n.samplename+" expression rank",dslabel:l.mds.label,querykey:l.mds.queries[l.querykey].checkexpressionrank.querykey,sample:n.samplename,attributes:o.attributes};p.tklst.push(t)}}const d={bplengthUpperLimit:0,valueCutoff:l.valueCutoff,lohLengthUpperLimit:l.lohLengthUpperLimit,segmeanValueCutoff:l.segmeanValueCutoff,singlesample:{name:n.samplename}};if(l.iscustom){d.type=T.mdssvcnv;d.file=l.file;d.url=l.url;d.indexURL=l.indexURL;d.iscustom=true;d.legend_vorigin=l.legend_vorigin}else{d.mds=l.mds;d.querykey=l.querykey;for(const t in l.mds.queries[l.querykey]){if(t=="bplengthUpperLimit"||t=="valueCutoff"){continue}d[t]=l.mds.queries[l.querykey][t]}}if(l.iscustom&&l.checkvcf){d.checkvcf=l.checkvcf}p.tklst.push(d);if(e){if(e.dt==h||e.dt==g){const t=Math.ceil((e.stop-e.start)/2);p.chr=e.chr;p.start=Math.max(0,e.start-t);p.stop=Math.min(i.genome.chrlookup[e.chr.toUpperCase()].len,e.stop+t)}else if(e.dt==k||e.dt==v){if(e.chrA==e.chrB){const t=Math.ceil(Math.abs(e.posA-e.posB)/4);p.chr=e.chrA;p.start=Math.max(0,Math.min(e.posA,e.posB)-t);p.stop=Math.min(i.genome.chrlookup[e.chrA.toUpperCase()].len,Math.max(e.posA,e.posB)+t)}else{const t=1e4;p.chr=e.chrA;p.start=Math.max(0,e.posA-t);p.stop=Math.min(i.genome.chrlookup[e.chrA.toUpperCase()].len,e.posA+t);p.subpanels.push({chr:e.chrB,start:Math.max(0,e.posB-t),stop:Math.min(i.genome.chrlookup[e.chrB.toUpperCase()].len,e.posB+t),width:600,leftpad:10,leftborder:"rgba(50,50,50,.1)"})}}}if(!p.chr){const t=i.tkarg_maygm(l)[0];if(e&&e.dt==x){const n=1e4;if(n<t.stop-t.start){p.chr=e.chr;p.start=Math.max(0,e.pos-n);p.stop=Math.min(i.genome.chrlookup[e.chr.toUpperCase()].len,e.pos+n)}}if(!p.chr){p.chr=t.chr;p.start=t.start;p.stop=t.stop}}let f;if(!l.iscustom){const t=await H("mdssvcnv",{method:"POST",body:JSON.stringify({genome:i.genome.name,dslabel:l.mds.label,querykey:l.querykey,gettrack4singlesample:n.samplename})});if(t.error)throw t.error;if(t.tracks){f=t.tracks;for(const e of t.tracks){p.tklst.push(JSON.parse(JSON.stringify(e)))}}}const m=i.newblock(p);if(e){if(e.dt==h||e.dt==g){m.addhlregion(e.chr,e.start,e.stop,Ge)}}if(f){c.style("display","inline-block").style("margin","0px 10px 20px 10px").append("div").style("margin-bottom","3px").text("Show/hide available assay tracks for "+n.samplename).style("font-size",".7em").style("opacity",.5);const t=c.append("div").style("border","solid 1px #ccc").style("border-radius","7px");for(const e of f){const n=t.append("div").style("display","inline-block").style("white-space","nowrap").style("margin","10px").style("font-size",".8em").append("label");n.append("input").attr("type","checkbox").style("margin-right","3px").property("checked",!e.hidden).on("change",(t=>{if(t.target.checked){m.turnOnTrack(e)}else{m.turnOffTrack(e)}}));n.append("span").text(e.name)}}}function Ln(t,e,n){if(!t.checkrnabam)return;e.checkrnabam={};for(const n in t.checkrnabam){if(n=="samples")continue;if(n=="legend")continue;e.checkrnabam[n]=t.checkrnabam[n]}if(n){e.checkrnabam.samples={};for(const n in 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D({padding:"0px"});if(t.singlesample){if(!t.midpad)t.midpad=3;if(!t.stem1){t.stem1=10;t.stem2=0;t.stem3=5}if(!t.legheight)t.legheight=40;if(!t.discradius)t.discradius=8;if(!t.valueCutoff)t.valueCutoff=.2;if(!Number.isInteger(t.bplengthUpperLimit))t.bplengthUpperLimit=2e6;if(!Number.isInteger(t.lohLengthUpperLimit))t.lohLengthUpperLimit=2e6;if(!t.segmeanValueCutoff)t.segmeanValueCutoff=.1;if(t.fixname){t.name=t.fixname;t.tklabel.text(t.name);delete t.fixname}else{t.tklabel.text((t.name?t.name+", 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Press ENTER to update.")}{const a=n.append("div");a.append("span").html("Copy number gain&nbsp;");a.append("input").attr("type","color").property("value",t.cnvcolor.gain.str).on("change",(n=>{t.cnvcolor.gain.str=n.target.value;const a=V(t.cnvcolor.gain.str);t.cnvcolor.gain.r=a.r;t.cnvcolor.gain.g=a.g;t.cnvcolor.gain.b=a.b;t.cnvcolor.cnvlegend.gain_stop.attr("stop-color",t.cnvcolor.gain.str);if(t.singlesample){be(t,e)}else{dn(t,e)}}));a.append("span").html("&nbsp;&nbsp;loss&nbsp;");a.append("input").attr("type","color").property("value",t.cnvcolor.loss.str).on("change",(n=>{t.cnvcolor.loss.str=n.target.value;const a=V(t.cnvcolor.loss.str);t.cnvcolor.loss.r=a.r;t.cnvcolor.loss.g=a.g;t.cnvcolor.loss.b=a.b;t.cnvcolor.cnvlegend.loss_stop.attr("stop-color",t.cnvcolor.loss.str);if(t.singlesample){be(t,e)}else{dn(t,e)}}))}if(t.cnvcolor.lohlegend){n.append("hr").style("margin","20px");{const a=n.append("div").style("margin-bottom","15px");a.append("span").html("LOH seg.mean cutoff&nbsp;");a.append("input").property("value",t.segmeanValueCutoff||0).attr("type","number").style("width","50px").on("keyup",(n=>{if(n.code!="Enter"&&n.code!="NumpadEnter")return;let a=Number.parseFloat(n.target.value);if(!a||a<0){a=0}if(a==0){if(t.segmeanValueCutoff){t.segmeanValueCutoff=0;an(t,e)}return}if(t.segmeanValueCutoff){if(t.segmeanValueCutoff==a);else{t.segmeanValueCutoff=a;an(t,e)}}else{t.segmeanValueCutoff=a;an(t,e)}}));a.append("div").style("font-size",".7em").style("color","#858585").html("Only show LOH with seg.mean no less than cutoff.<br>Set to 0 to show all. Press ENTER to update.")}{const a=n.append("div").style("margin-bottom","15px");a.append("span").html("LOH segment size limit&nbsp;");a.append("input").property("value",t.lohLengthUpperLimit||0).attr("type","number").style("width","80px").on("keyup",(n=>{if(n.code!="Enter"&&n.code!="NumpadEnter")return;let a=Number.parseInt(n.target.value);if(!a||a<0){a=0}if(a==0){if(t.lohLengthUpperLimit){t.lohLengthUpperLimit=0;an(t,e)}return}if(t.lohLengthUpperLimit){if(t.lohLengthUpperLimit==a);else{t.lohLengthUpperLimit=a;an(t,e)}}else{t.lohLengthUpperLimit=a;an(t,e)}}));a.append("span").text("bp");a.append("div").style("font-size",".7em").style("color","#858585").html("Limit the LOH segment length to show only focal events.<br>Set to 0 to show all. Press ENTER to update.")