@sjcrh/proteinpaint-client 2.76.2 → 2.77.1

package/dist/tk-ac524564.js

@@ -1 +0,0 @@
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e=m();if(t.skewer){if(e.has("hlaachange")){t.hlaachange=e.get("hlaachange")}if(e.has("hlssmid")){t.hlssmid=e.get("hlssmid").split(",")}}}function wt(t){if(!t.mds.has_skewer)return;t.skewer={g:t.glider.append("g"),hlBoxColor:t.mds.hlBoxColor||"red",hideDotLabels:false,pointup:true};kt(t)}function bt(t){let e=t.mds.termdbConfig?.queries?.cnv;if(!e){if(t.mds.has_cnv){e={}}}if(!e)return;t.cnv={g:t.glider.append("g"),cnvMaxLength:e.cnvMaxLength,cnvGainCutoff:e.cnvGainCutoff,cnvLossCutoff:e.cnvLossCutoff,absoluteValueRenderMax:e.absoluteValueRenderMax||5,gainColor:e.gainColor||"#D6683C",lossColor:e.lossColor||"#67a9cf"}}function kt(t){t.skewer.viewModes=t.skewerModes;delete t.skewerModes;if(!t.skewer.viewModes)t.skewer.viewModes=[];const e=t.skewer.viewModes;if(!Array.isArray(e))throw"skewerModes[] is not array";if(t.mds.skewerModes){for(const s of t.mds.skewerModes)e.push(s)}if(!e.find((t=>t.type=="skewer")))e.push({type:"skewer"});for(const t of e){if(typeof t!="object")throw"one of skewerModes[] is not object";if(t.type=="skewer"){if(!t.label)t.label="lollipops"}else if(t.type=="numeric"){if(t.byAttribute){if(!t.label)t.label=t.byAttribute}else if(t.byInfo);else{throw"unknown data method for a type=numeric mode"}}else{throw"unknown type from a skewerModes[]"}}if(!e.find((t=>t.inuse)))e[0].inuse=true}function xt(t){if(t.mds.hiddenmclass){for(const e of t.mds.hiddenmclass)t.legend.mclass.hiddenvalues.add(e)}}async function vt(t,e){if(t.dslabel){const s=await u("getDataset",{body:{genome:e.genome.name,dsname:t.dslabel}});if(s.error)throw"Error: "+s.error;if(!s.ds)throw"data.ds{} missing";t.mds=s.ds;t.name=s.ds.label;return}if(!t.name)t.name="Custom data";t.mds={};if(t.bcf){if(!t.bcf.file&&!t.bcf.url)throw"file or url missing for tk.bcf{}";t.mds.has_skewer=true;await Ot(t,e.genome)}else if(t.custom_variants){Lt(t,e);Rt(t)}else{throw"unknown data source for custom track"}yt(t)}function yt(t){if(!t.sampleAnnotation)return;if(!Array.isArray(t.sampleAnnotation.terms))throw"sampleAnnotation.terms is not array";if(!t.mds.termdb)t.mds.termdb={};t.mds.termdb.terms=t.sampleAnnotation.terms;t.mds.termdb.annotations=t.sampleAnnotation.annotations}async function _t(t,e){const s=t.mds.termdb;if(!s)return;{const a={};if(t.mds.label){a.vocab={genome:e.genome.name,dslabel:t.mds.label}}else if(s.terms){a.vocab={terms:s.terms,sampleannotation:s.annotations}}else{throw"do not know how to init vocab"}const n=await import("./FilterRxComp-02e68f1b.js").then((function(t){return t.k}));s.vocabApi=n.vocabInit(a);if(!s.vocabApi.app){s.vocabApi.app={opts:{genome:e.genome}}}}t.mds.termdbConfig=await s.vocabApi.getTermdbConfig();if(t.mds.termdb.allowCaseDetails){t.mds.termdb.allowCaseDetails.get=async t=>{}}}function jt(t,e){if(!t.mds.queries?.snvindel?.m2csq)return;t.mds.queries.snvindel.m2csq.get=async s=>{const a={genome:e.genome.name,dslabel:t.mds.label,m2csq:1};if(t.mds.queries.snvindel.m2csq.by=="ssm_id"){a.ssm_id=s.ssm_id}else{return{error:"unknown query method"}}const n={"Content-Type":"application/json",Accept:"application/json"};if(t.token)n["X-Auth-Token"]=t.token;return await u("mds3",{body:a,headers:n},{serverData:t.cache})}}function Mt(t,e){if(!t.mds.queries?.singleSampleMutation)return;t.mds.queries.singleSampleMutation.get=async s=>{const a={genome:e.genome.name,dslabel:t.mds.label,sample:s};const n={"Content-Type":"application/json",Accept:"application/json"};if(t.token)n["X-Auth-Token"]=t.token;const i=await u("termdb/singleSampleMutation",{body:a,headers:n});if(i.error)throw i.error;if(!Array.isArray(i.mlst))throw"data.mlst is not array";return i.mlst}}async function At(t,e){if(!t.mds.variant2samples)return;if(t.custom_variants){St(t)}else{qt(t,e)}if(t.mds.variant2samples.twLst){if(!Array.isArray(t.mds.variant2samples.twLst))throw"v2s.twLst[] not array";if(!t.mds.termdb?.vocabApi)throw"mds.termdb.vocabApi should be present for initiating v2s.twLst";for(const e of t.mds.variant2samples.twLst)await G(e,t.mds.termdb.vocabApi)}}function St(t,e){t.mds.variant2samples.get=e=>{if(e.querytype==t.mds.variant2samples.type_samples){const t=[];for(const s of e.mlst){if(!s.samples)continue;for(const e of s.samples){const a=JSON.parse(JSON.stringify(e));a.ssm_id=s.ssm_id;t.push(a)}}return{samples:t}}if(e.querytype==t.mds.variant2samples.type_summary){throw"todo: summary"}if(e.querytype==t.mds.variant2samples.type_sunburst){throw"todo: sunburst"}throw"unknown querytype"};t.mds.getSamples=()=>{const e=new Map;for(const s of t.custom_variants){if(!s.samples)continue;for(const t of s.samples){if(e.has(t.sample_id)){e.get(t.sample_id).ssm_id_lst.push(s.ssm_id)}else{const a=JSON.parse(JSON.stringify(t));a.ssm_id_lst=[s.ssm_id];e.set(t.sample_id,a)}}}return{samples:[...e.values()]}}}function qt(t,e){t.mds.variant2samples.get=async s=>{const a={genome:e.genome.name,variant2samples:1,get:s.querytype};if(t.mds.label){a.dslabel=t.mds.label}else if(t.bcf){if(t.bcf.file)a.bcffile=t.bcf.file;else if(t.bcf.url)a.bcfurl=t.bcf.url;else throw"tk.bcf{}: file/url missing"}else{throw"no dslabel or tk.bcf"}if(s.groupSsmBySample){a.groupSsmBySample=1}if(s.mlst){if(t.mds.variant2samples.variantkey=="ssm_id"){a.ssm_id_lst=s.mlst.map((t=>t.ssm_id)).join(",")}else{throw"unknown variantkey for variant2samples"}}if(s.isoform){a.isoform=s.isoform}if(s.rglst){a.rglst=s.rglst}const