@sjcrh/proteinpaint-client 2.74.2 → 2.76.0

package/dist/block.legend-b2987cd9.js

@@ -1 +0,0 @@
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s=t.hover(r);if(s!=undefined){e.attr("title",s)}}if(t.tablecellwidth){e.style("width",t.tablecellwidth).style("word-break","break-all")}if(t.ismaf){const s=t.get(r);if(s){if(s.v2==0){e.text("0/0");e.attr("title","No coverage")}else{g(e,s,t)}}}else{e.html(t.get(r))}}}}}function ot(t){return'<span style="font-size:70%;color:#858585">'+t+"</span>"}function at(t,e,s,o,a){if(!e){s.append("p").text("vcfobj config object missing");return}const n=s.append("div").style("margin-top","10px");n.append("span").text(t.type).style("padding-right","10px");n.append("span").text(t.chr+":"+(t.pos+1)).style("padding-right","10px");if(t.dt==c){n.append("span").style("padding-right","10px").html(ot("REF")+" "+t.ref+" "+ot("ALT")+" "+t.alt);if(a.variantPageCall_snv){const e={chr:t.chr,position:t.pos+1,refallele:t.ref,altallele:t.alt,container:n.append("span").style("padding-left","20px")};a.variantPageCall_snv(e)}if(o.button4variant){zt(n,t,o.button4variant)}if(o.url4variant){At(n,t,o.url4variant)}}if(e.info&&e.info.CSQ&&e.info.CSQ.csqheader&&t.csq){vt(t.csq,n,o,e.info.CSQ.csqheader)}if(e.info&&e.info.ANN&&e.info.ANN.annheader&&t.ann){wt(t.ann,n,o,e.info.ANN.annheader)}if(o.variant2img){_t(t,n,s.append("div"),o)}const r=s.append("div");if(Pt(t,o,r)){r.style("margin-top","10px")}else if(t.sampledata){const e=r.append("div");Promise.resolve().then((()=>{if(t.sampledata.length==0&&o.ds.vcfcohorttrack){e.text("Loading ...");return Mt(t,o,a).then((e=>{if(!e){return}t.sampledata=e.sampledata;return}))}return})).then((()=>{e.remove();if(t.sampledata.length==0){return}if(t.sampledata.length==1){St(t,o,r);return}if(Nt(t,o,r)){r.style("margin-top","10px")}else if(jt(t,o,r)){r.style("margin-top","10px")}else if(Pt(t,o,r)){r.style("margin-top","10px")}else{kt(t,n,o)}})).catch((t=>{e.text(t)}))}if(e.infopipejoin){const o=[];if(t.altinfo){for(const s of e.infopipejoin){const e=t.altinfo[s.key];if(e){if(Array.isArray(e)){o.push(e)}else{o.push(e.split(/[,|]/))}}else{o.push([])}}}if(o.length){const t=s.append("div");for(let s=0;s<o[0].length;s++){const a=[];for(let t=0;t<e.infopipejoin.length;t++){const n=e.infopipejoin[t];a.push({k:n.label,v:n.values?n.values[o[t][s]]:o[t][s]})}d(t,a).style("display","inline-block").style("border","solid 1px black").style("margin","20px")}}}nt(t,s,o);rt(t,s,o);const i={};const l={};if(o.vcfinfofilter){for(const t of o.vcfinfofilter.lst){if(t.categories){if(t.altalleleinfo){i[t.altalleleinfo.key]=t.categories}else if(t.locusinfo){l[t.locusinfo.key]=t.categories}}}}{const o=[];for(const s in t.altinfo){const a=Array.isArray(t.altinfo[s])?t.altinfo[s]:[t.altinfo[s]];let n;if(i[s]){n=a.map((t=>{const e=i[s][t];if(e){return'<span style="padding:1px 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image")}}))}function jt(t,e,s){if(!e.ds.vaf2coverageplot){return false}if(!t.sampledata){return false}const o=[];const a={};const n=new Map;let r=0;for(const s of t.sampledata){if(!s.allele2readcount){r++;continue}if(s.DP==undefined){s.DP=0;for(const t in s.allele2readcount){s.DP+=s.allele2readcount[t]}}const i=s.allele2readcount[t.alt]||0;if(i>s.DP){console.log("alt coverage > DP: "+i+" "+s.DP);continue}const l={sampleobj:{},mut:i,total:s.DP,maf:s.DP==0?0:i/s.DP,genotype:s.genotype};if(s.sampleobj){if(e.ds.cohort&&e.ds.cohort.annotation&&e.ds.cohort.key4annotation){const t=s.sampleobj[e.ds.cohort.key4annotation];if(t){const s=e.ds.cohort.annotation[t];if(s){if(e.ds.cohort.levels){for(const t of e.ds.cohort.levels){if(!s[t.k])continue;l.sampleobj[t.label||t.k]=s[t.k]+(t.full&&s[t.full]?' <span style="font-size:.8em;color:#858585">'+s[t.full]+"</span>":"")}l.sampleobj[e.ds.cohort.key4annotation]=t}else{for(const t in s){l.sampleobj[t]=s[t]}}}}}else{for(const t in 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Yt(t,e){if(t.textlabel){C(t.textlabel).attr("font-size",t._labfontsize)}e.pica.g.selectAll("*").remove()}async function Jt(t,e,s,o){if(t.dt==i||t.dt==l){$({mlst:[t],pane:true,x:e.left-10,y:e.top-10,tk:s,block:o,svgraph:true});return}if(t.occurrence>1){if(await Ut(t.occurrence,[t],t.aa.x+t.xoff,s.numericmode.toplabelheight+s.numericmode.axisheight-t._y,s,o))return}$({mlst:[t],pane:true,x:e.left-10,y:e.top-10,tk:s,block:o})}function Qt(t){const e=[];for(const s of t.data){for(const t of s.mlst){e.push({m:t,w:2*(t.radius+t.rimwidth),x:s.x0,y:t._y})}}e.sort(((t,e)=>e.y-t.y));for(let t=0;t<e.length;t++){const s=e[t];let o=false;for(let a=0;a<t;a++){const t=e[a];if(Math.abs(s.x-t.x)<(s.w+t.w)/2-2){o=true;break}}if(!o){s.m.labattop=true}}for(let t=e.length-1;t>=0;t--){const s=e[t];if(s.m.labattop)continue;let o=false;for(let a=e.length-1;a>t;a--){const t=e[a];if(t.m.labatbottom&&Math.abs(t.x-s.x)<(t.w+s.w)/2-2){o=true;break}}if(!o){s.m.labatbottom=true}}}function Wt(t,e){if(t.mlst.length==1){return"M0,0v"+e.stem1+"l"+-t.xoffset+","+e.stem2+"v"+e.stem3}return"M0,0"+"v"+e.stem1+"l"+-t.xoffset+","+e.stem2+"v"+e.stem3+"v-"+e.stem3+"l"+(t.stemw+t.xoffset-1)+",-"+e.stem2+"v-"+e.stem1}function Zt(t,e){t.numericmode;const s=100;let o=0;for(const e of t.data){let t=0;for(const s of e.mlst){t+=2*(s.radius+s.rimwidth)}if(e.mlst.length==1){e.width=t}else{e.width=Math.min(s,t);const o=e.mlst[0];const a=e.mlst[e.mlst.length-1];e.fixedgew=o.radius+o.rimwidth+a.radius+a.rimwidth}o+=e.width}if(o<=e.width){let s=0;for(const e of t.data){e.x=s+e.mlst[0].radius+e.mlst[0].rimwidth;s+=e.width;if(e.mlst.length==1){e.stemw=0}else{e.stemw=e.width-e.fixedgew}}Kt(t.data,e.width);for(const e of t.data){e.xoffset=e.x-e.x0;if(e.mlst.length==1){e.mlst[0].xoff=0;e.stemw=0}else{e.stemw=e.width-e.fixedgew;const t=e.stemw/(e.mlst.length-1);for(let s=0;s<e.mlst.length;s++){e.mlst[s].xoff=t*s}}}return true}else{for(const e of t.data){e.x=e.x0;e.xoffset=0;for(const t of e.mlst){t.xoff=0}}return false}}function Kt(t,e){for(let s=0;s<t.length;s++){if(t[s].x0<0)continue;if(t[s].x0>e)break;while(1){let o=0,a=0;for(let n=s;n<t.length;n++){const s=t[n];if(s.x0>e){return}o+=Math.abs(s.x-s.x0-s.stemw/2);s.x++;a+=Math.abs(s.x-s.x0-s.stemw/2)}if(t[s].x>t[s].x0-t[s].stemw/2){for(let e=s;e<t.length;e++){t[e].x--}break}const n=t[t.length-1];if(n.x+n.width/2>=e){return}if(a<=o);else{for(let o=s;o<t.length;o++){if(t[o].x0>e){break}t[o].x--}break}}}}const $t="Not annotated";const te=.3;const ee=1;const se=4;const oe=0;const ae=1;async function ne(t,e){try{if(!t)throw"no tk";if(!t.ds)throw"no ds";if(!e.gmmode||e.gmmode==F.genomic){if(e.viewrangeabovelimit(t.viewrangeupperlimit)){t.mlst=[];t.viewrangeupperlimit_above=true;fe(t,e);return}}delete t.viewrangeupperlimit_above;if(t.isvcf){e.tkcloakon(t);Rt(e,t);return}if(e.ds2handle[t.ds.label]){t.