}{const a=n.append("div").style("margin-bottom","1px");a.append("span").html("LOH color&nbsp;");a.append("input").attr("type","color").property("value",t.cnvcolor.loh.str).on("change",(n=>{t.cnvcolor.loh.str=n.target.value;const a=V(t.cnvcolor.loh.str);t.cnvcolor.loh.r=a.r;t.cnvcolor.loh.g=a.g;t.cnvcolor.loh.b=a.b;t.cnvcolor.lohlegend.loh_stop.attr("stop-color",t.cnvcolor.loh.str);if(t.singlesample){be(t,e)}else{dn(t,e)}}))}}}function Fn(t,e){if(t.singlesample)return;const n=t.tkconfigtip.d.append("div").style("background","#FAF9DE").style("margin-bottom","20px").style("padding","15px");const a=Math.random().toString();const s=Math.random().toString();const o=Math.random().toString();const l=n.append("div").style("margin-bottom","5px");t.mode_radio_1=l.append("input").attr("type","radio").attr("id",a).attr("name",o).property("checked",t.isdense).on("change",(()=>{Cn(t,e)}));l.append("label").attr("for",a).attr("class","sja_clbtext").html('&nbsp;Dense <span style="font-size:.7em;color:#858585;">Showing densities of SV breakpoints and SNV/indels, over all samples</span>');const i=n.append("div");t.mode_radio_2=i.append("input").attr("type","radio").attr("id",s).attr("name",o).property("checked",t.isfull).on("change",(()=>{Cn(t,e)}));i.append("label").attr("for",s).attr("class","sja_clbtext").html('&nbsp;Expanded <span style="font-size:.7em;color:#858585;">Showing SV/SNV/indel for each sample</span>')}function Hn(t,e){if(t.singlesample)return;t.tkconfigtip.d.append("div").style("margin-bottom","5px").text("Show text labels in expanded mode").style("opacity",.5);const n=t.tkconfigtip.d.append("div").style("margin-bottom","20px");{const a=Math.random().toString();n.append("input").attr("type","checkbox").attr("id",a).property("checked",!t.multihidelabel_vcf).on("change",(()=>{t.multihidelabel_vcf=!t.multihidelabel_vcf;dn(t,e)}));n.append("label").attr("for",a).attr("class","sja_clbtext").html("&nbsp;SNV/indel")}if(!t.nocnvlohsv){{const a=Math.random().toString();n.append("input").attr("type","checkbox").style("margin-left","20px").attr("id",a).property("checked",!t.multihidelabel_sv).on("change",(()=>{t.multihidelabel_sv=!t.multihidelabel_sv;dn(t,e)}));n.append("label").attr("for",a).attr("class","sja_clbtext").html("&nbsp;DNA SV")}{const a=Math.random().toString();n.append("input").attr("type","checkbox").style("margin-left","20px").attr("id",a).property("checked",!t.multihidelabel_fusion).on("change",(()=>{t.multihidelabel_fusion=!t.multihidelabel_fusion;dn(t,e)}));n.append("label").attr("for",a).attr("class","sja_clbtext").html("&nbsp;RNA fusion")}}}function Pn(t,e,n){const a=n.tkarg_maygm(e)[0];if(t.chr==a.chr&&Math.max(t.start,a.start)<Math.min(t.stop,a.stop)){t.x1=n.seekcoord(t.chr,Math.max(t.start,a.start))[0].x;t.x2=n.seekcoord(t.chr,Math.min(t.stop,a.stop-1))[0].x}let s=n.width;for(const e of n.subpanels){s+=e.leftpad;if(t.chr==e.chr&&Math.max(t.start,e.start)<Math.min(t.stop,e.stop)){const n=s+(Math.max(t.start,e.start)-e.start)*e.exonsf;const a=s+(Math.min(t.stop,e.stop)-e.start)*e.exonsf;if(t.x1==undefined){t.x1=n;t.x2=a}else{t.x2=a}}s+=e.width}if(t.x1!=undefined&&n.gmmode&&n.gmmode!=Y.genomic){const e=n.width+n.subpanels.reduce(((t,e)=>e.width+e.leftpad),0);if(t.x1<t.x2){if(t.x2<0||t.x1>e){t.x1=undefined;t.x2=undefined;return}if(t.x1<0){t.x1=0}if(t.x2>e){t.x2=e}}else if(t.x1>t.x2){if(t.x1<0||t.x2>e){t.x1=undefined;t.x2=undefined;return}if(t.x2<0){t.x2=0}if(t.x1>e){t.x1=e}}}}function Tn(t,e){const n=e.seekcoord(t._chr,t._pos);for(const a of n){if(a.ridx!=undefined){if(a.x>0&&a.x<e.width){t.x=a.x;break}}else if(a.subpanelidx!=undefined){t.x=a.x}}}function Dn(t,e){if(!t.data_vcf)return;for(const n of t.data_vcf){if(n.dt==x){n._chr=n.chr;n._pos=n.pos;Tn(n,e);if(n.x==undefined){console.log("snvindel unmapped: "+n.chr+":"+n.pos)}else{delete n._chr;delete n._pos}}else{console.error("may_map_vcf: unknown dt")}}}function Yn(t,e){if(!t._data_vcf||t._data_vcf.length==0){t.data_vcf=null;return}const n=t._data_vcf;t.data_vcf=[];for(const a of n){if(a.dt==x){G(a,e)}else{throw"unknown dt "+a.dt}if(!t.legend_mclass.hiddenvalues.has(a.class)){t.data_vcf.push(a)}}}function Gn(t){const e=new Map;for(const n of t){e.set(n.sample+"."+n.chrA+"."+n.posA+"."+n.strandA+"."+n.chrB+"."+n.posB+"."+n.strandB,n)}return[...e.values()]}function Xn(t,e){if(!t)return false;if(e.legend_vorigin&&e.legend_vorigin.key){const n=t[e.legend_vorigin.key];if(n){if(n.toLowerCase()==e.legend_vorigin.germline)return true}}return false}export{Je as coverbarcolor_active,Xe as coverbarcolor_silent,Gn as dedup_sv,jn as draw_colorscale_cnv,Mn as draw_colorscale_loh,zn as focus_singlesample,Ye as intrasvcolor,yn as itemname_svfusion,en as labelspace,an as loadTk,Pn as map_cnv,An as multi_expressionstatus_ase_outlier,wn as multi_rnabam_asestatus,kn as multi_sample_addhighlight,vn as multi_sample_removehighlight,Ln as rnabamtk_copyparam,cn as trackclear,Xn as vcfvariantisgermline};
+import{p as t,bY as e,ac as n,Z as a,am as s,bZ as o,b_ as l,c as i,x as r,aa as c,a as p,q as d,a9 as f,b$ as m,j as u,ap as h,aq as g,ar as b,as as k,at as v,ak as x,z as y,ae as _,aN as w,aA as A,c0 as j,v as M,b as z,b6 as L,b7 as S,I as N,ah as U,ag as q,d as B,a8 as C,B as E,an as R,r as V,aW as I,bw as O,f as F,a7 as H,ao as P,ad as T,M as D,be as Y,bb as G}from"./app-488d9fd6.js";import{a as X,s as J,u as Z,m as W,i as $}from"./block.mds.expressionstat-483c9bc9.js";import{s as K}from"./legacy-d3-polyfill-bdb2d792.js";import{l as Q}from"./block.legend-aa831169.js";import{c as tt,d as et}from"./axis-747c801e.js";import{l as nt}from"./log-1001ca83.js";import{v as at}from"./vcf-55bf2c83.js";import{r as st,c as ot}from"./block.mds.svcnv.share-6575b7cf.js";import"./partition-db811f6b.js";import"./arc-3d6751aa.js";import"./constant-426a1483.js";import"./math-2fb199c6.js";const lt="svcnv";const it="vcf";const rt="expression";async function ct(t){const{feature:n,tk:p,block:d,limitsamplebyeitherannotation:f,limitbysamplesetgroup:m}=t;const u=a({x:100,y:100,close:()=>{e(u.pane,p.config_handle);u.pane.style("display","none")}});if(f){const t=f[0];if(t){u.header.html('<span style="font-size:.8em;opacity:.5">'+p.name+"</span> "+t.value)}}else if(m){u.header.html('<span style="font-size:.8em;opacity:.5">'+p.name+"</span> "+m.name)}else{u.header.text(p.name)}const h={debugmode:d.debugmode,genome:d.genome,features:[n],hostURL:d.hostURL,limitsamplebyeitherannotation:f,limitbysamplesetgroup:m,jwt:d.jwt,holder:u.body.append("div").style("margin","20px")};if(p.iscustom){h.iscustom=1;h.querykey2tracks={};h.querykey2tracks[lt]={type:s.mdssvcnv,file:p.file,url:p.url,indexURL:p.indexURL};if(p.checkexpressionrank){h.querykey2tracks[rt]={type:s.mdsexpressionrank};for(const t in p.checkexpressionrank){h.querykey2tracks[rt][t]=p.checkexpressionrank[t]}}if(p.checkvcf){h.querykey2tracks[it]={type:s.mdsvcf};for(const t in p.checkvcf){if(t=="stringifiedObj")continue;h.querykey2tracks[it][t]=p.checkvcf[t]}}}else{h.dslabel=p.mds.label}if(window.location.search.includes("smx=3")){h.client=o;h.common=l;h.string2pos=i;h.invalidcoord=r;h.block=import("./block-2f22e7fd.js").then((function(t){return t.c}));const t=await c();t.dthm(h).then((t=>{t._pane=u;p.samplematrices.push(t)}))}else{import("./samplematrix-2bb2480b.js").then((t=>{const e=new t.Samplematrix(h);e._pane=u;p.samplematrices.push(e)}))}}function