n={"Content-Type":"application/json",Accept:"application/json"};if(t.set_id)a.set_id=t.set_id;if(t.token)n["X-Auth-Token"]=t.token;if(t.filter0)a.filter0=t.filter0;if(t.filterObj)a.filterObj=t.filterObj;if(s.tid2value)a.tid2value=s.tid2value;if(s.querytype==t.mds.variant2samples.type_sunburst){if(t.mds.variant2samples.sunburst_twLst){a.twLst=t.mds.variant2samples.sunburst_twLst}}else if(s.querytype==t.mds.variant2samples.type_samples){if(t.mds.variant2samples.twLst)a.twLst=t.mds.variant2samples.twLst}else if(s.querytype==t.mds.variant2samples.type_summary){if(t.mds.variant2samples.twLst)a.twLst=t.mds.variant2samples.twLst}else{throw"unknown querytype"}a.skewerRim=t.mds.queries.snvindel?.skewerRim;if(t.legend.formatFilter){const e={};for(const s in t.legend.formatFilter){if(t.legend.formatFilter[s].hiddenvalues.size){e[s]=[...t.legend.formatFilter[s].hiddenvalues]}}if(Object.keys(e).length){a.formatFilter=e}}if(t.legend.mclass?.hiddenvalues?.size){a.hiddenmclasslst=[...t.legend.mclass.hiddenvalues].join(",")}const i=await u("mds3",{body:a,headers:n},{serverData:t.cache});if(i.error)throw i.error;const o=i.variant2samples;if(!o)throw"result error";if(s.querytype==t.mds.variant2samples.type_sunburst){if(!Array.isArray(o.nodes))throw"nodes[] not array from return"}else if(s.querytype==t.mds.variant2samples.type_samples){if(!Array.isArray(o.samples))throw"samples[] not array from return"}else if(s.querytype==t.mds.variant2samples.type_summary){if(!Array.isArray(o.summary))throw"summary[] not array from return"}else{throw"unknown querytype"}return o};t.mds.getSamples=async(s={})=>{if(s.isSummary){s.querytype=t.mds.variant2samples.type_summary}else{s.querytype=t.mds.variant2samples.type_samples;s.groupSsmBySample=1}Cs(t,e,s);return await t.mds.variant2samples.get(s)}}function Ct(t,e){return async()=>await As(t,e)}function zt(t,e){if(t.altalleleinfo){if(!e.altinfo)return["no .altinfo"];const s=e.altinfo[t.altalleleinfo.key];if(s==undefined){if(t.numericfilter){return[null,[0]]}return[null,undefined]}let a=Array.isArray(s)?s:[s];if(t.altalleleinfo.separator){a=a[0].split(t.altalleleinfo.separator)}return[null,a]}if(t.locusinfo){if(!e.info)return["no .info"];const s=e.info[t.locusinfo.key];if(s==undefined){if(t.numericfilter){return[null,[0]]}return[null,undefined]}let a=Array.isArray(s)?s:[s];if(t.locusinfo.separator){a=a[0].split(t.locusinfo.separator)}return[null,a]}return["no trigger"]}function Lt(t,e){for(const a of t.custom_variants){if(a.dt==p){t.mds.has_skewer=true;$t(a);continue}if(a.dt==l||a.dt==r){t.mds.has_skewer=true;Nt(a,e);continue}if(a.dt==s){t.mds.has_cnv=true;a.ssm_id=a.chr+"."+a.start+"."+a.stop+"."+a.class;continue}throw"unknown dt for a custom variant"}}function $t(t){if(!t.chr)throw".chr missing for custom snvindel";if(!Number.isInteger(t.pos))throw".pos not integer for custom snvindel";if(!t.ssm_id){t.ssm_id=t.chr+"."+t.pos+"."+(t.ref&&t.alt?t.ref+"."+t.alt:t.mname)}}function Nt(t,e){if(t.pairlst);else{if(!t.chr1)throw".chr1 missing for custom sv/fusion";if(!Number.isInteger(t.pos1))throw".pos1 not integer for custom svfusion";if(t.strand1!="+"&&t.strand1!="-")throw".strand1 not +/- for custom svfusion";if(!t.chr2)throw".chr1 missing for custom sv/fusion";if(!Number.isInteger(t.pos2))throw".pos1 not integer for custom svfusion";if(t.strand2!="+"&&t.strand2!="-")throw".strand1 not +/- for custom svfusion";t.pairlst=[{a:{chr:t.chr1,pos:t.pos1,strand:t.strand1,name:t.gene1||""},b:{chr:t.chr2,pos:t.pos2,strand:t.strand2,name:t.gene2||""}}];delete t.chr1;delete t.pos1;delete t.strand1;delete t.gene1;delete t.chr2;delete t.pos2;delete t.strand2;delete t.gene2}const s=[t.dt];const a=e.seekcoord(t.pairlst[0].a.chr,t.pairlst[0].a.pos);if(a.length&&a[0].x>0&&a[0].x<e.width){s.push(...[t.pairlst[0].a.chr,t.pairlst[0].a.pos,t.pairlst[0].a.strand,0,t.pairlst[0].a.name]);t.mname=t.pairlst[0].b.name||"";t.chr=t.pairlst[0].a.chr;t.pos=t.pairlst[0].a.pos;t.pairlstIdx=0}else{const a=e.seekcoord(t.pairlst[0].b.chr,t.pairlst[0].b.pos);if(a.length&&a[0].x>0&&a[0].x<e.width){s.push(...[t.pairlst[0].b.chr,t.pairlst[0].b.pos,t.pairlst[0].b.strand,1,t.pairlst[0].b.name]);t.mname=t.pairlst[0].a.name||"";t.chr=t.pairlst[0].b.chr;t.pos=t.pairlst[0].b.pos;t.pairlstIdx=1}}t.ssm_id=s.join(".")}function Rt(t){if(t.custom_variants.find((t=>t.occurrence!=undefined))){return}for(const e of t.custom_variants){if(e.sample){e.sample_id=e.sample;delete e.sample}}if(!t.custom_variants.find((t=>t.sample_id))){return}const e=[];const s=new Map;for(const a of t.custom_variants){if(a.dt!=p){a.occurrence=1;a.samples=[{sample_id:a.sample_id}];delete a.sample_id;e.push(a);continue}const t=a.mname+"."+a.chr+"."+a.pos+"."+a.ref+"."+a.alt;const n=s.get(t);if(n){n.occurrence++;n.samples.push({sample_id:a.sample_id})}else{a.occurrence=1;a.samples=[{sample_id:a.sample_id}];delete a.sample_id;s.set(t,a)}}t.custom_variants=e;for(const e of s.values())t.custom_variants.push(e);if(!t.mds.variant2samples)t.mds.variant2samples={};const a=t.mds.variant2samples;a.type_samples="samples";a.type_summary="summary";a.type_sunburst="sunburst"}async function Ot(t,e){const s={genome:e.name};if(t.bcf.file){s.file=t.bcf.file}else{s.url=t.bcf.url;if(t.bcf.indexURL)s.indexURL=t.bcf.indexURL}const a=await u("vcfheader",{body:s});if(a.error)throw a.error;const[n,i,o,r]=F(a.metastr.split("\n"));if(r)throw"Error parsing VCF meta lines: "+r.join("; ");t.mds.bcf={info:n,format:i};if(o?.length){t.mds.bcf.samples=o;t.mds.variant2samples={type_samples:"samples",variantkey:"ssm_id"}}if(!t.mds.queries)t.mds.queries={};t.mds.queries.snvindel={forTrack:true}}function It(t){const e=t.allow2selectSamples;if(!e)return;if(!e.buttonText)e.buttonText="Select samples";if(typeof e.buttonText!