__handlesays=e.ds2handle[t.ds.label].handlesays}if(t.ds.bulkdata||t.ds.mlst){return await ie(t,e)}await le(t,e);re(t,e);t.ds.busy=false;e.tkcloakoff(t,{})}catch(s){if(s.stack)console.log(s.stack);t.ds.busy=false;e.tkcloakoff(t,{error:s.message||s});e.setllabel(t);e.block_setheight()}}function re(t,e){if(!t.legacyDsFilter)return;if(!t.legacyDsFilter.key||!t.legacyDsFilter.value)throw"legacyDsFilter is not {key,value}";const s=t.mlst.filter((e=>e[t.legacyDsFilter.key]==t.legacyDsFilter.value));const o={label:t.ds.label+" - "+t.legacyDsFilter.value,bulkdata:{},parentname:t.ds.label,iscustom:true,sampleselectable:t.ds.sampleselectable};o.bulkdata[e.usegm.name.toUpperCase()]=s;e.addchilddsnoload(o);const a=e.block_addtk_template({type:D.ds,ds:o});ne(a,e)}async function ie(t,e){if(e.usegm){if(t.__handlesays){t.__handlesays.style("background-color","#ddd").style("color","black")}let s=[];if(t.ds.bulkdata){const o=t.ds.bulkdata[e.usegm.name.toUpperCase()];if(o){s=[...o]}}if(t.ds.mlst){for(const o of t.ds.mlst){if(o.gene.toUpperCase()==e.usegm.name.toUpperCase()){s.push(o)}}}if(s.length){const o=[];for(const t of s){if(t.isoform&&t.isoform==e.usegm.isoform){o.push(t)}}if(o.length){ce([{lst:o}],e,t)}else{throw"No data from "+t.ds.label+" for "+e.usegm.isoform}}else{throw"No data from "+t.ds.label+" for "+e.usegm.name}if(t.ds.dbexpression&&(!t.eplst||t.eplst.length==0)){const s={jwt:e.jwt,db:t.ds.dbexpression.dbfile,tablename:t.ds.dbexpression.tablename,keyname:t.ds.dbexpression.keyname,key:e.usegm.name};const o=await w("dbdata",{method:"POST",body:JSON.stringify(s)});if(o.error)throw o.error;if(!t.eplst)t.eplst=[];if(t.ds.dbexpression.tidy)t.ds.dbexpression.tidy(o.rows);const a={data:o.rows,expp:t.ds.dbexpression.config,block:e,genome:e.genome,genename:e.usegm.name,dsname:t.ds.label};const n=await import("./ep-a86b185a.js");t.eplst.push(new n.default(a))}}else{const s=[];const f=new Map;for(const t of e.rglst){if(!f.has(t.chr)){f.set(t.chr,[])}f.get(t.chr).push(t)}const d=[];if(t.ds.bulkdata){for(const e in t.ds.bulkdata){d.push(...t.ds.bulkdata[e])}}if(t.ds.mlst){d.push(...t.ds.mlst)}for(const t of d){switch(t.dt){case c:case r:case o:case n:case a:if(!t.pos){break}if(!t.chr&&!f.has(t.chr)){break}for(const e of f.get(t.chr)){if(t.pos>=e.start&&t.pos<e.stop){s.push(t);break}}break;case l:case i:if(!t.pairlst){break}let e=false;for(const s of t.pairlst){if(s.a.chr&&f.has(s.a.chr)){const t=s.a.position||s.a.pos;if(t){for(const o of f.get(s.a.chr)){if(t>=o.start&&t<o.stop){e=true;break}}}}if(s.b.chr&&f.has(s.b.chr)){const t=s.b.position||s.b.pos;if(t){for(const o of f.get(s.b.chr)){if(t>=o.start&&t<o.stop){e=true;break}}}}}if(e){s.push(t)}break}}if(s.length){ce([{lst:s}],e,t)}}}async function le(t,e){if(t.__handlesays)t.__handlesays.text("Loading...");t.ds.busy=true;e.tkcloakon(t);const s={genome:e.genome.name,dsname:t.ds.label,range:e.tkarg_maygm(t)[0]};if(e.usegm){s.genename=e.usegm.name;s.isoform=e.usegm.isoform}if(t.eplst){s.noexpression=1}if(e.hidedatasetexpression){s.noexpression=1}const o=await w("dsdata",{method:"POST",body:JSON.stringify(s)});if(t.__handlesays){t.__handlesays.text(t.ds.label).style("background-color","#ddd").style("color","black")}if(o.error)throw o.error;ce(o.data,e,t)}function ce(t,e,s){if(s.dsuninitiated){for(let t=0;t<e.tklst.length;t++){if(e.tklst[t].tkid==s.tkid){e.tklst.splice(t,1);break}}delete s.dsuninitiated;let t=-1;for(let s=0;s<e.tklst.length;s++){const o=e.tklst[s];if(o.type==D.usegm&&!o.hidden){t=s;break}}let o=true;if(t==-1){o=true;e.tklst.push(s)}else{let a=false;for(let s=0;s<t;s++){const t=e.tklst[s];if(!t.hidden&&t.type==D.ds){a=true;break}}if(a){o=false;e.tklst.splice(t+1,0,s)}else{o=true;if(t==0){e.tklst.unshift(s)}else{e.tklst.splice(t-1,0,s)}}}if(s.aboveprotein==undefined){s.aboveprotein=o}s.eplst=[]}s.mlst=[];const o=[];for(const a of t){if(a.isgeneexpression){o.push(Me(a,s,e));continue}if(a.vcfid){It(a,s,e);continue}if(a.lst){Ae(a.lst,s,e);Ee(a,s);continue}e.error("unknown data/query type from "+s.ds.label);return}Promise.all(o).then((()=>{if(s.eplst.length>1){for(let t=1;t<s.eplst.length;t++){const e=s.eplst[t];e.pane.pane.style("left",Number.parseInt(s.eplst[0].pane.pane.style("left"))+50*t+"px");e.pane.pane.style("top",Number.parseInt(s.eplst[0].pane.pane.style("top"))+50*t+"px")}}}));fe(s,e)}function fe(t,e){e.tkcloakoff(t,{});de(t);if(t.vcfinfofilter&&t.vcfinfofilter.setidx4numeric!=undefined){if(!t.numericmode){t.numericmode={axisheight:t.axisheight}}}else{delete t.numericmode}const s=new Set;for(const t in L){if(L[t].hidden){s.add(t)}}Pe(t);if(t.numericmode){Ot(t,e,s)}else{pe(t,e,s)}e.setllabel(t);e.block_setheight();e.tkchangeaffectlegend(t);Ne(t,e);Re(t,e);{const s=Ie(t,e);if(s)console.log("showlegend_sampleattribute: "+s)}}function de(t){if(t.vcfinfofilter&&t.vcfinfofilter.setidx4occurrence!=undefined){const e=t.vcfinfofilter.lst[t.vcfinfofilter.setidx4occurrence];if(!e)throw"mcset not found by setidx4occurrence";for(const s of t.mlst){const[t,o]=Se(e,s);if(t||o==undefined){s.occurrence=1}else{s.occurrence=o[0]}}}else{for(const e of t.mlst){e.occurrence=1}}}function pe(t,e,s){t.leftaxis.selectAll("*").remove();if(e.usegm&&e.gmmode!=F.genomic&&e.pannedpx!=undefined&&t.skewer){De(t,e);t.skewer.attr("transform",(t=>"translate("+t.x+","+t.y+")"));ye(t,e)}else{t.glider.selectAll("*").remove();qe(t,e,s);const o=new Map;for(const e of t.mlst){if(e.__x==undefined){continue}if(!o.has(e.__x)){o.set(e.__x,[])}o.get(e.__x).push(e)}const a=[];if(e.exonsf>=se){for(const[t,e]of o){a.push({chr:e[0].chr,pos:e[0].pos,mlst:e,x:t,groups:ue(e)})}}else{if(e.usegm&&e.usegm.coding&&e.gmmode!=F.genomic){const t=new Map;for(const[s,a]of o){if(a[0].chr!=e.usegm.chr){continue}let n=undefined;for(const t of a){if(Number.isFinite(t.aapos))n=t.aapos}if(n==undefined){n=_(a[0].pos,e.usegm).aapos}if(n==undefined){console.error("data item cannot map to aaposition");console.log(a[0]);continue}o.delete(s);if(!t.has(n)){t.set(n,[])}let r=true;for(const s of t.get(n)){if(Math.abs(s[0].__x-a[0].