pt(a,s){if(!a.samplematrices||a.samplematrices.length==0)return;const o=a.tkconfigtip.d.append("table").style("margin-bottom","5px");for(const s of a.samplematrices){const l=o.append("tr");{const a=[];if(s.limitsamplebyeitherannotation){const t=s.limitsamplebyeitherannotation[0];a.push(t.value)}else if(s.limitbysamplesetgroup){a.push(s.limitbysamplesetgroup.name)}else{a.push("Any sample")}const o=s.features.length;a.push(o+" feature"+(o>1?"s":""));a.push(s.samples.length+" samples");const i=l.append("td").append("div").attr("class","sja_menuoption").style("border","solid 1px #ededed").text(a.join(", "));if(s._pane.pane.style("display")=="none"){i.style("border-color","black")}i.on("click",(()=>{if(s._pane.pane.style("display")=="none"){t(s._pane.pane);e(i,s._pane.pane);i.style("border-color","#ededed")}else{e(s._pane.pane,i);n(s._pane.pane);i.style("border-color","black")}}))}{l.append("td").attr("class","sja_menuoption").html("&times;").on("click",(()=>{l.remove();s._pane.pane.remove();for(const[t,e]of a.samplematrices.entries()){if(s.limitsamplebyeitherannotation){if(e.limitsamplebyeitherannotation){const n=s.limitsamplebyeitherannotation[0];const o=e.limitsamplebyeitherannotation[0];if(n.key==o.key&&n.value==o.value){a.samplematrices.splice(t,1);return}}}else{if(!e.limitsamplebyeitherannotation){a.samplematrices.splice(t,1);return}}}}))}}}async function dt(t,e){if(t.iscustom)return;if(t.singlesample)return;const n=t.tkconfigtip.d.append("div").style("margin-bottom","15px");const s=n.append("input").attr("size",20).attr("placeholder","Find sample");const o=n.append("div").style("margin-top","10px");s.on("keyup",p.debounce(l,300));async function l(){o.selectAll("*").remove();const n=s.property("value").trim();if(!n)return;const l={genome:e.genome.name,dslabel:t.mds.label,querykey:t.querykey,findsamplename:n};try{const n=await d("mdssvcnv",l);if(n.error)throw n.error;if(!n.result)return;for(const s of n.result){const n=o.append("div");n.append("span").text(s.name);if(s.grouplabel){n.append("span").style("margin-left","10px").style("font-size",".7em").text(s.grouplabel)}if(s.num_assay_tracks){n.append("span").style("font-size",".7em").style("padding","1px 5px").style("margin-left","10px").style("background","#bbb").style("color","white").style("border-radius","3px").text(s.num_assay_tracks+" track"+(s.num_assay_tracks>1?"s":""))}if(s.disco){n.append("span").style("font-size",".7em").style("padding","1px 5px").style("margin-left","10px").style("background","#bbb").style("color","white").style("border-radius","3px").text("Genome view")}if(s.mutation_signature){n.append("span").style("font-size",".7em").style("padding","1px 5px").style("margin-left","10px").style("background","#bbb").style("color","white").style("border-radius","3px").text("Mutation signature")}n.attr("class","sja_menuoption").on("click",(()=>{t.tkconfigtip.hide();const n=[];Ft(n,{tk:t,block:e,sample:{samplename:s.name},samplegroup:{attributes:s.attributes}});Pt(n,{tk:t,block:e,sample:{samplename:s.name}});Ht(n,{tk:t,block:e,sample:{samplename:s.name}});Tt(n,s.name,t,e);if(s.attr&&t.sampleAttribute&&t.sampleAttribute.attributes){n.push({label:"Attributes",callback:e=>{for(const e of s.attr){const n=t.sampleAttribute.attributes[e.k];if(n)e.k=n.label}f(e,s.attr)}})}const o=a({x:100,y:100});o.header.text(s.name);m(o.body.style("padding-top","10px"),n)}))}}catch(t){u(o,err.message||err);if(err.stack)console.log(err.stack)}}}function ft(t,e,n){if(e.sampleset)return mt(t,e,n);if(e.iscustom)return;if(!t.attributes){return}const a=t=>u(e.tip2.d,t);if(!e.sampleAttribute)return a("tk.sampleAttribute missing");if(!e.sampleAttribute.attributes)return a("tk.sampleAttribute.attributes{} missing");e.tip2.d.append("div").style("margin","4px 10px").style("font-size",".7em").text(t.name);e.tip2.d.append("div").attr("class","sja_menuoption").text("Hide").on("click",(()=>{e.tip2.clear();gt(t,e,true);e.tip2.hide();an(e,n)}));e.tip2.d.append("div").attr("class","sja_menuoption").text("Show only").on("click",(()=>{e.tip2.clear();for(const t of e._data){gt(t,e,true)}gt(t,e,false);e.tip2.hide();an(e,n)}));{const[a,s,o]=ht(t,e);if(a);else if(o.hiddenvalues.size>0){e.tip2.d.append("div").attr("class","sja_menuoption").text("Show all").on("click",(()=>{e.tip2.hide();o.hiddenvalues.clear();an(e,n)}))}}e.tip2.d.append("div").attr("class","sja_menuoption").text("Table view").on("click",(()=>{e.tip2.hide();kt(t,e,n)}));e.tip2.d.append("div").attr("class","sja_menuoption").text("Matrix view").on("click",(()=>{e.tip2.hide();ut(e,n,t)}));Ct(t,e,n);Gt({tk:e,block:n,samplegroup:t,holder:e.tip2.d});Xt(e,n,e.tip2.d,t)}function mt(t,e,n){e.tip2.d.append("div").style("margin","4px 10px").style("font-size",".7em").text(t.name);e.tip2.d.append("div").attr("class","sja_menuoption").text("Table view").on("click",(()=>{e.tip2.hide();kt(t,e,n)}));e.tip2.d.append("div").attr("class","sja_menuoption").text("Matrix view").on("click",(()=>{e.tip2.hide();ut(e,n,t)}))}function ut(e,n,a){const s=n.rglst[n.startidx];const o={ismutation:1,width:60,chr:s.chr,start:s.start,stop:s.stop,cnv:{valuecutoff:e.valueCutoff,focalsizelimit:e.bplengthUpperLimit},loh:{valuecutoff:e.segmeanValueCutoff,focalsizelimit:e.lohLengthUpperLimit},itd:{},sv:{},fusion:{},snvindel:{excludeclasses:{}}};if(e.legend_mclass&&e.legend_mclass.hiddenvalues){for(const t of e.legend_mclass.hiddenvalues){if(typeof t=="string"){o.snvindel.excludeclasses[t]=1}else{if(t==h){o.cnv.hidden=1}else if(t==g){o.loh.hidden=1}else if(t==b){o.itd.hidden=1}else if(t==k){o.sv.hidden=1}else if(t==v){o.fusion.hidden=1}else{console.error("unknown hidden dt?? "+t)}}}}if(e.showinggene){o.label=e.showinggene}else{o.label=s.chr+":"+s.start+"-"+s.stop}const l={tk:e,block:n,feature:o};o.querykeylst=[];if(e.iscustom){if(e.file||e.url)o.querykeylst.push(lt);if(e.checkvcf)o.querykeylst.push(it)}else if(e.querykey){o.querykeylst.push(e.querykey);if(e.checkvcf)o.querykeylst.push(e.checkvcf.querykey)}if(e.sampleset){for(const n of e.samplematrices){if(n.limitbysamplesetgroup&&n.limitbysamplesetgroup.name==a.name){t(n._pane.pane);n.addnewfeature_update(o);return}}l.limitbysamplesetgroup={name:a.name,samples:JSON.parse(JSON.stringify(e.sampleset.find((t=>t.name==a.name)).samples))}}else if(a.attributes){const n=a.attributes[a.attributes.length-1];for(const a of e.samplematrices){if(a.limitsamplebyeitherannotation){const e=a.limitsamplebyeitherannotation[0];if(e&&e.key==n.k&&e.value==n.kvalue){t(a._pane.pane);a.addnewfeature_update(o);return}}}l.limitsamplebyeitherannotation=[{key:n.k,value:n.kvalue}]}ct(l)}function ht(t,e){if(!t.attributes)return[".attributes[] missing for group "+t.name];if(t.attributes.length==0)return[".attributes[] zero