@sjcrh/proteinpaint-client 2.74.2 → 2.76.0

package/dist/table-eee91e14.js

@@ -1 +0,0 @@
-import{controlsInit as t}from"./controls-0bacec22.js";import{h as e,d as s}from"./app-a8c4854a.js";import"./controls.btns-1cb2bfab.js";import"./controls.config-0ccc9d79.js";import"./controls.overlay-fe20d41d.js";import"./roundValue-b0d0517c.js";import"./tslib.es6-1f85f553.js";import"path";import"./FilterRxComp-242f4615.js";import"./table-79e3e776.js";import"./termdb.bins-9faa5170.js";import"./controls.term1-faa2efcf.js";import"./controls.divide-a9fe9466.js";class o{constructor(t){this.type="table"}async init(){const t=this.opts;const e=t.controls?null:t.holder.append("div");const s=t.controls?t.holder:t.holder.append("div");this.dom={header:t.header,controls:e,holder:s,div:s.style("margin","10px 0px").style("display","none"),inputs:["term1","overlay"]};if(this.dom.header)this.dom.header.html("Crosstab");i(this);l(this);await this.setControls()}async setControls(){if(this.opts.controls){this.opts.controls.on("downloadClick.boxplot",this.download)}else{this.dom.holder.attr("class","pp-termdb-plot-viz").style("display","inline-block").style("min-width","300px").style("margin-left","50px");this.components={controls:await t({app:this.app,id:this.id,holder:this.dom.controls.attr("class","pp-termdb-plot-controls").style("display","inline-block")})};this.components.controls.on("downloadClick.boxplot",this.download)}}getState(t,e){const s=t.plots.find((t=>t.id===this.id));if(!s){throw`No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`}return{activeCohort:t.activeCohort,termfilter:t.termfilter,config:{term:s.term,term2:s.term2,settings:{common:s.settings.common,table:s.settings.table}}}}async main(){try{this.config=structuredClone(this.state.config);if(!this.config.term2){this.dom.div.style("display","none");throw"term2 is required for table view"}const t=this.state.config;if(this.dom.header)this.dom.header.html(t.term.term.name+" vs "+t.term2.term.name);const e=this.getDataRequestOpts();this.data=await this.app.vocabApi.getNestedChartSeriesData(e);this.app.vocabApi.syncTermData(this.state.config,this.data);const[s,o]=this.processData(this.data);this.render(s,o)}catch(t){throw t}}getDataRequestOpts(){const t=this.config;const e={term:t.term,filter:this.state.termfilter.filter};if(t.term2)e.term2=t.term2;if(t.term0)e.term0=t.term0;if(this.state.ssid)e.ssid=this.state.ssid;return e}processData(t){const e=this.config.term2.term;const s=t.refs.rows.map((t=>{const s=e.values&&t in e.values?e.values[t].label:t;return{key:t,label:s}}));const o=t.refs.rows;const i=this.config.term.term;const l=t.refs.cols.map((e=>{const s=t.charts[0].serieses.find((t=>t.seriesId==e));const l=i.values&&e in i.values?i.values[e].label:e;return{label:l,lst:!s?[]:s.data.slice().sort(((t,e)=>o.indexOf(t.dataId)-o.indexOf(e.dataId))).map((t=>({label:t.dataId,value:t.total})))}}));return[s,l]}}function i(t){t.download=()=>{if(!t.state||!t.state.isVisible)return;const e=[];t.dom.div.selectAll("tr").each((function(){const t=[];s(this).selectAll("th, td").each((function(){t.push(s(this).text())}));e.push(t)}));const o=e.map((t=>t.join("\t"))).join("\n");const i=document.createElement("a");document.body.appendChild(i);i.addEventListener("click",(function(){i.download=t.config.term.term.name+" table.txt";i.href=URL.createObjectURL(new Blob([o],{type:"text/tab-separated-values"}));document.body.removeChild(i)}),false);i.click()}}function l(t){t.render=function e(s,o){t.dom.div.style("display","inline-block").selectAll("*").remove();const i=t.dom.div.append("table").style("margin-right","20px").style("border-spacing","3px").style("border-collapse","collapse").style("border","1px solid black");const l=i.append("tr").style("white-space","normal").style("background-color","#ececec");l.append("td");for(const t of s){const e=t.label;l.append("th").text(e.length>20?e.slice(0,16)+"...":e).attr("title",e).style("border","1px solid black").style("padding","3px").style("text-align","center").style("min-width","80px").style("max-width","150px").style("word-break",e.length>12?"break-word":"normal").style("vertical-align","top")}let a=0;for(const t of o){const e=i.append("tr").style("background-color",a++%2==0?"#fff":"#ececec");e.append("th").text(t.label.length>20?t.label.slice(0,20)+"...":t.label).attr("title",t.label).style("border","1px solid black").style("padding","3px").style("word-break",t.label.length>12?"break-all":"normal");const o=s.map((t=>t.key));for(const s of o){const o=e.append("td").style("border","1px solid black").style("padding","3px 5px").style("text-align","center");const i=t.lst.find((t=>t.label==s));if(i){o.html(i.value)}}}}}const a=e(o);export{a as tableInit};