__x)<=e.exonsf*3){for(const t of a){s.push(t)}r=false;break}}if(r){t.get(n).push(a)}}e.usegm.utr5?e.usegm.utr5.reduce(((t,e)=>t+e[1]-e[0]),0):0;for(const e of t.values()){for(const t of e){let e=null;for(const s of t){if(Number.isFinite(s.rnapos))e=s}if(e==null){console.log("trying to map mlst to codon, but no rnapos found");for(const e of t){console.log(e)}continue}a.push({chr:t[0].chr,pos:e.pos,mlst:t,x:t[0].__x,groups:ue(t)})}}}const t=[];const s=2;for(const[e,a]of o){const o=Math.floor(e/s);if(!t[o]){t[o]=[]}t[o]=[...t[o],...a]}for(const e of t){if(!e)continue;const t=e.reduce(((t,e)=>t+e.__x),0);a.push({isbin:true,chr:e[0].chr,pos:e[0].pos,mlst:e,x:t/e.length,groups:ue(e)})}}a.sort(((t,e)=>t.x-e.x));if(t.data&&e.pannedpx!=undefined&&(!e.usegm||e.gmmode==F.genomic)){const e={};for(const s of t.data){e[s.chr+"."+s.pos]={mode:s.showmode,xoffset:s.xoffset,slabelrotate:s.slabelrotate}}for(const t of a){const s=t.chr+"."+t.pos;if(e[s]){t.showmode=e[s].mode;t.xoffset=e[s].xoffset;t.slabelrotate=e[s].slabelrotate}}}t.data=a;for(const e of t.data){e.occurrence=e.groups.reduce(((t,e)=>t+e.occurrence),0)}me(t,e);t.height_main=t.toppad+t.maxskewerheight+t.stem1+t.stem2+t.stem3+t.bottompad}if(!t.data||t.data.length==0){Le(t,e);return}if(t.hlaachange||t.hlvariants){const s=[];const o=[];if(t.hlaachange){for(const e of t.data){let a=false;for(const s of e.groups){if(t.hlaachange.has(s.mlst[0].mname)){a=true;t.hlaachange.delete(s.mlst[0].mname);break}}if(a){o.push(e)}else{s.push(e)}}if(t.hlaachange.size){if(!e.usegm){e.error("cannot add items from hlaachange: not in gene-mode")}else{ze(t,e)}}delete t.hlaachange}if(t.hlvariants){const e={};for(const s of t.hlvariants){e[s.chr+"."+s.pos+"."+s.ref+"."+s.alt]=1}for(const a of t.data){let t=false;for(const s of a.groups){if(t){break}for(const o of s.mlst){if(e[o.chr+"."+o.pos+"."+o.ref+"."+o.alt]){t=true;break}}}if(t){o.push(a)}else{s.push(a)}}}_e(s,t);xe(o,t,e)}else{ye(t,e)}}function ue(t,e){const s=new Map;for(const e of t){switch(e.dt){case c:if(!s.has(e.dt)){s.set(e.dt,new Map)}if(!s.get(e.dt).has(e.class)){s.get(e.dt).set(e.class,new Map)}const t=e.mname||"";if(!s.get(e.dt).get(e.class).has(t)){s.get(e.dt).get(e.class).set(t,[])}s.get(e.dt).get(e.class).get(t).push(e);break;case l:case i:if(!s.has(e.dt)){s.set(e.dt,new Map)}if(!s.get(e.dt).has(e.class)){s.get(e.dt).set(e.class,{use5:new Map,use3:new Map})}if(e.useNterm){if(!s.get(e.dt).get(e.class).use5.has(e.mname)){s.get(e.dt).get(e.class).use5.set(e.mname,[])}s.get(e.dt).get(e.class).use5.get(e.mname).push(e)}else{if(!s.get(e.dt).get(e.class).use3.has(e.mname)){s.get(e.dt).get(e.class).use3.set(e.mname,[])}s.get(e.dt).get(e.class).use3.get(e.mname).push(e)}break;case r:case o:case n:case a:if(!s.has(e.dt)){s.set(e.dt,[])}s.get(e.dt).push(e);break;default:console.log("unknown datatype: "+e.dt);console.log(e);return}}const f=[];for(const[t,e]of s){switch(t){case c:for(const s of e.values()){for(const e of s.values()){f.push({dt:t,mlst:e})}}break;case l:case i:for(const s of e.values()){for(const e of s.use5.values()){f.push({dt:t,useNterm:true,mlst:e})}for(const e of s.use3.values()){f.push({dt:t,useNterm:false,mlst:e})}}break;case r:case o:case n:case a:f.push({dt:t,mlst:e})}}for(const t of f){let e=0,s=0;for(const o of t.mlst){if(o.isrim1)e++;else if(o.isrim2)s++}t.rim1count=e;t.rim2count=s;t.occurrence=t.mlst.reduce(((t,e)=>t+e.occurrence),0)}f.sort(((t,e)=>e.occurrence-t.occurrence));return f}function me(t,e){delete t.skewer2;const s=e=>{if(t.vcfinfofilter&&t.vcfinfofilter.setidx4mclass!=undefined){const s=t.vcfinfofilter.lst[t.vcfinfofilter.setidx4mclass];const[o,a]=Se(s,e);if(o||a==undefined)return"black";for(const t of a){if(s.categories[t]){return s.categories[t].color}else{return"black"}}}if(f[e.class]){return f[e.class].color}return"black"};const d=[];for(const s of t.data){s.x0=s.x;if(s.xoffset!=undefined){s.x=s.x0+s.xoffset}for(const t of s.groups){t.aa=s;let a=null;if(t.dt==r){a=t.mlst[0].rnaduplength;for(const e of t.mlst){a=Math.max(a,e.rnaduplength)}}else if(t.dt==o){a=t.mlst[0].rnadellength;for(const e of t.mlst){a=Math.max(a,e.rnadellength)}}else{continue}if(!Number.isFinite(a)||a<0){console.log("no rnaspan for stack bar from itd/del");console.log(t.mlst);continue}let n=null;if(e.usegm){const 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_=Q().innerRadius((t=>t.radius)).outerRadius((t=>t.radius+t.rimwidth)).startAngle(0).endAngle((t=>{t.rim1_startangle=Math.PI*2*t.rim1count/t.occurrence;return t.rim1_startangle}));x.append("path").attr("d",_).attr("fill",(t=>s(t.mlst[0]))).attr("class","sja_aa_discrim").attr("fill-opacity",0);const j=Q().innerRadius((t=>t.radius+.5)).outerRadius((t=>t.radius+.5+t.rimwidth)).startAngle((t=>t.rim1_startangle)).endAngle((t=>t.rim1_startangle+Math.PI*2*t.rim2count/t.occurrence));x.filter((t=>t.rim2count>0)).append("path").attr("d",j).attr("stroke",(t=>s(t.mlst[0]))).attr("fill","none").attr("class","sja_aa_discrim").attr("stroke-opacity",0);{let e=0;let s=0;for(const o of t.data){if(o.x-o.maxradius-o.maxrimwidth<s){e++}s=Math.max(s,o.x+o.width-o.maxradius-o.maxrimwidth)}t.stem1=e==0?0:u;t.stem2=R().domain([0,1,t.data.length]).range([0,u,u*3])(e)}const M=u*.7;let A=0;for(const e of t.data){for(const t of e.groups){A=Math.max(A,t.occurrence)}}t.stem3=Math.max(p+2,M+u*Math.min(5,A));t.skewer.append("circle").attr("class","sja_aa_skkick").attr("fill","white").attr("fill-opacity",0).attr("stroke","none").attr("r",(t=>t.maxradius+1)).attr("cy",(e=>(t.aboveprotein?-1:1)*e.maxradius)).attr("transform",(t=>"scale("+(t.showmode==oe?1:0)+")")).on("mouseover",((e,o)=>{je(t,o.mlst,true);const a=t.aboveprotein;let n=0;let r=0;const i=5;const l=a?7:14;for(const e of o.groups){e.pica_fontsize=Math.max(11,e.radius);n+=e.pica_fontsize+1;t.pica.g.append("text").text(e.mlst[0].mname+(e.occurrence>1?" x"+e.occurrence:"")).attr("font-size",e.pica_fontsize).each((function(){r=Math.max(r,this.getBBox().width)})).remove()}r+=i*2;const c=n+5;t.pica.g.append("rect").attr("y",a?-c:0).attr("width",r).attr("height",c).attr("fill","white").attr("fill-opacity",.8).attr("stroke","#ccc").attr("shape-rendering","crispEdges");n=0;const f=t.pica.g.selectAll().data(o.groups).enter().append("g").attr("transform",((t,e)=>{n+=t.pica_fontsize+1;return"translate("+i+","+n*(a?-1:1)+")"}));f.append("text").text((t=>t.mlst[0].mname)).attr("font-size",(t=>t.pica_fontsize)).each((function(t){t.pica_mlabelwidth=this.getBBox().width})).attr("fill",(t=>s(t.mlst[0]))).attr("dominant-baseline",a?"hanging":"auto");const d=o.groups[0].pica_mlabelwidth;t.pica.x=o.x-i-d/2;t.pica.y=o.y+(a?