length for group "+t.name];const n=t.attributes[t.attributes.length-1];const a=e.sampleAttribute.attributes[n.k];if(!a)return['"'+n.k+'" not registered in sampleAttribute for group '+t.name];return[null,n,a]}function gt(t,e,n){const[a,s,o]=ht(t,e);if(a)return a;if(n){o.hiddenvalues.add(s.kvalue)}else{o.hiddenvalues.delete(s.kvalue)}return null}function bt(t,e){const n=e.tktip.clear().d.append("div");if(t.attributes){for(const e of t.attributes){n.append("div").html(e.kvalue+(e.fullvalue?' <span style="opacity:.5;font-size:.8em;">'+e.fullvalue+"</span>":""))}}else if(t.name){n.append("div").text(t.name)}const a=[t.samples.length+" sample"+(t.samples.length>1?"s":"")];if(t.sampletotalnum)a.push(t.sampletotalnum+" samples total, "+Math.ceil(100*t.samples.length/t.sampletotalnum)+"%");if(e.sampleset){const n=e.sampleset.find((e=>e.name==t.name));if(n){a.push(n.samples.length+" samples total, "+Math.ceil(100*t.samples.length/n.samples.length)+"%")}}e.tktip.d.append("div").style("margin-top","10px").style("color","#858585").html(a.join("<br>"));e.tktip.show(event.clientX,event.clientY)}function kt(t,e,n){const s=a({x:event.clientX+100,y:Math.max(100,event.clientY-100)});s.header.html(t.name+' <span style="font-size:.7em">'+e.name+"</span>");if(t.samples.length==1){const a=t.samples[0];const o=s.body.append("table").style("margin","10px").style("border-spacing","4px");{const t=o.append("tr");t.append("td").text("Sample").style("opacity",.5);t.append("td").text(a.samplename)}if(a.sampletype){const t=o.append("tr");t.append("td").text("Sample type").style("opacity",.5);t.append("td").text(a.sampletype)}const[l,i,r,c,p,d,f,m,u,h]=Bt(a.samplename,a.items,e);if(l.length){const s=o.append("tr");s.append("td").text("CNV").style("opacity",.5);const i=s.append("td");for(let 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i=l.append("tr");i.append("td").text("Sample").style("font-size",".8em").style("opacity",.5);i.append("td").text("SV").style("font-size",".8em").style("opacity",.5);i.append("td").text("RNA fusion").style("font-size",".8em").style("opacity",.5);let r=0;for(const[t,a]of o){const s=l.append("tr");if(!(r++%2)){s.style("background","#f1f1f1")}s.append("td").text(t);const o=s.append("td");for(const t of a.sv){const a=qt(t,e);o.append("div").attr("class","sja_clbtext").html(t.cytogeneticname?t.cytogeneticname+' <span style="font-size:.7em">'+a+"</span>":a).on("mouseover",(()=>{At({item:t,sample:t._sample,samplegroup:t._samplegroup,tk:e})})).on("mouseout",(()=>{e.tktip.hide();vn(t._sample)})).on("click",(()=>{wt({item:t,sample:t._sample,samplegroup:t._samplegroup,tk:e,block:n})}))}const i=s.append("td");for(const t of a.fusion){i.append("div").attr("class","sja_clbtext").html(yn(t)+' <span 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a.sampledata){const[s,o]=Nt({m:a,m_sample:t,tk:e});i.append("div").text(t.sampleobj.name).attr("class","sja_clbtext").on("mouseover",(()=>{At({item:a,m_sample:t,sample:s,samplegroup:o,tk:e,block:n})})).on("mouseout",(()=>{e.tktip.hide();vn(s)})).on("click",(()=>{wt({item:a,m_sample:t,sample:s,samplegroup:o,tk:e,block:n})}))}Ot(a,n,o)}else{throw"Unknown dt: "+a.dt}return}const o=s.body.append("table").style("margin-top","10px").style("border-spacing","4px");for(const a of t.items){const t=o.append("tr");t.append("td").text(a.mname).style("color",y[a.class].color).style("font-weight","bold").style("vertical-align","top");{const e=t.append("td");if(a.dt==x){e.style("opacity",".5").text(a.ref+" > "+a.alt).style("vertical-align","top")}}{const s=t.append("td");if(a.dt==x){for(const t of 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n=[];n.push({label:"Details",callback:e=>{t.holder=e;jt(t)}});Ft(n,t);Rt(n,t);Pt(n,t);Ht(n,t);Tt(n,t.sample.samplename,t.tk,t.block);Yt(n,{tk:t.tk,block:t.block,m:t.item,sample:t.sample});Dt(n,{tk:t.tk,block:t.block,m:t.item,sample:t.sample,samplegroup:t.samplegroup});m(e.body.style("padding-top","10px"),n)}function At(t){kn(t.sample);t.holder=t.tk.tktip.clear().d;jt(t);t.tk.tktip.show(event.clientX,event.clientY)}function jt(t){const e=[];if(t.sample){e.push({k:"Sample",v:t.sample.samplename});Et(t.sample.samplename,t.tk,e)}const n=t.item;let a;if(n.dt==b){e.push({k:"ITD",v:n.chr+":"+(n.start+1)+"-"+(n.stop+1)});if(n.gene||n.isoform){const t=[];if(n.gene)t.push(n.gene);if(n.isoform)t.push(n.isoform);e.push({k:"Gene",v:t.join(", ")})}if(n.rnaduplength){e.push({k:"RNA duplicated",v:n.rnaduplength+" bp"})}if(n.aaduplength){e.push({k:"AA duplicated",v:n.aaduplength+" aa"})}a=n.mattr}else if(n.dt==h||n.dt==g){if(n.dt==g){e.push({k:"LOH seg.mean",v:n.segmean.toFixed(2)})}else{e.push({k:"CNV 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s=t.tk.checkvcf?t.tk.checkvcf.format:null;for(const o in t.m_sample){if(o=="sampleobj"){continue}if(t.tk.mds&&t.tk.mds.mutation_signature){const n=t.tk.mds.mutation_signature.sets[o];if(n){const a=t.m_sample[o];const s=n.signatures[a];if(!s.nodata){const t=s?s.name:"Unknown ("+a+")";const o=s?s.color:"black";e.push({k:n.name,v:'<span style="background:'+o+'">&nbsp;&nbsp;&nbsp;</span> '+t})}continue}}if(t.tk.mutationAttribute&&t.tk.mutationAttribute.attributes){if(t.tk.mutationAttribute.attributes[o]){a[o]=t.m_sample[o];continue}}const l=s?s[o]:null;if(l){let a=l.Number=="R"||l.Number=="A";if(!a){if(o=="AD"){a=true}}if(a){const a=[];const s=[];let i;for(const e in t.m_sample[o]){if(e==n.ref)continue;a.push(e);i=t.m_sample[o][e];s.push(i)}const r=t.m_sample[o][n.ref];if(r!=undefined){a.push(n.ref);s.push(r)}let c;if(r+i>0){c=w(null,{f:i/(i+r)})}e.push({k:o,v:(c?c+" ":"")+'<span style="font-size:.8em;opacity:.5">'+a.join(" / ")+"</span> "+s.join(" / ")+(l.Description?' <span 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5px;background:'+n.gecfg.ase.color_uncertain+';color:white">ASE uncertain</span>')}else if(t.estat.ase_biallelic){e.push('<span style="padding:0px 5px;background:'+n.gecfg.ase.color_biallelic+';color:white">Bi-allelic</span>')}else if(t.estat.ase_monoallelic){e.push('<span style="padding:0px 5px;background:'+n.gecfg.ase.color_monoallelic+';color:white">Mono-allelic</span>')}}e.push("</td>");s.push("<tr>"+e.join("")+"</tr>")}if(n.gecfg.fixed){for(const e of n.gecfg.fixed){if(e.sample2rnabam){const a=e.sample2rnabam[t.sample.samplename];if(a){const t=["<td><b>"+e.gene+"</b></td>"+'<td><span style="font-size:.8em;opacity:.5">'+n.gecfg.datatype+"</span> "+a.fpkm+"</td>"+"<td>"];if(a.estat){if(a.estat.ase_uncertain){t.push('<span style="padding:0px 5px;background:'+n.gecfg.ase.color_uncertain+';color:white">ASE uncertain</span>')}else if(a.estat.ase_biallelic){t.push('<span style="padding:0px 