="string")throw"allow2selectSamples.buttonText value is not string";if(!e.attributes)e.attributes=[{from:"sample_id",to:"sample_id"}];if(!Array.isArray(e.attributes))throw"allow2selectSamples.attributes[] is not array";if(e.attributes.length==0)throw"allow2selectSamples.attributes[] blank array";for(const t of e.attributes){if(typeof t.from!="string"||!t.from)throw"allow2selectSamples.attributes.from is not string";if(typeof t.to!="string"||!t.to)throw"allow2selectSamples.attributes.to is not string"}if(typeof e.callback!="function")throw"allow2selectSamples.callback() is not function";e._cart=[]}async function Dt(t){for(const e of t.mlst){if(e.dt!=p&&e.dt!=l&&e.dt!=r&&e.dt!=s)throw"mlst[] contains unknown dt"}if(t.mlst.length==1){await Bt(t)}else{await Ft(t)}Tt(t)}function Tt(t){if(!t.tipDiv){return}const e=[];for(const s of t.div.selectAll("div").selectAll("table")){if(s)e.push(s)}if(!e.length)return;let s=0;for(const t of e){const e=t.firstChild;if(e.tagName!="THEAD")continue;const a=e.firstChild;if(a.tagName!="TR")continue;s=Math.max(s,a.childNodes?.length)}if(s>5){t.tipDiv.style("left","50px")}}async function Bt(t){const e=h({holder:t.div});const a=t.mlst[0];if(a.dt==p){Ut(t,e)}else if(a.dt==r||a.dt==l){await Wt(t,e)}else if(a.dt==s){Kt(t,e)}else{throw"oneItem: unknown dt"}t.singleSampleDiv=e;if(t.tk.mds.variant2samples){if(a.occurrence){await Zt(t)}}}async function Ft(t){const e=t.div.append("div").style("margin-bottom","10px").style("display","none");e.append("span").html("&#8810; Back to list").attr("class","sja_clbtext").on("click",(()=>{m.style("display","");e.style("display","none");a.style("display","none")}));const a=t.div.append("div").style("display","none");const n=[{label:"Click a variant to see details"}];const o=t.mlst.some((t=>t.occurrence));if(o){n.push({label:"Occurrence"})}let c=null;if(t.tk.mds.bcf?.info){c=[];for(const e in t.tk.mds.bcf.info){if(t.tk.mds.bcf.info[e].categories){c.push(e);n.push({label:t.tk.mds.bcf.info[e].name||e})}}if(c.length==0)c=null}let d;if(t.tk.skewer){d=t.tk.skewer.viewModes.find((t=>t.inuse&&t.type=="numeric"&&t.byAttribute!="occurrence"));if(d){n.push({label:d.label})}}t.mlst.sort(((t,e)=>t.__x-e.__x));const f=[];for(const e of t.mlst){const s=[{}];if(o){s.push({value:"occurrence"in e?e.occurrence:""})}if(c){for(const a of c){const n=e.info[a];if(n==undefined){s.push({})}else{const e=t.tk.mds.bcf.info[a].categories[n];if(e?.color){s.push({html:`<span style="background:${e.color}">&nbsp;&nbsp;</span> ${e.label||n}`})}else{s.push({value:n})}}}}if(d){s.push({value:e[d.byAttribute]})}f.push(s)}const m=t.div.append("div");R({div:m,columns:n,rows:f,striped:false,resize:true});for(const[n,o]of t.mlst.entries()){const c=f[n][0].__td.append("div").attr("class","sja_menuoption").on("click",(()=>{m.style("display","none");e.style("display","");a.style("display","").selectAll("*").remove();const s=Object.assign({},t);s.mlst=[o];s.div=a;Dt(s)}));if(o.dt==p){c.append("span").text(t.tk.mnamegetter(o));c.append("span").text(i[o.class].label).style("font-size",".8em").style("margin-left","10px").style("color",i[o.class].color);c.append("span").text(`${o.chr}:${o.pos+1}${o.ref?", "+o.ref+">"+o.alt:""}`).style("font-size",".8em").style("margin-left","10px")}else if(o.dt==r||o.dt==l){c.append("span").text(i[o.class].label).style("font-size",".7em").style("margin-right","8px");Qt(o.pairlst[0],c)}else if(o.dt==s){c.append("span").style("background",t.tk.cnv.colorScale(o.value)).text(o.value).style("font-size",".8em").style("padding","0px 3px");c.append("span").style("margin-left","10px").text(`${o.chr}:${o.start}-${o.stop}`)}else{c.text("error: unknown m.dt")}}if(!t.doNotListSample4multim&&t.tk.mds.variant2samples){const e=t.mlst.reduce(((t,e)=>t+(e.occurrence||0)),0);if(e){t.div.append("div").style("margin-top","10px").append("span").attr("class","sja_clbtext").text("List all samples").on("click",(async e=>{e.target.remove();m.remove();await Zt(t);Tt(t)}))}}}function Ut({mlst:t,tk:e,block:s},a){const n=t[0];{const[t,e]=a.addRow();t.text(s.mclassOverride?s.mclassOverride.className:"Consequence");Ht(e,n)}{const[t,i]=a.addRow();t.text(n.ref&&n.alt?"Mutation":"Position");Vt(i,n,e,s)}if(n.occurrence>1){const[t,e]=a.addRow();t.text("Occurrence");e.text(n.occurrence)}Gt(n,e,a);Pt(n,e,a);Yt(n,e,a);if(n.info){for(const t in n.info){if(t=="CSQ"){continue}const[s,i]=a.addRow();s.text(t);const o=n.info[t];const r=e.mds?.bcf?.info?.[t];if(Array.isArray(o)){for(const t of o){Et(n,r,t,i)}}else{Et(n,r,o,i)}if(r?.Description){i.append("span").style("margin-left","10px").style("font-size",".8em").style("opacity",.6).text(r.Description)}}}}function Gt(t,e,s){const a=e.skewer.viewModes.find((t=>t.inuse));if(a.type!="numeric"||a.byAttribute=="occurrence")return;if(a.tooltipPrintValue){const e=a.tooltipPrintValue(t);if(Array.isArray(e)){for(const t of e){const[e,a]=s.addRow();e.text(t.k);a.text(t.v)}}else{console.log("unknown return value")}return}const[n,i]=s.addRow();n.text(a.label);i.text(t.__value_missing?"NA":t.