-1:1)*(o.maxradius*2+l+2);t.pica.g.attr("transform","translate("+t.pica.x+","+t.pica.y+")");f.filter((t=>t.occurrence>1)).append("text").text((t=>"x"+t.occurrence)).attr("x",(t=>t.pica_mlabelwidth+5)).attr("font-size",(t=>t.pica_fontsize)).attr("dominant-baseline",a?"hanging":"auto").attr("fill","#9e9e9e");const p=t.pica.g.append("g").attr("transform","translate("+(i+d/2)+","+(a?1:-1)+")");p.append("line").attr("y2",(a?1:-1)*l).attr("stroke","#858585").attr("shape-rendering","crispEdges");p.append("line").attr("x1",-1).attr("x2",-1).attr("y2",(a?1:-1)*l).attr("stroke","white").attr("shape-rendering","crispEdges");p.append("line").attr("x1",1).attr("x2",1).attr("y2",(a?1:-1)*l).attr("stroke","white").attr("shape-rendering","crispEdges")})).on("mouseout",((e,s)=>{t.pica.g.selectAll("*").remove();je(t,s.mlst,false)})).on("click",((s,o)=>{t.pica.g.selectAll("*").remove();xe([o],t,e)}));let z=0;for(const e of t.data){z=Math.max(z,e.occurrence)}const N=R().domain([1,z]).range([M,t.stem3-y]);t.skewer.attr("transform",(e=>{e.foldyoffset=N(e.occurrence);e.y=ge(e,t);return"translate("+e.x+","+e.y+")"}));if(d.length>0){t.skewer.filter((t=>t.hasstackbar)).selectAll().data((t=>{const e=[];for(const s of t.groups){if(s.stackbar){e.push(s.stackbar)}}return e})).enter().append("g").attr("class","sja_aa_stackbar_g").attr("transform",(e=>"translate(0,"+(t.aboveprotein?1:-1)*(t.stem1-e.y)+")")).append("rect").attr("y",(e=>t.aboveprotein?-e.height:0)).attr("class","sja_aa_stackbar_rect").attr("width",0).attr("shape-rendering","crispEdges").attr("fill-opacity",.5).attr("stroke","none").attr("stroke-width",1).attr("height",(t=>t.height)).attr("fill",(t=>s(t.grp.mlst[0]))).on("mouseover",((e,a)=>{const n=s(a.grp.mlst[0]);C(e.target).attr("stroke",n);const i=t.pica;let l="wrong label";let c="wrong label, ";switch(a.grp.mlst[0].dt){case r:l=f[a.grp.mlst[0].class].desc;c=Math.ceil(a.grp.mlst[0].rnaduplength/3)+" aa, ";break;case o:l=f[a.grp.mlst[0].class].label;c=Math.ceil(a.grp.mlst[0].rnadellength/3)+" aa, ";break}if(a.grp.occurrence==1){const t=a.grp.mlst[0];if(t.sample){c+=t.sample}else if(t.patient){c+=t.patient}else{c+="1 sample"}}else{c+=a.grp.occurrence+" samples"}const d=14,p=10,u=2,m=4;let h=0;i.g.append("text").text(l).attr("font-size",d).attr("font-family",I).each((function(){h=this.getBBox().width})).remove();i.g.append("text").text(c).attr("font-size",p).attr("font-family",I).each((function(){h=Math.max(h,this.getBBox().width)})).remove();const g=u*3+d+p;i.x=a.grp.aa.x0+3;i.y=t.aboveprotein?t.height_main-t.toppad-t.bottompad-a.y-a.height-3-g:a.y+a.height+3;i.g.attr("transform","translate("+i.x+","+i.y+")");i.g.append("rect").attr("width",h+m*2).attr("height",g).attr("stroke",n).attr("stroke-width",1).attr("shape-rendering","crispEdges").attr("fill","white").attr("fill-opacity",.8);i.g.append("text").text(l).attr("x",m).attr("y",u+d/2).attr("dominant-baseline","middle").attr("font-size",d).attr("font-family",I).attr("fill",n);i.g.append("text").text(c).attr("x",m).attr("y",u*2+d+p/2).attr("dominant-baseline","middle").attr("font-size",p).attr("font-family",I).attr("fill","#858585")})).on("mouseout",((e,s)=>{C(e.target).attr("stroke","none");t.pica.g.selectAll("*").remove()})).on("click",((s,o)=>{$({mlst:o.grp.mlst,pane:true,x:s.clientX,y:s.clientY,tk:t,block:e})}))}t.skewer.append("path").attr("class","sja_aa_stem").attr("d",(e=>be(e,t))).attr("stroke",(t=>s(t.groups[0].mlst[0]))).attr("fill","none");const P=t.skewer.filter((t=>t.groups.length>1));P.append("rect").attr("class","sja_aa_ssk_bg").attr("shape-rendering","crispEdges").attr("fill-opacity",0).attr("height",t.stem1).attr("fill",(t=>s(t.groups[0].mlst[0]))).attr("width",(t=>{t.ssk_width=Math.max(t.occurrence.toString().length*8+6,2*(t.maxradius+t.maxrimwidth));return t.ssk_width})).attr("x",(t=>-t.ssk_width/2));P.append("text").attr("class","sja_aa_ssk_text").attr("fill","white").attr("fill-opacity",0).attr("font-weight","bold").attr("text-anchor","middle").attr("dominant-baseline","central").text((t=>t.occurrence)).each((e=>{e.ssk_fontsize=Math.min(t.stem1,e.ssk_width/(e.occurrence.toString().length*S))})).attr("font-size",(t=>t.ssk_fontsize));P.append("rect").attr("class","sja_aa_ssk_kick").attr("fill","white").attr("fill-opacity",0).attr("stroke","none").attr("height",t.stem1).attr("x",(t=>-t.ssk_width/2)).attr("width",(t=>t.ssk_width)).on("mouseover",((e,s)=>{const 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o=t.skewer.filter((t=>t.hasstackbar));o.selectAll(".sja_aa_stackbar_g").transition().duration(s).attr("transform",(s=>{const o=s.grp.aa;return"translate("+(o.showmode==oe?0:o.x0-o.x)+","+(e?1:-1)*(o.showmode==oe?t.stem1-s.y:t.stem1+t.stem2+t.stem3-s.y)+")"}));o.filter((t=>t.showmode==ae)).selectAll(".sja_aa_stackbar_rect").transition().duration(s).attr("y",(t=>e?-t.height:0));t.skewer.transition().duration(s).attr("transform",(e=>{e.y=ge(e,t);return"translate("+e.x+","+e.y+")"}));t.skewer.selectAll(".sja_aa_stem").transition().duration(s).attr("d",(e=>be(e,t)));t.skewer.selectAll(".sja_aa_discg").transition().duration(s).attr("transform",(t=>{t.y=(e?-1:1)*(t.aa.showmode==oe?t.aa.maxradius:t.yoffset);return"translate(0,"+t.y+")"}));t.skewer.selectAll(".sja_aa_ssk_kick").attr("y",e?0:-t.stem1);t.skewer.selectAll(".sja_aa_ssk_bg").attr("y",e?0:-t.stem1);t.skewer.selectAll(".sja_aa_ssk_text").attr("y",(e?1:-1)*t.stem1/2);t.skewer.selectAll(".sja_aa_skkick").attr("cy",(t=>(e?-1:1)*t.maxradius));t.skewer.filter((t=>t.showmode==ae&&t.groups.length==1)).selectAll(".sja_aa_disclabel").transition().duration(s).attr("transform",(t=>"scale(1) 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t=e.skewer.filter((t=>r.has(t.x0)));t.transition().duration(o).attr("transform",(t=>"translate("+t.x+","+t.y+")"));t.selectAll(".sja_aa_discg").transition().duration(o).attr("transform",(t=>{t.y=t.yoffset*(a?