5px;background:'+n.gecfg.ase.color_biallelic+';color:white">Bi-allelic</span>')}else if(a.estat.ase_monoallelic){t.push('<span style="padding:0px 5px;background:'+n.gecfg.ase.color_monoallelic+';color:white">Mono-allelic</span>')}}t.push("</td>");s.push("<tr>"+t.join("")+"</tr>")}}}}if(s.length){e.push({k:"Gene expression",v:"<table>"+s.join("")+"</table>"})}}function Lt(t,e){const n=t.tk;if(!n)return;const a=t.sample;if(!a)return;if(!a.expressionrank)return;const s=[];for(const t in a.expressionrank){const e=a.expressionrank[t];const o=["<tr>"+"<td><b>"+t+"</b></td>"+'<td>&nbsp;<span style="font-size:.7em">RANK</span> '+j(e.rank)+"</td>"+'<td>&nbsp;<span style="font-size:.7em">'+n.gecfg.datatype+"</span> "+e.value+"</td>"+"<td>"];if(e.estat){if(e.estat.ase_uncertain){o.push('<span style="padding:0px 5px;background:'+n.gecfg.ase.color_uncertain+';color:white">ASE uncertain</span>')}else if(e.estat.ase_biallelic){o.push('<span style="padding:0px 5px;background:'+n.gecfg.ase.color_biallelic+';color:white">Bi-allelic</span>')}else if(e.estat.ase_monoallelic){o.push('<span style="padding:0px 5px;background:'+n.gecfg.ase.color_monoallelic+';color:white">Mono-allelic</span>')}if(e.estat.outlier){o.push('<span style="padding:0px 5px;background:'+n.gecfg.outlier.color_outlier+';color:white">Outlier HIGH</span>')}else if(e.estat.outlier_asehigh){o.push('<span style="padding:0px 5px;background:'+n.gecfg.outlier.color_outlier_asehigh+';color:white">ASE HIGH</span>')}}o.push("</td></tr>");s.push(o.join(""))}if(n.gecfg&&n.gecfg.fixed){for(const t of n.gecfg.fixed){if(t.sample2rank&&t.sample2rank[a.samplename]){const e=t.sample2rank[a.samplename];const o=["<tr>"+"<td><b>"+t.gene+"</b></td>"+'<td>&nbsp;<span style="font-size:.7em">RANK</span> '+j(e.rank)+"</td>"+'<td>&nbsp;<span style="font-size:.7em">'+n.gecfg.datatype+"</span> "+e.value+"</td>"+"<td>"];if(e.estat){if(e.estat.ase_uncertain){o.push('<span style="padding:0px 5px;background:'+n.gecfg.ase.color_uncertain+';color:white">ASE uncertain</span>')}else if(e.estat.ase_biallelic){o.push('<span style="padding:0px 5px;background:'+n.gecfg.ase.color_biallelic+';color:white">Bi-allelic</span>')}else if(e.estat.ase_monoallelic){o.push('<span style="padding:0px 5px;background:'+n.gecfg.ase.color_monoallelic+';color:white">Mono-allelic</span>')}if(e.estat.outlier){o.push('<span style="padding:0px 5px;background:'+n.gecfg.outlier.color_outlier+';color:white">Outlier HIGH</span>')}else if(e.estat.outlier_asehigh){o.push('<span style="padding:0px 5px;background:'+n.gecfg.outlier.color_outlier_asehigh+';color:white">ASE HIGH</span>')}}o.push("</td></tr>");s.push(o.join(""))}}}if(s.length){e.push({k:"Expression",v:'<table style="font-size:.9em">'+s.join("")+"</table>"})}}function St(t,e){const n=[];{const e=y[t.class];n.push({k:"Mutation",v:(t.mname?'<span style="color:'+e.color+'">'+t.mname+"</span>":"")+' <span style="font-size:.7em">'+e.label+"</span>"})}{const e=[];if(t.gene)e.push(t.gene);if(t.isoform)e.push(t.isoform);if(e.length){n.push({k:"Gene",v:e.join(" ")})}}n.push({k:"Position",v:t.chr+":"+(t.pos+1)});n.push({k:"Alleles",v:'<span style="font-size:.8em;opacity:.5">REF/ALT</span> '+t.ref+" / "+t.alt});if(e&&e.alleleAttribute&&e.alleleAttribute.attributes){for(const a in e.alleleAttribute.attributes){const s=e.alleleAttribute.attributes[a];n.push({k:s.label,v:t.altinfo?t.altinfo[a]:""})}}if(e&&e.locusAttribute&&e.locusAttribute.attributes){for(const a in e.locusAttribute.attributes){const s=e.locusAttribute.attributes[a];const o=t.info?t.info[a]:"";if(s.appendto_link){if(!o){continue}n.push({k:s.label,v:o.split(",").map((t=>"<a target=_blank href="+s.appendto_link+t+">"+t+"</a>")).join(" ")});continue}n.push({k:s.label,v:t.info?t.info[a]:""})}}return n}function Nt(t){let e;if(t.m.dt==x){if(!t.m_sample)throw"m_sample missing";e=t.m_sample.sampleobj.name}else{throw"unknown dt"}for(const n of t.tk._data){for(const t of n.samples){if(t.samplename==e){return[t,n]}}}return[-1,-1]}function 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s=t.attributes.find((t=>t.k==e.mds.annotationsampleset2matrix.key));if(!s)return;const o=e.mds.annotationsampleset2matrix.groups[s.kvalue];if(!o)return;if(!o.groups)return;for(const t of o.groups){if(!t.name||!t.matrixconfig)continue;e.tip2.d.append("div").html(t.name+' <span style="font-size:.8em;opacity:.5">SUMMARY</span>').attr("class","sja_menuoption").on("click",(()=>{e.tip2.hide();const s=a({x:100,y:100});s.header.text(t.name+" summary");const o={dslabel:e.mds.label,debugmode:n.debugmode,genome:n.genome,hostURL:n.hostURL,jwt:n.jwt,holder:s.body.append("div").style("margin","20px")};for(const e in t.matrixconfig){o[e]=t.matrixconfig[e]}import("./samplematrix-2bb2480b.js").then((t=>{new t.Samplematrix(o)}))}))}}function Et(t,e,n){if(!e.sampleAttribute)return;if(!e.sampleAttribute.attributes||!e.sampleAttribute.samples)return;const a=e.sampleAttribute.samples[t];if(!a)return;for(const t in a){const s=e.sampleAttribute.attributes[t]||{};const o=a[t];if(o==undefined)continue;let l=o;if(s.values){const t=s.values[o];if(t&&t.name){l=t.name}}n.push({k:s.label||t,v:l})}}function Rt(t,e){if(!e.item)return;if(e.item.dt!=k&&e.item.dt!=v)return;t.push({label:"Fusion graph",callback:async t=>{const n=M(t);await Vt(e,t);n.remove()}})}async function Vt(t,e){const n={a:{chr:t.item.chrA,position:t.item.posA,strand:t.item.strandA},b:{chr:t.item.chrB,position:t.item.posB,strand:t.item.strandB}};const a=e.append("div");try{{a.text("Loading gene at "+n.a.chr+":"+n.a.position+" ...");const e=await It(t,n.a.chr,n.a.position);const s=e.find((t=>t.isdefault))||e[0];if(s){n.a.name=s.name;n.a.gm={isoform:s.isoform}}}{a.text("Loading gene at "+n.b.chr+":"+n.b.position+" ...");const e=await It(t,n.b.chr,n.b.position);const s=e.find((t=>t.isdefault))||e[0];if(s){n.b.name=s.name;n.b.gm={isoform:s.isoform}}}a.remove();const s={pairlst:[n],genome:t.block.genome,holder:e};import("./svgraph-76e34d5e.js").then((t=>{t.default(s)}))}catch(t){if(t.stack)console.log(t.stack);a.text("Error: "+(t.message||t))}}function It(t,e,n){return z(`isoformbycoord?genome=${t.block.genome.name}&chr=${e}&pos=${n}`).then((t=>{if(t.error)throw t.error;return t.lst}))}async function Ot(t,e,n){if(!e||!e.genome||!e.genome.hasSNP)return;const a=n.append("tr");a.append("td").attr("colspan",2).text("dbSNP").style("opacity",.4).style("padding","3px");const s=a.append("td");const o=s.append("div").text("Loading...");try{const n=await L(t.chr,[t.pos],e.genome,[t.ref,t.altstr]);if(!n||n.length==0){o.text("No match");return}o.remove();for(const t of n){const e=s.append("div");S(t,e)}}catch(t){o.text(t.message||t)}}function Ft(t,e){t.push({label:"Sample