__value_use)}function Pt(t,e,s){if(!t.htmlSections)return;if(!Array.isArray(t.htmlSections))throw"htmlSections[] is not array";for(const e of t.htmlSections){const[t,a]=s.addRow();if(e.key&&e.html){t.text(e.key);a.html(e.html)}}}function Et(t,e,s,a,n){if(!e){a.append("span").text(s);return}if(e.urlBase){a.append("a").text(s).attr("href",e.urlBase+s).attr("target","_blank");return}const i=a.append("span").text(s);if(e&&e.categories){const t=e.categories[s];if(t){i.style("padding","1px 4px").style("background",t.color);if(t.textcolor){i.style("color",t.textcolor)}}}}function Ht(t,e){t.append("span").text(e.mname);t.append("span").style("margin-left","5px").style("color",i[e.class].color).style("font-size",".8em").text(i[e.class].label.toUpperCase())}function Vt(t,e,s,a){const n=t.append("span").text(`${e.chr}:${e.pos+1} ${e.ref&&e.alt?e.ref+">"+e.alt:""}`);const i=s.mds.termdbConfig?.urlTemplates?.ssm||s.mds.queries?.snvindel?.ssmUrl;if(i){const s=z(i,e,n,a.genome.name);if(s?.length){t.append("span").style("margin-left","10px").html(s.join(" "))}}}async function Wt(t,e){await Xt(t.mlst[0],e.scrollDiv.insert("div",":first-child"),t.block);{const[s,a]=e.addRow();s.text("Data type");a.text(i[t.mlst[0].class].label)}{const[s,a]=e.addRow();s.text("Break points");for(const e of t.mlst[0].pairlst){Qt(e,a.append("div"))}}}function Kt(t,e){const s=t.mlst[0];{const[a,n]=e.addRow();a.text("Copy number change");n.html(`<span style="background:${t.tk.cnv.colorScale(s.value)}">&nbsp;&nbsp;</span> ${s.value}`)}{const[t,a]=e.addRow();t.text("Position");a.text(s.chr+":"+s.start+"-"+s.stop)}if(s.samples){const[t,a]=e.addRow();t.text("Sample");for(const t of s.samples){a.append("div").text(t.sample_id)}}}function Qt(t,e){if(t.a.name)e.append("span").text(t.a.name).style("font-weight","bold").style("margin-right","5px");e.append("span").text(`${t.a.chr}:${t.a.pos} ${t.a.strand=="+"?"forward":"reverse"} > ${t.b.chr}:${t.b.pos} ${t.b.strand=="+"?"forward":"reverse"}`);if(t.b.name)e.append("span").text(t.b.name).style("font-weight","bold").style("margin-left","5px")}async function Xt(t,e,s){const a=e.append("div").text("Loading...");try{if(!t.pairlst)throw".pairlst[] 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e.mds.queries.ld.mOverlay.data||[]){if(s.pos==t.pos&&s.alleles==t.ref+"."+t.alt){a=s.r2;break}}if(a==null){s.html("No r<sup>2</sup> value is found.")}else{s.html(e.mds.queries.ld.mOverlay.ldtkname+" r<sup>2</sup> = "+a)}}}n.append("div").html("Click a button to overlay LD r<sup>2</sup> values against this variant:").style("font-size",".8em").style("opacity",.5);for(const s of e.mds.queries.ld.tracks){const a=n.append("button").text(s.name);if(i&&i.ssm_id==t.ssm_id){if(s.name==e.mds.queries.ld.mOverlay.ldtkname){a.property("disabled",true);continue}}a.on("click",(()=>{e.itemtip.hide();e.mds.queries.ld.mOverlay={ldtkname:s.name,m:{chr:t.chr,pos:t.pos,ref:t.ref,alt:t.alt,ssm_id:t.ssm_id}};e.load()}))}}async function Zt(t){const e=t.div.append("div").text("Loading...").style("padding","10px").style("color","#8AB1D4").style("font-size","1.25em").style("font-weight","bold");t.tid2value_orig=new Set;if(t.tid2value)Object.keys(t.tid2value).forEach(t.tid2value_orig.add,t.tid2value_orig);try{t.querytype=t.tk.mds.variant2samples.type_samples;const s=await t.tk.mds.variant2samples.get(t);await te(s.samples,t);e.remove()}catch(t){e.text("Error: "+(t.message||t));if(t.stack)console.log(t.stack)}}async function te(t,e){if(t.length==1){return await se(t[0],e)}const[s,a]=await oe(t,e.tk);const n={rows:a,columns:s,div:e.div,resize:a.length>10,dataTestId:"sjpp_mds3tk_sampletable"};n.columnButtons=[];if(e.tk.mds.queries?.singleSampleMutation){const s={text:"Disco",dataTestId:"sja_sample_table_disco_button",callback:async(s,a)=>{e.tk.itemtip.hide();e.tk.menutip.hide();let n;if(t[a].ssm_id_lst?.[0]){n=(e.tk.skewer.rawmlst||e.tk.custom_variants).find((e=>e.ssm_id==t[a].ssm_id_lst[0]))}await ie(e.tk,e.block,t[a],n)}};n.columnButtons.push(s)}if(e.tk.mds.queries?.singleSampleGenomeQuantification){for(const s in e.tk.mds.queries.singleSampleGenomeQuantification){const a={text:s,dataTestId:`${s}_button`,callback:async(a,n)=>{const i=g(e.tk.newChartHolder||e.block.holder0);i.header.text(t[n].sample_id);await(await import("./plot.ssgq-d33113d5.js")).plotSingleSampleGenomeQuantification(e.tk.mds,e.tk.mds.label,s,t[n],i.body.append("div").style("margin","20px"),e.block.genome,e.block.usegm?.name)}};n.columnButtons.push(a)}}if(e.tk.allow2selectSamples){n.buttons=[{text:e.tk.allow2selectSamples.buttonText,class:e.tk.allow2selectSamples.class,callback:s=>{ee(e.tk,e.block,t,s);e.tk.itemtip.hide();e.tk.menutip.hide()}}]}return R(n)}async function ee(t,e,s,a){const n=[...s];const i=a.map((t=>n[t]));t.allow2selectSamples.callback({samples:await t.mds.termdb.vocabApi.convertSampleId(i,t.allow2selectSamples.attributes),source:"Samples with "+le(e)})}async function se(t,e){const s=e.singleSampleDiv||h({holder:e.div});if(t.sample_id){const[a,n]=s.addRow();a.text(e.tk.mds.termdbConfig?.lollipop?.sample||"Sample");let i;if(t.ssm_id_lst?.[0]){i=e.tk.skewer.rawmlst.find((e=>e.ssm_id==t.ssm_id_lst[0]))}ne(t,e.tk,n,e.block,i)}if("caseIsOpenAccess"in t){const[e,a]=s.addRow();e.text("Access");a.text(t.caseIsOpenAccess?"Open":"Controlled")}if(e.tk.mds.variant2samples.twLst){for(const a of e.tk.mds.variant2samples.twLst){const[e,n]=s.addRow();e.text(a.term.name).style("text-overflow","ellipsis");n.style("text-overflow","ellipsis");if(a.term.id in t){if(Array.isArray(t[a.term.id])){if(a.baseURL){n.html(t[a.term.id].map((t=>`<a href=${a.baseURL+t} target=_blank>${t}</a>`)).join("<br>"))}else{n.html(t[a.term.id].join("<br>"))}}else{const e=ae(t,a);if(a.baseURL){n.html(`<a href=${a.baseURL+e} target=_blank>${e}</a>`)}else{n.text(e)}}}}}if(t.ssmid2format){for(const a of t.ssm_id_lst){if(t.ssm_id_lst.length>1){const[t,n]=s.addRow();n.style("padding-top","20px");const i=e.tk.skewer.rawmlst.find((t=>t.ssm_id==a));if(i){if(i.dt==p){Vt(n,i,e.tk,e.block)}else if(i.dt==r||i.dt==l){Qt(i.pairlst[0],n)}else{n.text(a)}}else{n.text(a)}}for(const n in t.ssmid2format[a]){const i=t.ssmid2format[a][n];const[o,r]=s.addRow();const l=e.tk.mds?.bcf?.format?.