-1:1);return"translate(0,"+t.y+")"}));setTimeout((function(){t.selectAll(".sja_aa_disckick").attr("transform","scale(1)")}),o);t.selectAll(".sja_aa_discnum").transition().duration(o).attr("fill-opacity",1).attr("stroke-opacity",1);t.filter((t=>t.groups.length>1)).selectAll(".sja_aa_disclabel").transition().duration(o).attr("fill-opacity",1).attr("transform","scale(1)");t.selectAll(".sja_aa_discrim").transition().duration(o).attr("fill-opacity",1).attr("stroke-opacity",1);t.selectAll(".sja_aa_ssk_kick").attr("transform","scale(1)").attr("y",a?0:-e.stem1);t.selectAll(".sja_aa_ssk_bg").attr("transform","scale(1)").attr("y",a?0:-e.stem1);t.selectAll(".sja_aa_ssk_text").attr("transform","scale(1)").attr("y",(a?1:-1)*e.stem1/2);t.selectAll(".sja_aa_skkick").attr("transform","scale(0)");t.filter((t=>t.hasstackbar)).selectAll(".sja_aa_stackbar_g").attr("transform",(t=>"translate(0,"+(a?1:-1)*(e.stem1+e.stem2+e.stem3-t.y)+")"));let n=0;t.selectAll(".sja_aa_stem").transition().duration(o).attr("d",(t=>be(t,e))).each((()=>++n)).on("end",(()=>{if(! --n){ke(e,s)}}))}else{ke(e,s)}}function ke(t,e){const s=1e3;const o=t.aboveprotein;const a=[];const n=new Set;const r=0;const i=e.width;for(const e of t.data){if(e.x0<r||e.x0>i)continue;if(e.showmode==ae){e.x=e.x0;a.push(e);n.add(e.x0)}}if(a.length==0){return}ve(a,t,e);for(const t of a){t.xoffset=t.x-t.x0}for(let e=0;e<a.length;e++){const s=a[e];if(s.groups.length>1)continue;const o=s.groups[0];if(t.slabel_forcerotate){s.slabelrotate=true}else{const t=a[e+1];const n=t?t.x-t.maxradius-t.maxrimwidth:i;s.slabelrotate=n-s.x-o.radius-o.rimwidth-1<s.slabelwidth}s.width=(o.radius+o.rimwidth)*2+(s.slabelrotate?0:2+s.slabelwidth)}const l=t.skewer.filter((t=>n.has(t.x0)));l.transition().duration(s).attr("transform",(t=>"translate("+t.x+","+t.y+")"));l.selectAll(".sja_aa_stem").transition().duration(s).attr("d",(e=>be(e,t)));l.filter((t=>t.groups.length==1)).selectAll(".sja_aa_disclabel").transition().duration(s).attr("fill-opacity",1).attr("transform",(t=>"scale(1) rotate("+(t.aa.slabelrotate?(o?"-":"")+"90":"0")+")"));t.slabel_forcerotate=false;const c=l.filter((t=>t.hasstackbar));c.selectAll(".sja_aa_stackbar_g").transition().duration(s).attr("transform",(e=>"translate("+(e.grp.aa.x0-e.grp.aa.x)+","+(o?1:-1)*(t.stem1+t.stem2+t.stem3-e.y)+")"));c.selectAll(".sja_aa_stackbar_rect").transition().duration(s).attr("width",(t=>t.pxspan)).attr("y",(t=>o?-t.height:0))}function ve(t,e,s){const o=0;const a=s.width;let n=o;let r=false;for(const e of t){if(e.x0<o||e.x0>a)continue;if(e.groups.length==1){e.slabelrotate=true;const t=e.groups[0];e.width=(t.radius+t.rimwidth)*2}const t=e.x-e.maxradius-e.maxrimwidth;if(t<n){r=true}if(t+e.width>a){r=true}n=Math.max(n,t+e.width)}if(!r){return false}n=o;for(const e of t){if(e.x0<o||e.x0>a)continue;e.x=n+e.maxradius+e.maxrimwidth;n+=e.width}we(t,s.width)}function we(t,e){for(let s=0;s<t.length;s++){if(t[s].x0<0)continue;if(t[s].x0>e)break;while(1){let o=0,a=0;for(let n=s;n<t.length;n++){const s=t[n];if(s.x0>e){return}o+=Math.abs(s.x-s.x0);s.x++;a+=Math.abs(s.x-s.x0)}if(t[s].x>=t[s].x0){for(let e=s;e<t.length;e++){t[e].x--}break}const n=t[t.length-1];if(n.x+n.width/2>=e){return}if(a<=o);else{for(let o=s;o<t.length;o++){if(t[o].x0>e){break}t[o].x--}break}}}}function _e(t,e){if(t.length==0)return;const s=1e3;const o=e.aboveprotein;const a=new Set;for(const s of t){s.x=s.x0;a.add(s.x0);s.showmode=oe;s.y=ge(s,e)}const n=e.skewer.filter((t=>a.has(t.x0)));n.transition().duration(s).attr("transform",(t=>"translate("+t.x+","+t.y+")"));n.selectAll(".sja_aa_stem").transition().duration(s).attr("d",(t=>be(t,e)));n.selectAll(".sja_aa_discg").transition().duration(s).attr("transform",(t=>"translate(0,"+(o?"-":"")+t.aa.maxradius+")"));n.selectAll(".sja_aa_disckick").attr("transform","scale(0)");n.selectAll(".sja_aa_discnum").transition().duration(s).attr("fill-opacity",0).attr("stroke-opacity",0);n.selectAll(".sja_aa_disclabel").transition().duration(s).attr("fill-opacity",0).attr("transform","scale(0)");n.selectAll(".sja_aa_discrim").transition().duration(s).attr("fill-opacity",0).attr("stroke-opacity",0);n.selectAll(".sja_aa_ssk_kick").attr("transform","scale(0)");n.selectAll(".sja_aa_ssk_bg").attr("transform","scale(0)");n.selectAll(".sja_aa_ssk_text").attr("transform","scale(0)");n.selectAll(".sja_aa_skkick").transition().duration(s).attr("transform","scale(1)");const r=n.filter((t=>t.hasstackbar));r.selectAll(".sja_aa_stackbar_g").transition().duration(s).attr("transform",(t=>"translate(0,"+(o?1:-1)*(e.stem1-t.y)+")"));r.selectAll(".sja_aa_stackbar_rect").transition().duration(s).attr("width",0)}function je(t,e,s){if(!t.eplst)return;for(const o of t.eplst){o.may_hl(e,s)}}function Me(t,e,s){if(!t.config){s.error("config missing for expression data in "+e.ds.label);return}if(t.config.maf){try{t.config.maf.get=new Function(...t.config.maf.get)}catch(t){s.error("invalid javascript for config.maf.get of "+e.ds.label);return}}const o=t.config;if(o.usecohort){o.cohort=e.ds.cohort}const a={data:t.lst,expp:o,block:s,genome:s.genome,genename:s.usegm.name,dsname:e.ds.label};if(s.samplecart){if(e.ds.sampleselectable){a.samplecart=s.samplecart}}return import("./ep-a86b185a.js").then((t=>{e.eplst.push(new t.default(a))}))}function Ae(t,e,s){for(const f of t){switch(f.dt){case c:if(s.usegm){const t=_(f.pos,s.usegm);f.rnapos=t.rnapos;f.aapos=t.aapos}e.mlst.push(f);break;case l:case i:if(!f.pairlst){console.error("pairlst missing from sv/fusion");break}if(s.usegm&&f.dt==l){if(f.pairlst.length==1){const t=f.pairlst[0].a;const e=f.pairlst[0].b;if(t.chr!=null&&e.chr!=null&&t.chr==e.chr&&t.position!=null&&e.position!=null){if(t.position<e.position){if(s.usegm.strand=="+"){t.strand="+";e.strand="+"}else{t.strand="-";e.strand="-";f.pairlst[0].a=e;f.pairlst[0].b=t}}}}}if(s.usegm&&s.gmmode!=F.genomic){f.isoform=s.usegm.isoform;let t=true;for(let e=0;e<f.pairlst.length;e++){const o=f.pairlst[e];if(s.usegm.isoform==(o.a.isoform||o.a.name)){f.useNterm=e==0;f.chr=s.usegm.chr;f.strand=o.a.strand;if(o.a.position==undefined){if(o.a.rnaposition==undefined){if(o.a.codon==undefined){console.error("no position/rnaposition/codon available for "+s.usegm.isoform);break}else{f.pos=U(o.a.codon,s.usegm);o.a.position=f.pos}}else{f.pos=E(o.a.rnaposition-1,s.usegm);if(f.pos==null){console.error("failed to convert rnaposition to genomic position: "+o.a.rnaposition);break}o.a.position=f.pos}}else{f.pos=o.a.position}const a=_(f.pos,s.usegm);f.rnapos=a.rnapos;f.aapos=a.aapos;if(o.a.codon){f.aapos=o.a.codon}f.mname=o.b.name;t=false;break}if(s.usegm.isoform==(o.b.isoform||o.b.name)){f.useNterm=false;f.chr=s.usegm.chr;f.strand=o.b.strand;if(o.b.position==undefined){if(o.b.rnaposition==undefined){if(o.b.codon==undefined){console.error("no position/rnaposition/codon available for "+s.usegm.isoform);break}else{f.pos=U(o.b.codon,s.usegm);o.b.position=f.pos}}else{f.pos=E(o.b.rnaposition-1,s.usegm);if(f.pos==null){console.error("failed to convert rnaposition to genomic");break}o.b.position=f.pos}}else{f.pos=o.b.position}const