View",callback:t=>{zn({holder:t,m:e.item,sample:e.sample,samplegroup:e.samplegroup,tk:e.tk,block:e.block})}})}function Ht(t,e){if(!e.tk.mds)return;t.push({label:"Genome",callback:async t=>{const n=M(t);try{const a=await d("mdssvcnv",{genome:e.block.genome.name,dslabel:e.tk.mds.label,querykey:e.tk.mds.querykey,ifsamplehasvcf:e.sample.samplename});if(a.no)return;let s=0;for(const t in e.block.genome.majorchr){s=Math.max(s,e.block.genome.majorchr[t])}for(const n in e.block.genome.majorchr){const a=t.append("div").style("display","inline-block");const o={};if(e.tk.iscustom){}else{o.fixname=n.toUpperCase();o.mds=e.tk.mds;o.querykey=e.tk.querykey;o.singlesample={name:e.sample.samplename,waterfall:{inuse:1}};for(const t in e.tk.mds.queries[e.tk.querykey]){if(t=="bplengthUpperLimit"||t=="valueCutoff"){continue}o[t]=e.tk.mds.queries[e.tk.querykey][t]}}e.block.newblock({foldlegend:true,hide_mdsHandleHolder:1,width:Math.ceil(900*e.block.genome.majorchr[n]/s),holder:a,block:1,chr:n,start:0,stop:e.block.genome.majorchr[n],tklst:[o]})}n.remove()}catch(t){n.text("Error: "+(t.message||t));if(t.stack)console.log(t.stack)}}})}function Pt(t,e){if(!e.tk.mds||!e.tk.mds.singlesamplemutationjson)return;t.push({label:"Disco 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a={genome:e.block.genome,div:t,m:{chr:e.m.chr,pos:e.m.pos+1,ref:e.m.ref,alt:e.m.alt}};if(e.tk.iscustom){if(e.tk.checkexpressionrank){a.factor_profiles=[{isgenevalue:1,name:"Gene "+e.tk.gecfg.datatype,file:e.tk.checkexpressionrank.file,url:e.tk.checkexpressionrank.url,indexURL:e.tk.checkexpressionrank.indexURL}];if(e.sample){a.factor_profiles.push({isgenevalueonesample:1,name:e.sample.samplename+" "+e.tk.gecfg.datatype,samplename:e.sample.samplename,file:e.tk.checkexpressionrank.file,url:e.tk.checkexpressionrank.url,indexURL:e.tk.checkexpressionrank.indexURL})}}}else{if(e.tk.checkexpressionrank){const t={isgenevalue:1,datatype:e.tk.checkexpressionrank.datatype,querykey:e.tk.checkexpressionrank.querykey,mdslabel:e.tk.mds.label};if(e.samplegroup){if(e.samplegroup.attributes){t.name=e.samplegroup.name+" "+e.tk.gecfg.datatype;t.samplegroup_attrlst=e.samplegroup.attributes}}if(!t.name){t.name="Gene 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if(a.dt==g){s.chr=a.chr;s.start=a.start;s.stop=a.stop;s.loh={focalsizelimit:e.tk.lohLengthUpperLimit,valuecutoff:e.tk.segmeanValueCutoff}}else if(a.dt==k){s.chr=a._chr;s.start=a._pos;s.stop=a._pos;s.sv={}}else if(a.dt==v){s.chr=a._chr;s.start=a._pos;s.stop=a._pos;s.fusion={}}else if(a.dt==b){s.chr=a.chr;s.start=a.start;s.stop=a.stop;s.itd={}}const o={renderplot:1,samplerule:{full:{},set:s}};if(e.tk.mds.survivalplot.samplegroupattrlst&&e.sample){const t=e.tk.mds.survivalplot.samplegroupattrlst[0];const n=e.tk.sampleAttribute?e.tk.sampleAttribute.samples[e.sample.samplename]:null;if(n){const e=n[t.key];if(e){o.samplerule.full.byattr=1;o.samplerule.full.key=t.key;o.samplerule.full.value=e}}}else{}const l=await import("./mds.survivalplot-b04947ee.js");await l.init({genome:e.block.genome,mds:e.tk.mds,plotlist:[o]},t,e.block.debugmode);n.remove()}catch(t){n.text("Error: "+(t.message||t));if(t.stack)console.log(t.stack)}}})}function Gt(t){if(!t.tk.mds||!t.tk.mds.survivalplot){return}t.holder.append("div").text("Survival plot").attr("class","sja_menuoption").on("click",(()=>{t.tk.tip2.hide();t.m;const e={mutation:1};{const n=t.block.rglst;e.chr=n[t.block.startidx].chr;const a=n[t.block.startidx].start;const s=n[t.block.stopidx].stop;e.start=Math.min(a,s);e.stop=Math.max(a,s)}e.snvindel={hiddenclass:{}};{let n=false;for(const a of t.tk.legend_mclass.hiddenvalues){if(typeof a=="string"){e.snvindel.hiddenclass[a]=1;n=true}}if(!n){delete e.snvindel.hiddenclass}}if(!t.tk.legend_mclass.hiddenvalues.has(h)){e.cnv={focalsizelimit:t.tk.bplengthUpperLimit,valuecutoff:t.tk.valueCutoff}}if(!t.tk.legend_mclass.hiddenvalues.has(g)){e.loh={focalsizelimit:t.tk.lohLengthUpperLimit,valuecutoff:t.tk.segmeanValueCutoff}}if(!t.tk.legend_mclass.hiddenvalues.has(k)){e.sv={}}if(!t.tk.legend_mclass.hiddenvalues.has(v)){e.fusion={}}if(!t.tk.legend_mclass.hiddenvalues.has(b)){e.itd={}}const n={renderplot:1,samplerule:{full:{},set:e}};const 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i.samples){if(!i.name&&n.samplename&&n.height>=Ze){n.svglabel=t.cnvleftg.append("text").text(n.samplename).attr("text-anchor","end").attr("dominant-baseline","central").attr("fill","black").attr("x",-5).attr("y",r+n.height/2).attr("font-family",U).attr("font-size",Math.min(15,Math.max(Ze,n.height+1))).each((function(){})).on("mouseover",(()=>{kn(n)})).on("mouseout",(()=>{vn(n)}));t.leftLabelMaxwidth=Math.max(t.leftLabelMaxwidth,n.svglabel.node().getBBox().width)}const s=t.cnvmidg.append("g").attr("transform","translate(0,"+r+")");if(t.isfull){n.blockbg=s.append("rect").attr("width",a).attr("height",n.height).attr("fill",Je).attr("fill-opacity",0).on("mouseover",(()=>{kn(n)})).on("mouseout",(()=>{vn(n)}))}if(t.isfull&&n.sampletype==Qe){s.append("rect").attr("x",-5).attr("y",0).attr("width",5).attr("height",n.height).attr("fill","black").attr("shape-rendering","crispEdges")}for(const a of n.items){if(a.dt!=h&&a.dt!=g&&a.dt!=b)continue;let 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t.data_vcf){if(a.dt!=x)continue;if(a.x==undefined)continue;if(!a.sampledata)continue;const o=n.crossboxw;const l=bn(t,a,n);for(const r of a.sampledata){if(r.sampleobj.name!=n.samplename)continue;const c=s.append("g").attr("transform","translate("+a.x+","+n.height/2+")");const p=c.append("rect").attr("x",-o/2-1).attr("y",-o/2-1).attr("width",o+2).attr("height",o+2).attr("fill",l).attr("fill-opacity",0);let 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o}function bn(t,e,n){if(t.checkrnabam){const a=t.checkrnabam.samples[n.samplename];if(a&&a.genes){for(const n of a.genes){if(n.snps){const a=n.snps.find((t=>t.pos==e.pos&&t.ref==e.ref&&t.alt==e.alt));if(a&&a.rnacount&&a.rnacount.pvalue!=undefined){return t.checkrnabam.clientcolor_snpinuse}}}}return t.checkrnabam.clientcolor_markernotinuse}return y[e.class].color}function kn(t){if(!t)return;if(t.svglabel)t.svglabel.attr("fill",Je);if(t.blockbg)t.blockbg.attr("fill-opacity",.1);if(t.columnbars){for(const e of t.columnbars){e.attr("fill",Je)}}}function vn(t){if(!t)return;if(t.svglabel)t.svglabel.attr("fill",Xe);if(t.blockbg)t.blockbg.attr("fill-opacity",0);if(t.columnbars){for(const e of t.columnbars){e.attr("fill",Xe)}}}function xn(t,e){if(!t.samplegroups||t.samplegroups.length==0)return;if(t.isdense){for(const e of t.samplegroups){for(const t of e.samples){t.height=1;for(const e of t.items){if(e.dt==h||e.dt==g||e.dt==b){e.stack_y=0;e.stack_h=1}}}}return}for(const e of 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t.data_vcf){if(e.dt!