[n];o.text(l&&l.Description||n);r.html(re(l,i))}}}}function ae(t,e){if(!(e.term.id in t))return"";const s=t[e.term.id];if(e.term.values?.[s]?.label)return e.term.values[s].label;const a=e.term.valueConversion;if(a)return f(s,a.fromUnit,a.toUnit,a.scaleFactor);return s}function ne(t,e,s,a,n){const i=e.mds.termdbConfig?.urlTemplates?.sample;if(i){const e=s.append("a");e.attr("href",i.base+(t[i.namekey]||t.sample_id));e.attr("target","_blank");e.text(t.sample_id);e.style("word-break","break-word")}else{s.append("span").attr("class","pp_mds3_singleSampleNameSpan").text(t.sample_id)}const o=s.append("div");if(e.allow2selectSamples){const s=e.allow2selectSamples.buttonText;const n=o.append("button").style("margin-right","10px").text(s.endsWith("s")?s.substring(0,s.length-1):s).on("click",(()=>{ee(e,a,[t],[0]);e.itemtip.hide();e.menutip.hide()}));if(e.allow2selectSamples.class)n.attr("class",e.allow2selectSamples.class)}if(e.mds.queries?.singleSampleMutation){o.append("button").style("margin-right","10px").text("Disco plot").attr("data-testid","proteinpaint_disc_table_disco_button").on("click",(async()=>{e.itemtip.hide();await ie(e,a,t,n)}))}if(e.mds.queries?.singleSampleGenomeQuantification){for(const s in e.mds.queries.singleSampleGenomeQuantification){o.append("button").text(s).on("click",(async()=>{const n=g(e.newChartHolder||a.holder0);n.header.text(t.sample_id);await(await import("./plot.ssgq-d33113d5.js")).plotSingleSampleGenomeQuantification(e.mds,e.mds.label,s,t,n.body.append("div").style("margin","20px"),a.genome,a.usegm?.name)}))}}}async function ie(t,e,s,a){const n=g(t.newChartHolder||e.holder0);const i=[s.sample_id];if(a){i.push(", with ");if(e.usegm){i.push(e.usegm.name)}else{i.push(a.isoform)}i.push(" "+a.mname)}n.header.text(i.join(""));try{(await import("./plot.disco-1fdfee3c.js")).default(t.mds,t.mds.label,s,n.body,e.genome,{downloadImgName:i.join("")+" Disco",Disco:{prioritizeGeneLabelsByGeneSets:true}})}catch(t){n.body.append("div").text("Error: "+(t.message||t));if(t.stack)console.log(t.stack)}}async function oe(t,e){const s=t.some((t=>"caseIsOpenAccess"in t)),a=t.some((t=>t.ssm_id))||t.some((t=>t.ssm_id_lst)),n=t.some((t=>t.ssmid2format))&&e.mds?.bcf?.format;const o=new Set;const c=[{label:e.mds.termdbConfig?.lollipop?.sample||"Sample"}],d=[];if(s){c.push({label:"Access"})}if(e.mds.variant2samples.twLst){for(const t of e.mds.variant2samples.twLst){const e={label:t.term.name};c.push(e)}}if(a){c.push({label:"Mutations",isSsm:true})}if(n){for(const e of t){if(!e.ssmid2format)continue;for(const t in e.ssmid2format){for(const s in e.ssmid2format[t])o.add(s)}}for(const t in e.mds.bcf.format){if(!o.has(t))continue;const s=e.mds.bcf.format[t];c.push({label:s.Description||t})}}for(const c of t){const t=[{value:c.sample_id}];let f=c.ssm_id_lst;if(!f&&c.ssm_id)f=[c.ssm_id];{const s=e.mds.termdbConfig?.urlTemplates?.sample;if(s){t[0].url=s.base+(c[s.namekey]||c.sample_id)}}if(s){t.push({value:c.caseIsOpenAccess?"Open":"Controlled"})}if(e.mds.variant2samples.twLst){for(const s of e.mds.variant2samples.twLst){const e=ae(c,s);if(s.baseURL){t.push({html:`<a href=${s.baseURL+e} target=_blank>${e}</a>`})}else{t.push({value:e})}}}if(a){if(f){const s=[];for(const t of f){const a=[];const n=(e.skewer.rawmlst||e.custom_variants).find((e=>e.ssm_id==t));if(n){if(n.dt==p){if(e.mds.queries&&e.mds.queries.snvindel&&e.mds.queries.snvindel.url){a.push(`<a href=${e.mds.queries.snvindel.url.base+n.ssm_id} target=_blank>${n.mname}</a>`)}else{a.push(n.mname)}}else if(n.dt==r||n.dt==l){const t=n.pairlst[0];a.push(`${t.a.name||""} ${t.a.chr}:${t.a.pos} ${t.a.strand=="+"?"forward":"reverse"} > ${t.b.name||""} ${t.b.chr}:${t.b.pos} ${t.b.strand=="+"?"forward":"reverse"}`)}else{throw"unknown dt"}a.push(`<span style="color:${w(i[n.class].color).darker()};font-size:0.8em;">${i[n.class].label}</span>`);s.push(a.join(" "))}else{s.push(t)}}t.push({html:s.join("<br>")})}else{t.push({value:""})}}if(n){if(!f)throw"ssm_id_lst missing, cannot show format";for(const s in e.mds.bcf.format){if(!o.has(s))continue;if(!c.ssmid2format){t.push({value:""});continue}const a=e.mds.bcf.format[s];const n=[];for(const t of f){const e=c.ssmid2format?.[t]?.[s];n.push(re(a,e))}t.push({html:n.join("<br>")})}}d.push(t)}return[c,d]}function re(t,e){if(t&&e&&t.Number=="R"&&t.Type=="Integer"){const t=e.split(",").map(Number);if(t.length==2){const[e,s]=t;if(e>=0&&s>=0&&e+s>0){return`${b(null,{f:s/(s+e)})} <span style="font-size:.8em">${s}/${s+e}</span>`}}}return e}function le(t){if(t.gmmode=="genomic"){const e=t.rglst[0];return"mutations from "+e.chr+":"+e.start+"-"+e.stop}if(t.usegm)return"mutations in "+t.usegm.name;return"mutations"}const ce=10;async function de(t,e,s,a,n){try{if(e.click_snvindel){e.skewer.hlssmid=new Set(t.mlst.map((t=>t.ssm_id)));qe(e);e.click_snvindel(t.mlst[0]);return}if("occurrence"in t&&t.occurrence>=ce&&e.mds.variant2samples&&e.mds.variant2samples.sunburst_twLst){await fe(t,e,s,a);return}await me({mlst:t.mlst,tk:e,block:s,tippos:a})}catch(t){s.error(t.message||t);if(t.stack)console.log(t.stack)}}async function fe(t,e,s,a){e.glider.style("cursor","wait");const n=await e.mds.variant2samples.get({mlst:t.mlst,querytype:e.mds.variant2samples.type_sunburst});e.glider.style("cursor","auto");const i={nodes:n.nodes,occurrence:t.occurrence,boxyoff:e.yoff,boxheight:Math.min(800,e.height),boxwidth:s.width,svgheight:Number.parseFloat(s.svg.attr("height")),g:e.skewer.g.append("g"),pica:e.pica,click_listbutton:(n,i)=>{me({mlst:t.mlst,tk:e,block:s,tippos:a})},click_ring:async(a,n)=>{e.itemtip.clear();const i={mlst:t.mlst,tk:e,block:s,div:e.itemtip.d,tid2value:{}};i.tid2value[n.data.id0]=n.data.v0;if(n.data.id1)i.tid2value[n.data.id1]=n.data.v1;if(n.data.id2)i.tid2value[n.data.id2]=n.data.v2;i.mlst=t.mlst.map((t=>{if(e.mds.variant2samples.variantkey=="ssm_id"){return{ssm_id:t.ssm_id,occurrence:0}}throw"unknown variant2samples.variantkey"}));i.mlst[0].occurrence=n.value;const o=a.clientX;const r=a.clientY;await Zt(i);e.itemtip.show2(o,r)}};if(t.aa){i.cx=t.aa.x;i.cy=xe(t,e)+t.yoffset*(e.skewer.pointup?