e=_(f.pos,s.usegm);f.rnapos=e.rnapos;f.aapos=e.aapos;if(o.b.codon){f.aapos=o.b.codon}f.mname=o.a.name;t=false;break}}if(t){console.error("sv/fusion isoform no match to gm isoform: "+s.usegm.isoform)}else{e.mlst.push(f)}}else{for(const t of f.pairlst){let o=false,a=false;for(let e=s.startidx;e<=s.stopidx;e++){const n=s.rglst[e];if(t.a.chr==n.chr&&t.a.position>=n.start&&t.a.position<=n.stop){o=true}if(t.b.chr==n.chr&&t.b.position>=n.start&&t.b.position<=n.stop){a=true}}if(o){const s=G(f);const o=t.a;s.chr=o.chr;s.strand=o.strand;s.useNterm=o.strand=="+";s.pos=o.pos||o.position;s.mname=t.b.name||t.b.chr;if(!Number.isFinite(s.pos)){console.error("no genomic pos for breakend a")}else if(!s.chr){console.error("no chromosome for breakend a")}else{e.mlst.push(s)}}if(a){const s=G(f);const o=t.b;s.chr=o.chr;s.strand=o.strand;s.useNterm=o.strand=="+";s.pos=o.pos||o.position;s.mname=t.a.name||t.a.chr;if(!Number.isFinite(s.pos)){console.error("no genomic pos for breakend b")}else if(!s.chr){console.error("no chromosome for breakend b")}else{e.mlst.push(s)}}}}break;case r:case o:if(f.chrpos1&&f.chrpos2){let t=_(f.chrpos1,s.usegm);const e=t.rnapos;t=_(f.chrpos2,s.usegm);const a=t.rnapos;if(e<a){f.pos=f.chrpos1}else{f.pos=f.chrpos2}delete f.chrpos1;delete f.chrpos2;const n=Math.abs(e-a);if(f.dt==r){f.rnaduplength=n}else if(f.dt==o){f.rnadellength=n}}if(f.position){f.pos=f.position;delete f.position}if(!f.pos){if(f.dt==r){if(f.b){if(f.b.position){f.pos=f.b.position;f.chr=f.b.chr}}}}if(!f.pos){if(f.rnaposition){if(s.usegm){f.pos=E(f.rnaposition-1,s.usegm);f.chr=s.usegm.chr;if(f.pos==null){console.error("failed to convert rnaposition to genomic position: "+f.rnaposition);break}}}else if(f.aapos);}if(!f.pos){console.error("no genomic pos for itd");break}if(s.usegm){const t=_(f.pos,s.usegm);if(f.rnaposition){f.rnapos=f.rnaposition}else{f.rnapos=t.rnapos}f.aapos=t.aapos}if(f.dt==r){if(!f.rnaduplength){console.error("itd has no rnaduplength");f.rnaduplength=1}}else{if(!f.rnadellength){console.error("deletion has no rnadellength");f.rnadellength=1}}e.mlst.push(f);break;case n:case a:if(f.position){f.pos=f.position;delete f.position}if(!f.pos){if(f.rnaposition){if(s.usegm){f.pos=E(f.rnaposition-1,s.usegm);f.chr=s.usegm.chr;if(f.pos==null){console.error("failed to convert rnaposition to genomic position: "+f.rnaposition);break}}}else if(f.aapos);}if(!f.pos){console.error("no genomic pos for truncation");break}if(s.usegm){const t=_(f.pos,s.usegm);if(f.rnaposition){f.rnapos=f.rnaposition}else{f.rnapos=t.rnapos}f.aapos=t.aapos}e.mlst.push(f);break;default:console.error("unknown dt: "+f.dt)}}}function ze(t,e){const s=new Map;for(const t in f){s.set(f[t].label.toUpperCase(),t)}const o=[];for(const[a,n]of t.hlaachange){if(n==false){continue}if(!n.name){e.error("hlaachange item .name missing");continue}if(n.codon==undefined||!Number.isFinite(n.codon)){e.error("hlaachange invalid codon for "+n.name);continue}if(!n.class){e.error("hlaachange .class missing");continue}const t=f[n.class]?n.class:s.get(n.class.toUpperCase());if(!t){e.error("hlaachange invalid class: "+n.class);continue}n.class=t;n.mname=n.name;delete n.name;n.chr=e.usegm.chr;n.pos=U(n.codon,e.usegm);delete n.codon;n.dt=c;n.isoform=e.usegm.isoform;o.push(n)}if(o.length){const t={label:"Highlight",type:D.ds,iscustom:true,bulkdata:{}};t.bulkdata[e.usegm.name.toUpperCase()]=o;e.ownds[t.label]=t;const s=e.block_addtk_template({type:D.ds,ds:t});ne(s,e)}}function Ne(t,e){if(!t.vcfinfofilter)return;for(const s of t.vcfinfofilter.lst){s.holder.selectAll("*").remove();if(s.numericfilter){for(const t of s.numericfilter){t.count=0}for(const e of t.mlst){const[t,o]=Se(s,e);if(t){continue}if(!o)continue;const a=o[0];if(!Number.isFinite(a))continue;for(const t of s.numericfilter){if(t.side=="<"){if(a<t.value){t.count++}}else{if(a>t.value){t.count++}}}}for(const o of s.numericfilter){const a=s.holder.append("div").style("display","inline-block").style("padding","10px").attr("class","sja_clb").on("click",(()=>{if(s.numericCutoff==o.value&&s.numericCutoffSide==o.side){delete s.numericCutoff}else{s.numericCutoff=o.value;s.numericCutoffSide=o.side}fe(t,e)}));if(s.numericCutoff==o.value&&s.numericCutoffSide==o.side){a.style("border-bottom","solid 2px #ccc").style("background-color","#f1f1f1")}if(o.count>0){a.append("div").style("display","inline-block").attr("class","sja_mcdot").style("padding","1px 5px").style("background-color","#ccc").style("color","white").html(o.count>1?o.count:"&nbsp;").style("margin-right","5px")}a.append("span").text(o.side+o.value)}continue}if(!s.categories){continue}const o=new Map;let a=0;for(const e of t.mlst){const[t,n]=Se(s,e);if(t){continue}if(n==undefined){a++}else{for(const t of n){if(!o.has(t)){o.set(t,0)}o.set(t,o.get(t)+1)}}}const n=[...o];if(a){n.push([$t,a])}n.sort(((t,e)=>e[1]-t[1]));for(const[o,a]of n){const n=s.categories[o]||{color:"black",label:o};const r=s.holder.append("div").style("display","inline-block").style("padding","10px").attr("class","sja_clb").on("click",(()=>{t.vcfinfofilter.tip.showunder(r.node());Ce(s,o,t,e)}));r.append("div").style("display","inline-block").attr("class","sja_mcdot").style("padding","1px 5px").style("background-color",n.color).style("color","white").html(a>1?a:"&nbsp;").style("margin-right","5px");const i=r.append("span").text(n.label).style("color",n.color);if(s.categoryhidden[o]){i.style("text-decoration","line-through")}}}}function Pe(t,e){if(!t.vcfinfofilter)return;for(const e of t.vcfinfofilter.lst){if(e.numericfilter){continue}if(!e.autocategory){continue}const s=new Map;for(const o of t.mlst){const[t,a]=Se(e,o);if(t){continue}if(a!=undefined){for(const t of a){if(!s.has(t)){s.set(t,0)}s.set(t,s.get(t)+1)}}}const o=[...s];o.sort(((t,e)=>e[1]-t[1]));const a=M(Z);e.categories={};for(const[t,s]of o){e.categories[t]={label:t,color:a(t)}}}}function Se(t,e){if(t.altalleleinfo){if(!e.altinfo)return["no .altinfo"];const s=e.altinfo[t.altalleleinfo.key];if(s==undefined){if(t.numericfilter){return[null,[0]]}return[null,undefined]}let o=Array.isArray(s)?s:[s];if(t.altalleleinfo.separator){o=o[0].split(t.altalleleinfo.separator)}return[null,o]}if(t.locusinfo){if(!e.info)return["no .info"];const s=e.info[t.locusinfo.key];if(s==undefined){if(t.numericfilter){return[null,[0]]}return[null,undefined]}let o=Array.isArray(s)?s:[s];if(t.locusinfo.separator){o=o[0].split(t.locusinfo.separator)}return[null,o]}return["no trigger"]}function Ce(t,e,s,o){const a=s.vcfinfofilter.tip;a.clear();const n=t.categoryhidden[e];a.