=x||e.x==undefined||!e.sampledata)continue;const n=e.sampledata.find((t=>t.sampleobj.name==a.samplename));if(n){const a={dt:e.dt,x:e.x,obj:n.sampleobj};if(t.multihidelabel_vcf);else{a.name=e.mname}s.push(a)}}}if(s.length>0){s.sort(((t,e)=>t.x-e.x));for(let e=0;e<s.length;e++){const o=s[e];if(!o.name){continue}let l;t.g.append("text").text(o.name).attr("font-size",a.crossboxw+2).attr("font-family",U).each((function(){l=this.getBBox().width})).remove();l+=a.crossboxw/2+en;let i=false,r=false;if(l>o.x){i=true}else if(l>n-o.x){r=true}for(const t of a.items){if(i&&r)break;if(t.dt==h||t.dt==g||t.dt==b){if(t.x1==undefined||t.x2==undefined)continue;const e=Math.min(t.x1,t.x2);const n=Math.max(t.x1,t.x2);if(e<o.x){if(n<o.x){if(l>o.x-n){i=true}}else{i=true;r=true}}else{if(l>e-o.x){r=true}}}}if(i&&r){continue}if(!i){for(let t=e-1;t>=0;t--){const e=s[t];if(e.x==o.x){if(e.obj.labonleft){i=true}else 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D({padding:"0px"});if(t.singlesample){if(!t.midpad)t.midpad=3;if(!t.stem1){t.stem1=10;t.stem2=0;t.stem3=5}if(!t.legheight)t.legheight=40;if(!t.discradius)t.discradius=8;if(!t.valueCutoff)t.valueCutoff=.2;if(!Number.isInteger(t.bplengthUpperLimit))t.bplengthUpperLimit=2e6;if(!Number.isInteger(t.lohLengthUpperLimit))t.lohLengthUpperLimit=2e6;if(!t.segmeanValueCutoff)t.segmeanValueCutoff=.1;if(t.fixname){t.name=t.fixname;t.tklabel.text(t.name);delete t.fixname}else{t.tklabel.text((t.name?t.name+", 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t.lohcolor}if(t.iscustom){if(t.valueCutoff==undefined)t.valueCutoff=.2;if(t.bplengthUpperLimit==undefined)t.bplengthUpperLimit=2e6;if(t.segmeanValueCutoff==undefined)t.segmeanValueCutoff=.1;if(t.lohLengthUpperLimit==undefined)t.lohLengthUpperLimit=2e6}t.config_handle=e.maketkconfighandle(t).on("click",(()=>{En(t,e)}));if(t.checkrnabam){st(t.checkrnabam)}Kt(e,t);let n=false;if(t.iscustom){if(t.checkexpressionrank){n=true;if(!t.gecfg)t.gecfg={};t.gecfg.datatype=t.checkexpressionrank.datatype}else if(t.checkrnabam){n=true;if(!t.gecfg)t.gecfg={};t.gecfg.datatype="FPKM"}}else{if(t.mds.queries[t.querykey].checkexpressionrank){n=true;const e=t.mds.queries[t.mds.queries[t.querykey].checkexpressionrank.querykey];if(t.gecfg&&t.gecfg.fixed_pend){e.fixed_pend=t.gecfg.fixed_pend}t.gecfg=e}}if(n){if(!t.gecfg)t.gecfg={};if(!t.gecfg.fixed){t.gecfg.fixed=[]}if(!t.gecfg.no_ase){$(t.gecfg)}}}function Bn(t,e){const n=t.iscustom?t:t.customization;if(!n)return;if(n.singlesample){t.singlesample=n.singlesample}else if(n.sampleset){t.sampleset=n.sampleset}t.hide_cnvgain=n.hide_cnvgain;t.hide_cnvloss=n.hide_cnvloss;if(n.isfull){t.isdense=false;t.isfull=true}else if(n.isdense){t.isdense=true;t.isfull=false}if(n.sampleAttribute){if(!t.sampleAttribute)t.sampleAttribute={};if(!t.sampleAttribute.attributes)t.sampleAttribute.attributes={};for(const e in n.sampleAttribute){const a=n.sampleAttribute[e];if(!t.sampleAttribute.attributes[e]){t.sampleAttribute.attributes[e]={label:e}}const s=t.sampleAttribute.attributes[e];if(!s.hiddenvalues)s.hiddenvalues=new Set;if(a.hiddenvalues){for(const t of a.hiddenvalues)s.hiddenvalues.add(t)}}}t.legend_mclass={hiddenvalues:new Set};if(n.vcf){if(n.vcf.hiddenclass){for(const e of n.vcf.hiddenclass)t.legend_mclass.hiddenvalues.add(e)}}if(n.cnv){if(n.cnv.hidden)t.legend_mclass.hiddenvalues.add(h);if(Number.isInteger(n.cnv.upperlengthlimit))t.bplengthUpperLimit=n.cnv.upperlengthlimit}if(n.loh){if(n.loh.hidden)t.legend_mclass.hiddenvalues.add(g);if(Number.isInteger(n.loh.upperlengthlimit))t.lohLengthUpperLimit=n.loh.upperlengthlimit}if(n.fusion){if(n.fusion.hidden)t.legend_mclass.hiddenvalues.add(v)}if(n.sv){if(n.sv.hidden)t.legend_mclass.hiddenvalues.add(k)}if(n.itd){if(n.itd.hidden)t.legend_mclass.hiddenvalues.add(b)}if(n.fixedgeneexpression){if(!t.gecfg)t.gecfg={};t.gecfg.fixed_pend=n.fixedgeneexpression}}function Cn(t,e){t.tkconfigtip.hide();if(t.mode_radio_1.property("checked")){t.isdense=true;t.isfull=false}else if(t.mode_radio_2.property("checked")){t.isdense=false;t.isfull=true}if(!t._data){return}dn(t,e);e.block_setheight();e.setllabel()}function En(t,e){t.tkconfigtip.clear();pt(t);Fn(t,e);dt(t,e);Rn(t,e);Hn(t,e);In(t,e);On(t,e);ot(t,e,an);t.tkconfigtip.showunder(t.config_handle.node())}function Rn(t,e){if(t.singlesample)return;const n=t.tkconfigtip.d.append("div").style("margin-bottom","25px");if(t.sampleset){n.append("span").style("opacity",.5).style("padding-right","10px").text("Restricted to "+t.sampleset.reduce(((t,e)=>t+e.samples.length),0)+" samples");n.append("button").text("Edit").on("click",(()=>{Vn(t,e)}));n.append("button").text("Remove").on("click",(()=>{t.tkconfigtip.hide();delete t.sampleset;an(t,e)}));return}n.append("button").text("Use a sample list").on("click",(()=>{Vn(t,e)}));if(t.iscustom||t.mds&&t.mds.allow_getallsamples){n.append("button").style("margin-left","10px").text(t.getallsamples?"Only show samples with variants":"Show all samples").on("click",(()=>{t.getallsamples=!t.getallsamples;t.tkconfigtip.hide();an(t,e)}))}}function Vn(t,e){t.tkconfigtip.clear();const n=t.tkconfigtip.d.append("div");const a=n.append("textarea").attr("placeholder","One sample per row. 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Press ENTER to update.")}{const a=n.append("div").style("margin-bottom","15px");a.append("span").html("CNV segment size limit&nbsp;");a.append("input").property("value",t.bplengthUpperLimit||0).attr("type","number").style("width","80px").on("keyup",(n=>{if(n.code!="Enter"&&n.code!="NumpadEnter")return;let a=Number.parseInt(n.target.value);if(!a||a<0){a=0}if(a==0){if(t.bplengthUpperLimit){t.bplengthUpperLimit=0;an(t,e)}return}if(t.bplengthUpperLimit){if(t.bplengthUpperLimit==a);else{t.bplengthUpperLimit=a;an(t,e)}}else{t.bplengthUpperLimit=a;an(t,e)}}));a.append("span").text("bp");a.append("div").style("font-size",".7em").style("color","#858585").html("Limit the CNV segment length to show only focal events.<br>Set to 0 to show all. Press ENTER to update.")}{const a=n.append("div");a.append("span").html("Copy number gain&nbsp;");a.append("input").attr("type","color").property("value",t.cnvcolor.gain.str).on("change",(n=>{t.cnvcolor.gain.str=n.target.value;const a=V(t.cnvcolor.gain.str);t.cnvcolor.gain.r=a.r;t.cnvcolor.gain.g=a.g;t.cnvcolor.gain.b=a.b;t.cnvcolor.cnvlegend.gain_stop.attr("stop-color",t.cnvcolor.gain.str);if(t.singlesample){be(t,e)}else{dn(t,e)}}));a.append("span").html("&nbsp;&nbsp;loss&nbsp;");a.append("input").attr("type","color").property("value",t.cnvcolor.loss.str).on("change",(n=>{t.cnvcolor.loss.str=n.target.value;const a=V(t.cnvcolor.loss.str);t.cnvcolor.loss.r=a.r;t.cnvcolor.loss.g=a.g;t.cnvcolor.loss.b=a.b;t.cnvcolor.cnvlegend.loss_stop.attr("stop-color",t.cnvcolor.loss.str);if(t.singlesample){be(t,e)}else{dn(t,e)}}))}if(t.cnvcolor.lohlegend){n.append("hr").style("margin","20px");{const a=n.append("div").style("margin-bottom","15px");a.append("span").html("LOH seg.mean cutoff&nbsp;");a.append("input").property("value",t.segmeanValueCutoff||0).attr("type","number").style("width","50px").on("keyup",(n=>{if(n.code!