-1:1)}else{i.cx=t.x;i.cy=t.y+(e.skewer.pointup?1:-1)*e.skewer.stem1/2}if(t.mlst.length==1){i.chartlabel=t.mlst[0].mname}else{const e=new Set(t.mlst.map((t=>t.mname)));if(e.size==1){i.chartlabel=[...e][0]}else{i.chartlabel=t.mlst.reduce(((t,e)=>e.occurrence>t.occurrence?e:t)).mname+" etc"}}const o=await import("./sunburst-fe95832e.js");o.default(i)}async function me(t){t.tk.itemtip.clear().show(t.tippos.left-10,t.tippos.top-10);t.div=t.tk.itemtip.d;t.tipDiv=t.tk.itemtip.d;await Dt(t)}const 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u=m.append("circle");u.filter((t=>t.dt==p||t.dt==r||t.dt==l)).attr("fill",(e=>t.color4disc(e.mlst[0]))).attr("stroke","white").attr("r",(t=>t.radius-.5));m.filter((t=>t.dt==l||t.dt==r)).append("path").attr("fill","white").attr("stroke","none").attr("d",(t=>O()({innerRadius:0,outerRadius:t.radius-2,startAngle:t.useNterm?0:Math.PI,endAngle:t.useNterm?Math.PI:Math.PI*2})));const h=m.filter((t=>t.occurrence>1)).append("text").text((t=>t.occurrence)).attr("font-family",be).attr("class","sja_aa_discnum").attr("fill-opacity",(t=>t.aa.showmode==ue?0:1)).attr("stroke-opacity",(t=>t.aa.showmode==ue?0:1)).attr("text-anchor","middle").each((t=>{const 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if(s==0){t.menutip.d.append("div").text("Expand").attr("class","sja_menuoption").attr("data-testid","sja_expand_menuoption").style("border-radius","0px").on("click",(()=>{ye(t,e);t.menutip.hide()}))}t.menutip.d.append("div").text(t.skewer.pointup?"Point down":"Point up").attr("class","sja_menuoption").style("border-radius","0px").on("click",(()=>{t.skewer.pointup=!t.skewer.pointup;t.load();t.menutip.hide()}))}else if(s.type=="numeric"){t.menutip.d.append("div").text(t.skewer.hideDotLabels?"Show all variant labels":"Hide all variant labels").attr("class","sja_menuoption").style("border-radius","0px").on("click",(()=>{t.skewer.hideDotLabels=!t.skewer.hideDotLabels;t.load();t.menutip.hide()}))}}if(!t.custom_variants){t.menutip.d.append("div").text("Download").attr("class","sja_menuoption").attr("data-testid","sjpp_mds3tk_variantdownload_menuoption").style("border-radius","0px").on("click",(()=>{Te(t,e);t.menutip.hide()}))}Ie(t,e)}async function Oe(t,a){t.menutip.clear();const n=new Map;if(t.skewer){const e=t.skewer.viewModes.find((t=>t.inuse));let s;if(e.type=="skewer"){s=t.skewer.data.filter((t=>t.x>=0&&t.x<=a.width))}else if(e.type=="numeric"){s=e.data}else{throw"unknown mode type"}for(const t of s){for(const e of t.mlst){if(!n.has(e.dt))n.set(e.dt,[]);n.get(e.dt).push(e)}}}if(t.cnv?.cnvLst){n.set(s,t.cnv.cnvLst)}if(n.size==1){const e=t.menutip.d.append("div").style("margin","10px");await Dt({div:e,mlst:n.get([...n.keys()][0]),tk:t,block:a,doNotListSample4multim:true});return}const i=[];for(const[t,s]of n){i.push({label:s.length+" "+e[t]})}new T({holder:t.menutip.d.append("div").attr("class","sja_pp_vlb_dttabdiv").style("margin","10px"),tabs:i}).main();let o=0;for(const[e,s]of n){Dt({div:i[o++].contentHolder.append("div").style("margin-left","10px"),mlst:s,tk:t,block:a,doNotListSample4multim:true})}}function Ie(t,e){if(!t.skewer)return;if(t.skewer.viewModes.length<=1){return}const s=[];for(const[e,a]of t.skewer.viewModes.entries()){const t={label:De(a),value:e};if(a.inuse)t.checked=true;s.push(t)}B({holder:t.menutip.d.append("div").attr("class","sja_pp_vlb_viewmoderadiodiv").style("margin","10px"),options:s,callback:async s=>{for(const e of t.skewer.viewModes)e.inuse=false;t.skewer.viewModes[s].inuse=true;us({skewer:t.skewer.rawmlst},t,e);Pe(t,e);t._finish()}})}function De(t){if(!t)return"MISSING!!";if(t.type=="skewer")return"As lollipops";if(t.type=="numeric")return t.label+" as Y axis";return"unknown mode"}async function Te(t,e){if(!t.mds.variant2samples){console.log("TODO: variant-only");return}const s={querytype:"samples"};Cs(t,e,s);const a=(await t.mds.variant2samples.get(s)).samples;const[n,o]=await oe(a,t);const c=[];for(const t of n){if(t.isSsm){c.push("AAchange");c.push("Consequence");c.push("Mutation");continue}if(t.isMaf){c.push("Alternative allele depth in tumor");c.push("Total depth in tumor");continue}c.push(t.label)}const d=[];for(const[e,s]of a.entries()){let 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n=N().scale(a).ticks(4);if(e.isinteger){n.tickFormat(y("d"));if(e.maxvalue-e.minvalue<3){n.ticks(e.maxvalue-e.minvalue)}}L({axis:e.axisg.call(n),showline:true,fontsize:e.dotwidth});e.axisWidth=0;e.axisg.selectAll("text").each((function(){e.axisWidth=Math.max(e.axisWidth,this.getBBox().width)}));e.axisWidth+=15;let i;e.axisg.append("text").attr("fill","black").attr("font-size",e.dotwidth).attr("dominant-baseline","central").attr("text-anchor","end").attr("class","sjpp-mds3-nm-axislabel