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">&#10003;</div> show alone').on("click",(()=>{a.hide();t.categoryhidden={};for(const s in t.categories){if(s!=e){t.categoryhidden[s]=1}}if(e!=$t){t.categoryhidden[$t]=1}fe(s,o)}));if(n){a.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">&#10003;</div> show').on("click",(()=>{a.hide();delete t.categoryhidden[e];fe(s,o)}))}else{a.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">&times;</div> hide').on("click",(()=>{a.hide();t.categoryhidden[e]=1;fe(s,o)}))}let r=0;for(const e in t.categoryhidden){r++}if(r>1){a.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">&#10003;</div> show all').on("click",(()=>{a.hide();t.categoryhidden={};fe(s,o)}))}}function Fe(t,e){if(!t.vcfid)return[".vcfid missing"];if(!t.sampledata)return[".sampledata missing"];const s=e.ds.id2vcf[t.vcfid];if(!s)return["no vcf"];if(!s.samples||s.samples.length==0)return["vcf no samples"];let o=0;for(const e of t.sampledata){if(!e.gtallref)o++}return[null,o/s.samples.length]}function Re(t,e){if(!t.populationfrequencyfilter)return;for(const e of t.populationfrequencyfilter.lst){e.count=0}for(const e of t.mlst){const[s,o]=Fe(e,t);if(s){continue}for(const e of t.populationfrequencyfilter.lst){if(o<e.value){e.count++}}}t.populationfrequencyfilter.holder.selectAll("*").remove();for(const s of t.populationfrequencyfilter.lst){const o=t.populationfrequencyfilter.holder.append("div").style("display","inline-block").style("padding","10px").attr("class","sja_clb").on("click",(()=>{if(t.populationfrequencyfilter.cutoff==s.value){delete t.populationfrequencyfilter.cutoff}else{t.populationfrequencyfilter.cutoff=s.value}fe(t,e)}));if(t.populationfrequencyfilter.cutoff==s.value){o.style("border-bottom","solid 2px #ccc").style("background-color","#f1f1f1")}o.append("div").style("display","inline-block").attr("class","sja_mcdot").style("padding","1px 5px").style("background-color","#ccc").style("color","white").html(s.count>1?s.count:"&nbsp;").style("margin-right","5px");o.append("span").text("< "+s.value)}}function Ie(t,e){if(!t.ds||!t.ds.cohort||!t.ds.cohort.sampleattribute)return;if(!t.ds.cohort.annotation)return".ds.cohort.annotation 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Le(t,e){t.height_main=t.toppad+e.labelfontsize+t.bottompad;if(t.label_mcount&&t.label_mcount.text().length>0){t.height_main+=t.labyspace+e.labelfontsize}if(t.label_stratify){for(const s of t.label_stratify){if(s.svglabel.text().length>0){t.height_main+=t.labyspace+e.labelfontsize}}}t.glider.selectAll("*").remove();t.leftaxis.selectAll("*").remove();if(t.viewrangeupperlimit_above){e.tkerror(t,t.name+": zoom in under "+T(t.viewrangeupperlimit)+" to view data")}else{let s;if(!t.skewer.data||t.skewer.data.length==0){if(e.pannedpx!=undefined||e.zoomedin==true){s="view range"}else if(e.usegm&&e.gmmode!="genomic"){s=e.usegm.name||e.usegm.isoform}}e.tkerror(t,t.name+": no mutation in "+s)}if(t.hlaachange){ze(t,e);delete t.hlaachange}}function Ee(t,e){if(!t.stratifycount)return;for(const[s,o]of t.stratifycount){const t=e.label_stratify.find((t=>t.label==s));if(!t){console.error("unknown strat label: "+s);continue}t.servercount=o}}const Ue=new H({padding:"0px"});function Ge(t,e){const s=t.legend.holder.append("tr");const o=s.append("td").text(e).style("padding-right","10px").style("text-align","right").style("color","#555").style("border-right","solid 1px "+t.legend.legendcolor);const a=s.append("td");return[s,a,o]}function Ve(t){if(!t.legend){return}const e=new Set;for(const[s,o]of t.legend.mclasses){if(o.hidden){e.add(s)}}const s=new Map;for(const e of t.tklst){if(e.hidden||e.type!=D.ds)continue;if(!e.mlst){continue}for(const t of e.mlst){if(t.class){if(!s.has(t.class)){s.set(t.class,{count:0})}s.get(t.class).count++}}}const o=[];for(const[t,a]of s){if(e.has(t)){s.get(t).hidden=true}o.push({key:t,count:a.count})}t.legend.mclasses=s;if(s.size==0){t.legend.tr_mclass.style("display","none");return}t.legend.tr_mclass.style("display","table-row");o.sort(((t,e)=>e.count-t.count));t.legend.td_mclass.selectAll("*").remove();for(const s of o){const 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o=t.legend.td_morigin.append("div").style("display","inline-block").style("white-space","nowrap").style("padding",t.legend.vpad+" 20px "+t.legend.vpad+" 0px").classed("sja_clb",true).on("click",(()=>{Ue.clear();Ue.showunder(o.node());Ue.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">&#10003;</div> show alone').on("click",(()=>{Ue.hide();t.pannedpx=undefined;for(const e of t.legend.morigins.values()){e.hidden=true}t.legend.morigins.get(s.key).hidden=false;L[s.key].hidden=false;for(const e of t.tklst){if(!e.hidden&&e.type==D.ds){fe(e,t)}}}));if(t.legend.morigins.get(s.key).hidden){Ue.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">&#10003;</div> show').on("click",(()=>{Ue.hide();t.pannedpx=undefined;t.legend.morigins.get(s.key).hidden=false;L[s.key].hidden=false;for(const e of t.tklst){if(!e.hidden&&e.type==D.ds){fe(e,t)}}}))}else{Ue.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">&times;</div> hide').on("click",(()=>{Ue.hide();t.pannedpx=undefined;t.legend.morigins.get(s.key).hidden=true;for(const e of t.tklst){if(!e.hidden&&e.type==D.ds){fe(e,t)}}}))}if(e.size>1){Ue.d.append("div").attr("class","sja_menuoption").html('<div style="display:inline-block;width:25px">&#10003;</div> show all').on("click",(()=>{Ue.hide();t.pannedpx=undefined;for(const e of t.legend.morigins.values()){e.hidden=false}for(const e of t.tklst){if(!e.hidden&&e.type==D.ds){fe(e,t)}}}))}const 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package/dist/block.mds2-de6e0986.js

@@ -1 +0,0 @@