="Enter"&&n.code!="NumpadEnter")return;let a=Number.parseFloat(n.target.value);if(!a||a<0){a=0}if(a==0){if(t.segmeanValueCutoff){t.segmeanValueCutoff=0;an(t,e)}return}if(t.segmeanValueCutoff){if(t.segmeanValueCutoff==a);else{t.segmeanValueCutoff=a;an(t,e)}}else{t.segmeanValueCutoff=a;an(t,e)}}));a.append("div").style("font-size",".7em").style("color","#858585").html("Only show LOH with seg.mean no less than cutoff.<br>Set to 0 to show all. Press ENTER to update.")}{const a=n.append("div").style("margin-bottom","15px");a.append("span").html("LOH segment size limit&nbsp;");a.append("input").property("value",t.lohLengthUpperLimit||0).attr("type","number").style("width","80px").on("keyup",(n=>{if(n.code!="Enter"&&n.code!="NumpadEnter")return;let a=Number.parseInt(n.target.value);if(!a||a<0){a=0}if(a==0){if(t.lohLengthUpperLimit){t.lohLengthUpperLimit=0;an(t,e)}return}if(t.lohLengthUpperLimit){if(t.lohLengthUpperLimit==a);else{t.lohLengthUpperLimit=a;an(t,e)}}else{t.lohLengthUpperLimit=a;an(t,e)}}));a.append("span").text("bp");a.append("div").style("font-size",".7em").style("color","#858585").html("Limit the LOH segment length to show only focal events.<br>Set to 0 to show all. Press ENTER to update.")}{const a=n.append("div").style("margin-bottom","1px");a.append("span").html("LOH color&nbsp;");a.append("input").attr("type","color").property("value",t.cnvcolor.loh.str).on("change",(n=>{t.cnvcolor.loh.str=n.target.value;const a=V(t.cnvcolor.loh.str);t.cnvcolor.loh.r=a.r;t.cnvcolor.loh.g=a.g;t.cnvcolor.loh.b=a.b;t.cnvcolor.lohlegend.loh_stop.attr("stop-color",t.cnvcolor.loh.str);if(t.singlesample){be(t,e)}else{dn(t,e)}}))}}}function Fn(t,e){if(t.singlesample)return;const n=t.tkconfigtip.d.append("div").style("background","#FAF9DE").style("margin-bottom","20px").style("padding","15px");const a=Math.random().toString();const s=Math.random().toString();const o=Math.random().toString();const l=n.append("div").style("margin-bottom","5px");t.mode_radio_1=l.append("input").attr("type","radio").attr("id",a).attr("name",o).property("checked",t.isdense).on("change",(()=>{Cn(t,e)}));l.append("label").attr("for",a).attr("class","sja_clbtext").html('&nbsp;Dense <span style="font-size:.7em;color:#858585;">Showing densities of SV breakpoints and SNV/indels, over all samples</span>');const i=n.append("div");t.mode_radio_2=i.append("input").attr("type","radio").attr("id",s).attr("name",o).property("checked",t.isfull).on("change",(()=>{Cn(t,e)}));i.append("label").attr("for",s).attr("class","sja_clbtext").html('&nbsp;Expanded <span style="font-size:.7em;color:#858585;">Showing SV/SNV/indel for each sample</span>')}function Hn(t,e){if(t.singlesample)return;t.tkconfigtip.d.append("div").style("margin-bottom","5px").text("Show text labels in expanded mode").style("opacity",.5);const n=t.tkconfigtip.d.append("div").style("margin-bottom","20px");{const a=Math.random().toString();n.append("input").attr("type","checkbox").attr("id",a).property("checked",!t.multihidelabel_vcf).on("change",(()=>{t.multihidelabel_vcf=!t.multihidelabel_vcf;dn(t,e)}));n.append("label").attr("for",a).attr("class","sja_clbtext").html("&nbsp;SNV/indel")}if(!t.nocnvlohsv){{const a=Math.random().toString();n.append("input").attr("type","checkbox").style("margin-left","20px").attr("id",a).property("checked",!t.multihidelabel_sv).on("change",(()=>{t.multihidelabel_sv=!t.multihidelabel_sv;dn(t,e)}));n.append("label").attr("for",a).attr("class","sja_clbtext").html("&nbsp;DNA SV")}{const a=Math.random().toString();n.append("input").attr("type","checkbox").style("margin-left","20px").attr("id",a).property("checked",!t.multihidelabel_fusion).on("change",(()=>{t.multihidelabel_fusion=!t.multihidelabel_fusion;dn(t,e)}));n.append("label").attr("for",a).attr("class","sja_clbtext").html("&nbsp;RNA fusion")}}}function Pn(t,e,n){const a=n.tkarg_maygm(e)[0];if(t.chr==a.chr&&Math.max(t.start,a.start)<Math.min(t.stop,a.stop)){t.x1=n.seekcoord(t.chr,Math.max(t.start,a.start))[0].x;t.x2=n.seekcoord(t.chr,Math.min(t.stop,a.stop-1))[0].x}let s=n.width;for(const e of n.subpanels){s+=e.leftpad;if(t.chr==e.chr&&Math.max(t.start,e.start)<Math.min(t.stop,e.stop)){const n=s+(Math.max(t.start,e.start)-e.start)*e.exonsf;const a=s+(Math.min(t.stop,e.stop)-e.start)*e.exonsf;if(t.x1==undefined){t.x1=n;t.x2=a}else{t.x2=a}}s+=e.width}if(t.x1!=undefined&&n.gmmode&&n.gmmode!=Y.genomic){const e=n.width+n.subpanels.reduce(((t,e)=>e.width+e.leftpad),0);if(t.x1<t.x2){if(t.x2<0||t.x1>e){t.x1=undefined;t.x2=undefined;return}if(t.x1<0){t.x1=0}if(t.x2>e){t.x2=e}}else if(t.x1>t.x2){if(t.x1<0||t.x2>e){t.x1=undefined;t.x2=undefined;return}if(t.x2<0){t.x2=0}if(t.x1>e){t.x1=e}}}}function Tn(t,e){const n=e.seekcoord(t._chr,t._pos);for(const a of n){if(a.ridx!=undefined){if(a.x>0&&a.x<e.width){t.x=a.x;break}}else if(a.subpanelidx!=undefined){t.x=a.x}}}function Dn(t,e){if(!t.data_vcf)return;for(const n of t.data_vcf){if(n.dt==x){n._chr=n.chr;n._pos=n.pos;Tn(n,e);if(n.x==undefined){console.log("snvindel unmapped: "+n.chr+":"+n.pos)}else{delete n._chr;delete n._pos}}else{console.error("may_map_vcf: unknown dt")}}}function Yn(t,e){if(!t._data_vcf||t._data_vcf.length==0){t.data_vcf=null;return}const n=t._data_vcf;t.data_vcf=[];for(const a of n){if(a.dt==x){G(a,e)}else{throw"unknown dt "+a.dt}if(!t.legend_mclass.hiddenvalues.has(a.class)){t.data_vcf.push(a)}}}function Gn(t){const e=new Map;for(const n of t){e.set(n.sample+"."+n.chrA+"."+n.posA+"."+n.strandA+"."+n.chrB+"."+n.posB+"."+n.strandB,n)}return[...e.values()]}function Xn(t,e){if(!t)return false;if(e.legend_vorigin&&e.legend_vorigin.key){const n=t[e.legend_vorigin.key];if(n){if(n.toLowerCase()==e.legend_vorigin.germline)return true}}return false}export{Je as coverbarcolor_active,Xe as coverbarcolor_silent,Gn as dedup_sv,jn as draw_colorscale_cnv,Mn as draw_colorscale_loh,zn as focus_singlesample,Ye as intrasvcolor,yn as itemname_svfusion,en as labelspace,an as loadTk,Pn as map_cnv,An as multi_expressionstatus_ase_outlier,wn as multi_rnabam_asestatus,kn as multi_sample_addhighlight,vn as multi_sample_removehighlight,Ln as rnabamtk_copyparam,cn as trackclear,Xn as vcfvariantisgermline};