sja_clbtext2").attr("y",e.axisheight/2).attr("x",-e.axisWidth).text(e.label||Ye).each((function(){i=this.getBBox().width})).on("click",(a=>{t.menutip.clear().showunder(a.target).d.append("div").text("Cancel").attr("class","sja_menuoption").style("border-radius","0px").on("click",(()=>{t.menutip.hide();e.inuse=false;t.skewer.viewModes.find((t=>t.type=="skewer")).inuse=true;us({skewer:t.skewer.rawmlst},t,s);Pe(t,s);t._finish()}));I({holder:t.menutip.d.append("div").style("margin","10px"),noPercentile:true,callback:a=>{e.axisSetting=a;ts(t);es(e,t,s)},setting:e.axisSetting})}));t.skewer.maxwidth=e.axisWidth+i}function ds(t){return`M 0 -${t} L ${t} ${t*.7} h -${t*2} Z`}function fs(t){const e=t.mds.queries?.ld?.mOverlay?.m;if(!e)return;t.skewer.hlssmid=new Set([e.ssm_id]);qe(t)}const ms=10;function us(t,e,s){if(!e.skewer){e.subtk2height.skewer=0;return}e.skewer.maxwidth=0;bs(e,t.skewer);ps(e,t.skewer);const a=e.skewer.viewModes.find((t=>t.inuse));if(!a)throw"no mode!!";if(t.skewer){e.skewer.rawmlst=t.skewer}if(a.type=="numeric"){e.subtk2height.skewer=Ze(a,t,e,s);qe(e);return}if(a.type!="skewer")throw'mode.type is not "skewer"';if(t&&!t.skewer&&s.usegm&&s.gmmode!="genomic"&&s.pannedpx!=undefined){hs(e,s);e.skewer.selection.attr("transform",(t=>"translate("+t.x+","+t.y+")"));ye(e,s)}else{e.skewer.g.selectAll("*").remove();e.skewer.data=gs(e,s);ke(e,s)}if(!e.skewer.data||e.skewer.data.length==0){e.subtk2height.skewer=0;e.skewer.g.selectAll("*").remove();return}if(e.skewer.hlssmid){const t=[];const a=[];for(const s of e.skewer.data){let n=false;for(const t of s.groups){for(const s of t.mlst){if(e.skewer.hlssmid.has(s.ssm_id)){n=true;break}}}if(n){a.push(s)}else{t.push(s)}}Se(t,e);_e(a,e,s);qe(e)}else{ye(e,s)}e.subtk2height.skewer=e.skewer.maxheight+e.skewer.stem1+e.skewer.stem2+e.skewer.stem3}function ps(t,e){if(!t.hlaachange||!e)return;const s=new Set(t.hlaachange.split(","));delete t.hlaachange;t.skewer.hlssmid=new Set;for(const a of e){if(s.has(a.mname))t.skewer.hlssmid.add(a.ssm_id)}}function hs(t,e){for(const s of t.skewer.data){if(s.isbin){let t=0;for(const a of s.mlst){const s=e.seekcoord(a.chr,a.pos);if(a.usehitidx!=undefined&&s[a.usehitidx]){t+=s[a.usehitidx].x}else if(s.length==1){t+=s[0].x}else{console.log("cannot map item");console.log(a)}}s.x0=t/s.mlst.length;s.x=s.x0+(s.xoffset!=undefined?s.xoffset:0)}else{const t=e.seekcoord(s.chr,s.pos);if(t.length>0){s.x0=t[0].x;s.x=s.x0+(s.xoffset!=undefined?s.xoffset:0)}else{console.log("cannot map group of item");console.log(s)}}}}function gs(t,e){const s=ze(t,t.skewer.rawmlst,e);for(const t of s){t.groups=ws(t.mlst)}if(t.skewer.data&&e.pannedpx!=undefined){const e={};for(const s of t.skewer.data){e[s.chr+"."+s.pos]={mode:s.showmode,xoffset:s.xoffset,slabelrotate:s.slabelrotate}}for(const t of s){const s=t.chr+"."+t.pos;if(e[s]){t.showmode=e[s].mode;t.xoffset=e[s].xoffset;t.slabelrotate=e[s].slabelrotate}}}for(const t of s){t.occurrence=t.groups.reduce(((t,e)=>t+e.occurrence),0)}return s}function ws(t,e){const s=new Map;for(const e of t){if(!Number.isInteger(e.dt))continue;if(!s.has(e.dt))s.set(e.dt,new Map);switch(e.dt){case p: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 r:case l: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 n:case M:case j:case _: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 a=[];for(const[t,e]of s){switch(t){case p:for(const[s,n]of e){if(n.size>ms){const e=[];for(const t of n.values())e.push(...t);a.push({dt:t,mlst:e,mnameCompact:i[s].label})}else{for(const e of n.values()){a.push({dt:t,mlst:e})}}}break;case r:case l:for(const s of e.values()){if(s.use5.size>ms){const e=[];for(const t of s.use5.values())e.push(...t);a.push({dt:t,mlst:e,useNterm:true,mnameCompact:t==r?"SV":"fusion"})}else{for(const e of s.use5.values()){a.push({dt:t,mlst:e,useNterm:true})}}if(s.use3.size>ms){const e=[];for(const t of s.use3.values())e.push(...t);a.push({dt:t,mlst:e,useNterm:false,mnameCompact:t==r?"SV":"fusion"})}else{for(const e of s.use3.values()){a.push({dt:t,mlst:e,useNterm:false})}}}break;case n:case M:case j:case _:a.push({dt:t,mlst:e})}}for(const t of a){let e=0,s=0;for(const a of t.mlst){e+=a.rim1count||0;s+=a.rim2count||0}t.rim1count=e;t.rim2count=s}if(t.some((t=>Number.isFinite(t.occurrence)))){for(const t of a)t.occurrence=t.mlst.reduce(((t,e)=>t+e.occurrence),0)}else{for(const t of a)t.occurrence=t.mlst.length}a.sort(((t,e)=>e.occurrence-t.occurrence));return a}function bs(t,e){ks(t,e);for(const e of t.skewer.viewModes){if(e.type=="numeric"&&!e.inuse&&e.axisg){e.axisg.remove();delete e.axisg}}}function ks(t,e){if(e&&e.find((t=>Number.isFinite(t.occurrence)))){if(!t.skewer.viewModes.find((t=>t.type=="numeric"&&t.byAttribute=="occurrence"))){t.skewer.viewModes.push({type:"numeric",byAttribute:"occurrence",label:"Occurrence",isinteger:true})}}}function xs(t,e,s){e.cnv?.g.selectAll("*").remove();if(!t.cnv){delete e.subtk2height.cnv;return}const[a,n,i]=vs(t,e,s);e.cnv.cnvLst=n;e.cnv.absoluteMax=i;e.cnv.colorScale=d([-i,0,i],[e.cnv.lossColor,"white",e.cnv.gainColor]).clamp(true);const[o,r]=_s(a||n);if(a){for(const t of a){for(const a of t.cnvs){js(a,t.y*(o+r),o,e,s,t)}}}else{for(const t of n){js(t,t.y*(o+r),o,e,s)}}const l=(a||n).length;e.subtk2height.cnv=l*o+(l-1)*r}function vs(t,e,s){let a=0;const n=new Map;const i=[];for(const e of t.cnv){if(!e.chr)continue;if(!Number.isFinite(e.value)){if(typeof e.class=="string"){if(e.class==A){e.value=1}else if(e.class==S){e.value=-1}else{continue}}else{continue}}if(!Number.isInteger(e.start)||!Number.isInteger(e.stop))continue;const