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t=e.append("div").attr("class","sja_filter_tag_btn").style("position","absolute");const n=e.append("select").style("opacity",0).on("mouseover",(()=>{t.style("opacity","0.8").style("cursor","default")})).on("mouseout",(()=>{t.style("opacity","1")}));return[n,t]}function T(e,t,n,a,s){const o=D(t,s);console.log(o);return 0}const P=4;function B(e,t,n){if(!t.vcf)return 0;if(!e.vcf)return 0;if(!e.vcf.rglst)return 0;let a=0;for(const s of e.vcf.rglst){const o=t.g_vcfrow.append("g").attr("transform","translate("+s.xoff+",0)");if(s.rangetoobig){s.text_rangetoobig=o.append("text").text(s.rangetoobig).attr("text-anchor","middle").attr("dominant-baseline","central").attr("x",s.width/2);a=Math.max(a,50);continue}if(s.imgsrc){o.append("image").attr("width",s.width).attr("height",s.imgheight).attr("xlink:href",s.imgsrc);a=Math.max(a,s.imgheight);continue}if(s.variants){const i=q(e,s,o,t,n);a=Math.max(a,i);continue}}for(const t of e.vcf.rglst){if(t.rangetoobig){t.text_rangetoobig.attr("y",a/2)}}{const 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t=e.vcf.numerical_axis.AFtest;if(!t||!t.termfilter||!t.termfilter.inuse)return;if(t.termfilter.type!="categorical")throw"AFtest.termfilter.type is not categorical (hardcoded)";if(!t.termfilter.values)throw"termfilter.values missing";const n=t.termfilter.values[t.termfilter.value_index];if(!n)throw"unknown value selection by value_index in AFtest.termfilter";return{term:{id:t.termfilter.id,name:t.termfilter.name,type:"categorical"},values:[{key:n.key,label:n.label||n.key}]}}function Me(e,t){const n=e.vcf.numerical_axis.AFtest;const a=n.dom.holder.append("table").style("border-spacing","5px").style("border-collapse","separate").style("border-left","solid 1px #ccc");for(const[s,o]of n.groups.entries()){o.dom={};const n=a.append("tr");o.dom.td1=n.append("td").append("div").attr("class","sja_filter_tag_btn").text("GROUP "+(s+1)).style("white-space","nowrap").style("border-radius","6px").style("background-color","#ddd").style("color","#000").style("padding","6px").style("margin","3px 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t.populations){o.append("option").attr("value",e.key).text(e.label)}o.node().value=e.key;i.style("border-radius","6px").style("background-color","#ddd").style("color","black").style("padding","3px 6px 3px 6px").style("margin-left","5px").html(a.label+(t.populations.length>1?" &#9662;":""));o.style("width",i.node().offsetWidth+"px");const l=n.append("span");r(l);function r(n){n.selectAll("*").remove();const a=s.groups.find((t=>t.key==e.key));if(a.allowto_adjust_race){const e=n.append("label");e.append("input").attr("type","checkbox").style("margin-left","10px").property("disabled",!s.groups.find((e=>e.is_termdb))||!s.groups.find((e=>e.is_population))).property("checked",a.adjust_race).on("change",(async()=>{a.adjust_race=!a.adjust_race;o.html("&nbsp;Loading...");await t.load();o.html("&nbsp;Adjust race background")}));const o=e.append("span").html("&nbsp;Adjust race background")}}}function Je(e,t){const n=e.vcf.numerical_axis.AFtest.groups[t];if(!n)throw"index out of 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t=JSON.parse(JSON.stringify(e.mds.track.vcf));for(const n in t){if(e.vcf[n]==undefined)e.vcf[n]=t[n]}if(t.numerical_axis){for(const n in t.numerical_axis){if(e.vcf.numerical_axis[n]==undefined)e.vcf.numerical_axis[n]=t.numerical_axis[n]}if(t.numerical_axis.AFtest){for(const n in t.numerical_axis.AFtest){if(e.vcf.numerical_axis.AFtest[n]==undefined)e.vcf.numerical_axis.AFtest[n]=t.numerical_axis.AFtest[n]}}}}if(e.mds.track.ld){if(!e.ld)e.ld={};if(!e.ld.connheight)e.ld.connheight=50;const t=JSON.parse(JSON.stringify(e.mds.track.ld));for(const n in t){if(e.ld[n]==undefined)e.ld[n]=t[n]}e.ld.overlay.r2_to_color=L(e.ld.overlay.color_0,e.ld.overlay.color_1)}if(e.mds.track.info_fields){e.info_fields=JSON.parse(JSON.stringify(e.mds.track.info_fields))}if(e.mds.track.populations){e.populations=JSON.parse(JSON.stringify(e.mds.track.populations))}if(e.mds.track.sample_termfilter)e.sample_termfilter=JSON.parse(JSON.stringify(e.mds.track.sample_termfilter))}function yt(e){if(!e.info_fields)return;if(!Array.isArray(e.info_fields))throw"info_fields should be an array";for(const t of e.info_fields){if(!t.key)throw"key missing from one of info_fields";if(!t.label)t.label=t.key;if(!t.isfilter)continue;if(t.iscategorical){if(!t.values)throw".values[] missing from a categorical info field "+t.label;if(!Array.isArray(t.values))throw".values[] not an array from info field "+t.label;for(const e of t.values){if(!e.key)throw".key missing from a value of info field "+t.label;if(!e.label)e.label=e.key}}else if(t.isinteger||t.isfloat){if(!t.range)throw".range{} missing from a numeric info field "+t.label}else if(t.isflag);else{throw"info field "+t.label+" neither numerical or categorical"}}}async function xt(e,t){t.tkcloakon(e);t.block_setheight();const n=bt(e,t);try{if(e.uninitialized){await ft(e,t);delete e.uninitialized}e.tklabel.each((function(){e.leftLabelMaxwidth=this.getBBox().width}));const a=await _t(e,t);e.clear();const s=B(a,e,t);const o=at(a,e,t);if(e.g_ldrow){e.g_ldrow.transition().attr("transform","translate(0,"+s+")");e.gleft_ldrow.transition().attr("transform","translate(0,"+s+")")}e.height_main=s+o;n(a)}catch(t){if(e.clear)e.clear();e.height_main=50;n({error:t.message||t});if(t.stack)console.log(t.stack);return}}async function _t(e,t){const n=vt(e,t);return d("mds2",n).then((e=>{if(e.error)throw e.error;return e}))}function bt(e,t){return n=>{lt(n,e);t.tkcloakoff(e,{error:n.error});t.block_setheight();t.setllabel()}}function vt(e,t){const n={genome:t.genome.name};kt(n,e);if(e.legend.mclass.hiddenvalues.size){n.hidden_mclass=[...e.legend.mclass.hiddenvalues]}if(e.mds){n.dslabel=e.mds.label}else{if(e.vcf){n.vcf={file:e.vcf.file,url:e.vcf.url,indexURL:e.vcf.indexURL}}}if(e.vcf){n.trigger_vcfbyrange=1;Ne(e,n)}if(e.ld){const t=e.ld.tracks.filter((e=>e.shown));if(t.length){n.trigger_ld={tracks:t,connheight:e.ld.connheight}}}n.rglst=t.tkarg_rglst(e);if(t.usegm){const e=n.rglst[0];e.usegm_isoform=t.usegm.isoform;for(let a=1;a<n.rglst.length;a++){const s=n.rglst[a];e.width+=s.width+t.regionspace;e.start=Math.min(e.start,s.start);e.stop=Math.max(e.stop,s.stop)}n.rglst=[e]}let a=0;for(const e of n.rglst){e.xoff=0;a+=e.width+t.regionspace}if(t.subpanels.length==e.subpanels.length){for(const e of t.subpanels){n.rglst.push({chr:e.chr,start:e.start,stop:e.stop,width:e.width,exonsf:e.exonsf,xoff:a});a+=e.width+e.leftpad}}return n}function kt(e,t){if(t.info_fields){e.info_fields=t.info_fields.reduce(((e,t)=>{if(t.isfilter){if(t.iscategorical){const n={key:t.key,iscategorical:true,unannotated_ishidden:t.unannotated_ishidden,hiddenvalues:{}};for(const e of t.values){if(e.ishidden)n.hiddenvalues[e.key]=1}e.push(n)}else if(t.isinteger||t.isfloat){if(t.isactivefilter){e.push({key:t.key,isnumerical:true,missing_value:t.missing_value,range:t.range})}}else if(t.isflag){e.push({key:t.key,isflag:true,remove_no:t.remove_no,remove_yes:t.remove_yes})}else{throw"unknown type of info filter"}}return e}),[])}}export{vt as addparameter_rangequery,xt as loadTk};