t=s.seekcoord(e.chr,e.start)[0];if(!t)continue;const o=s.seekcoord(e.chr,e.stop)[0];if(!o)continue;const r=structuredClone(e);if(t.x>o.x){r.x1=o.x;r.x2=t.x}else{r.x1=t.x;r.x2=o.x}a=Math.max(a,Math.abs(e.value));i.push(r);if(Array.isArray(e.samples)){for(const t of e.samples){if(!n.has(t.sample_id))n.set(t.sample_id,[]);n.get(t.sample_id).push(structuredClone(r))}}}let o;if(n.size){o=[];for(const[t,e]of n){e.sort(((t,e)=>t.x1-e.x1));o.push({sample_id:t,cnvs:e,x1:Math.min(...e.map((t=>t.x1))),x2:Math.max(...e.map((t=>t.x2)))})}o.sort(((t,e)=>t.x1-e.x1));for(let t=0;t<o.length;t++)o[t].y=t}else{i.sort(((t,e)=>t.x1-e.x1));Ms(i,0)}return[o,i,Math.min(e.cnv.absoluteValueRenderMax,a)]}const ys=d([40,120],[10,1]);function _s(t){if(t.length>120)return[1,0];if(t.length<40)return[10,1];return[Math.ceil(ys(t.length)),1]}function js(t,e,s,a,n,i){const o=Math.max(0,t.x1),r=Math.min(t.x2,n.width);a.cnv.g.append("rect").attr("x",o).attr("y",e).attr("width",r-o).attr("height",s).attr("fill",a.cnv.colorScale(t.value)).on("mouseover",(e=>{e.target.setAttribute("stroke","black");a.itemtip.clear().show(e.clientX,e.clientY);const s=h({holder:a.itemtip.d});const n=structuredClone(t);if(i){n.samples=[{sample_id:i.sample_id}]}Kt({mlst:[n],tk:a},s)})).on("mouseout",(t=>{t.target.setAttribute("stroke","");a.itemtip.hide()}))}function Ms(t,e){const s=[];for(const a of t){for(let t=0;t<s.length;t++){if(s[t]+e<a.x1){s[t]=a.x2;a.y=t;break}}if(!("y"in a)){a.y=s.length;s.push(a.x2)}}}async function As(t,e){e.tkcloakon(t);e.block_setheight();try{if(!t.mds||t.uninitialized){await pt(t,e)}const s=await qs(t,e);if(t.uninitialized){t.clear();delete t.uninitialized}us(s,t,e);xs(s,t,e);await Ue(s,t,e);t._finish(s)}catch(e){if(t.clear)t.clear();if(t.subtk2height)t.subtk2height.skewer=50;if(t._finish)t._finish({error:e.message||e});if(e.stack)console.log(e.stack);return}}function Ss(t,e){const s={genome:e.genome.name,forTrack:1,skewerRim:t.mds.queries?.snvindel?.skewerRim};const a={"Content-Type":"application/json",Accept:"application/json"};if(t.mds.has_skewer){s.skewer=1}if(t.set_id){s.set_id=t.set_id}if(t.filter0){s.filter0=t.filter0}if(t.filterObj){if(t.filterObj?.lst.length){s.filterObj=t.filterObj}}if(t.token){a["X-Auth-Token"]=t.token}if(t.mds.label){s.dslabel=t.mds.label}else{if(t.bcf){if(t.bcf.file){s.bcffile=t.bcf.file}else if(t.bcf.url){s.bcfurl=t.bcf.url;if(t.bcf.indexURL)s.bcfindexURL=t.bcf.indexURL}else{throw".file and .url missing for tk.bcf{}"}}}Cs(t,e,s);if(t.legend.mclass.hiddenvalues.size){s.hiddenmclasslst=[...t.legend.mclass.hiddenvalues].join(",")}if(t.legend.bcfInfo){const e={};for(const s in t.legend.bcfInfo){if(t.legend.bcfInfo[s].hiddenvalues.size){e[s]=[...t.legend.bcfInfo[s].hiddenvalues]}}if(Object.keys(e).length){s.infoFilter=e}}if(t.legend.formatFilter){const e={};for(const s in t.legend.formatFilter){if(t.legend.formatFilter[s].hiddenvalues.size){e[s]=[...t.legend.formatFilter[s].hiddenvalues]}}if(Object.keys(e).length){s.formatFilter=e}}if(t.cnv){if(t.cnv.cnvMaxLength)s.cnvMaxLength=t.cnv.cnvMaxLength;if(t.cnv.cnvGainCutoff)s.cnvGainCutoff=t.cnv.cnvGainCutoff;if(t.cnv.cnvLossCutoff)s.cnvLossCutoff=t.cnv.cnvLossCutoff}return[s,a]}async function qs(t,e){let s;if(t.custom_variants){s=await zs(t,e)}else{const[a,n]=Ss(t,e);s=await u("mds3",{body:a,headers:n})}if(s.error)throw s.error;return s}function Cs(t,e,s){if(typeof s!="object")throw"par{} is not object";let a=[];if(e.usegm){const t={chr:e.rglst[0].chr,reverse:e.rglst[0].reverse,width:0,start:null,stop:null};for(let s=e.startidx;s<=e.stopidx;s++){const a=e.rglst[s];t.width+=a.width+e.regionspace;t.start=t.start==null?a.start:Math.min(t.start,a.start);t.stop=t.stop==null?a.stop:Math.max(t.stop,a.stop)}a.push(t);if(e.gmmode=="genomic");else{s.isoform=e.usegm.isoform;s.gene=e.usegm.name}}else{a=e.tkarg_rglst(t)}let n=0;for(const t of a){t.xoff=0;n+=t.width+e.regionspace}if(e.subpanels.length==t.subpanels.length){for(const t of e.subpanels){a.push({chr:t.chr,start:t.start,stop:t.stop,width:t.width,exonsf:t.exonsf,xoff:n});n+=t.width+t.leftpad}}s.rglst=a}async function zs(t,e){const a={skewer:[],cnv:[]};let n=null,o;for(let t=e.startidx;t<=e.stopidx;t++){if(n==null){n=e.rglst[t].start;o=e.rglst[t].stop}else{n=Math.min(n,e.rglst[t].start);o=Math.max(o,e.rglst[t].stop)}}const c=new Map;for(const d of t.custom_variants){if(d.dt==s){if(d.chr!=e.rglst[0].chr)continue;if(Math.max(d.start,n)>Math.min(d.stop,o))continue;a.cnv.push(d)}else if(d.dt==p||d.dt==r||d.dt==l){if(d.chr!=e.rglst[0].chr)continue;if(d.pos<=n||d.pos>=o)continue;if(!d.class)d.class="X";if(!i[d.class])d.class="X";if(t.legend.mclass.hiddenvalues.has(d.class))continue;a.skewer.push(d)}else{throw"unknown custom data dt"}c.set(d.class,1+(c.get(d.class)||0))}if(a.cnv.length==0)delete a.cnv;const d=new Set;if(a.skewer?.some((t=>t.samples))){for(const t of a.skewer){if(t.samples){for(const e of t.samples)d.add(e.sample_id)}}}if(a.cnv?.some((t=>t.samples))){for(const t of a.cnv){if(t.samples){for(const e of t.samples)d.add(e.sample_id)}}}if(d.size)a.sampleTotalNumber=d.size;a.mclass2variantcount=[...c];await Ls(t,a.skewer);return a}async function Ls(t){if(!t.mds.queries?.ld?.mOverlay)return;if(!t.mds.termdb?.vocabApi)return;delete t.mds.queries.ld.mOverlay.data;const e=await t.mds.termdb.vocabApi.getLDdata(t.mds.queries.ld.mOverlay.ldtkname,t.mds.queries.ld.mOverlay.m);if(e.error||!Array.isArray(e.lst))return;t.mds.queries.ld.mOverlay.data=e.lst}var $s=Object.freeze({__proto__:null,loadTk:As,rangequery_rglst:Cs});export{te as d,mt as g,Ee as m,$s as t};