package/dist/termInfo-f851b415.js

@@ -1 +0,0 @@
-import{i as t,P as e}from"./app-a8c4854a.js";const i={isVisible:false,term:null};class s{constructor(t){this.vocabApi=t.vocabApi||t.app&&t.app.vocabApi;this.state=Object.assign({},i,t.state?t.state:{});this.api=this;l(this);n(this);this.initUI(t)}async main(t={}){e(this.state,t);this.dom.content_holder.style("display",this.state.isVisible?"block":"none");this.dom.icon_holder.style("background-color",this.state.isVisible?"darkgray":"transparent").style("color",this.state.isVisible?"white":"#797a7a");if(!this.state.isVisible)return;const i=await this.vocabApi.getTermInfo(this.state.term.id);this.render(i)}}const o=t(s);function n(t){t.initUI=function(e){t.dom={content_holder:e.content_holder.style("margin-left","25px").attr("class","term_info_div").style("display",t.state.isVisible?"block":"none").style("white-space","normal").style("padding-bottom","20px"),details:e.content_holder.append("div"),tbody:e.content_holder.append("table").append("tbody"),icon_holder:e.icon_holder.style("margin","1px 0px 1px 5px").style("padding","2px 5px").style("font-family","Times New Roman").style("font-size","14px").style("font-weight","bold").style("cursor","pointer").style("background-color","transparent").style("color","#797a7a").style("align-items","center").style("justify-content","center").style("border","none").style("border-radius","3px").attr("title","Term Information").html("&#9432;").on("mouseenter",(()=>{if(t.state.isVisible==true)return;t.dom.icon_holder.style("color","blue")})).on("mouseleave",(()=>{if(t.state.isVisible==true)return;t.dom.icon_holder.style("color","#797a7a")})).on("click",t.toggleDescription)}};t.render=function(e){t.dom.tbody.selectAll("*").remove();if(e.terminfo.src){for(let i of e.terminfo.src){const e=t.dom.tbody.append("tr").append("td").style("padding","5px 0");e.append("div").style("font-weight","bold").text("Source");e.append("div").style("margin-left","20px").text(i.pub);e.append("div").style("margin-left","20px").html(i.title+":&nbsp;<i>"+i.section+"</i>")}}if(e.terminfo.rubric){const i=t.dom.tbody.append("tr").append("td").style("padding","5px 0").append("div").style("font-weight","bold").text("Grading Rubric").append("ol").style("margin","0px");for(let t of e.terminfo.rubric){i.append("li").style("font-weight","normal").text(t)}}t.dom.details.selectAll("*").remove();if(e.terminfo.description){t.dom.details.append("div").style("padding-top","20px").style("padding-bottom","10px").style("font-weight","bold").text("Description");for(const i of e.terminfo.description){t.renderDetail(i,t.dom.details.append("div").style("padding-bottom","3px"))}}};t.renderDetail=function(e,i){if(Array.isArray(e.value)){i.append("span").html("<i>"+e.label+"</i>");const s=i.append("div").style("padding-left","20px");for(const i of e.value){i.label="- "+i.label;t.renderDetail(i,s.append("div"))}}else{i.html("<i>"+e.label+":"+"</i>"+"&nbsp;"+e.value)}}}function l(t){t.toggleDescription=function(){t.state.isVisible=!t.state.isVisible;t.main({isVisible:t.state.isVisible})}}export{o as termInfoInit};

package/dist/tk-75566002.js

@@ -1 +0,0 @@
-import{M as t,B as e,ap as s,aq as a,ar as n,z as i,an as o,as as r,at as l,bL as c,I as d,V as f,u as m,b as u,ak as p,D as h,n as g,r as w,aN as b,d as k,be as x,aG as v,W as y,aQ as _,aR as j,aP as M,bE as A,bD as S}from"./app-a8c4854a.js";import{l as q}from"./block.legend-b2987cd9.js";import{s as C,m as z}from"./regression.results-c186a8dc.js";import{a as L}from"./axisstyle-fac7f76b.js";import{c as $,b as N}from"./axis-747c801e.js";import{r as R}from"./table-79e3e776.js";import{d as O}from"./arc-3d6751aa.js";import{m as I}from"./block-dcb130fb.js";import{t as D}from"./downloadTextfile-5723af95.js";import{T}from"./toggleButtons-002aeda1.js";import{m as B}from"./radiobutton-09bff425.js";import{v as F}from"./vcf-c4a23924.js";import{n as U}from"./niceNumLabels-6cfc1508.js";import{f as G}from"./roundValue-b0d0517c.js";import{r as P}from"./rehydrateFilter-12d118cb.js";const E="white",H="black";const V="Unannotated";function W(e,s){if(!e.legend)e.legend={};e.legend.tip=new t({padding:"0px"});const[a,n,i]=q(s,e.name);e.legend.headTd=i;e.tr_legend=a;const o=n.append("table").style("border-spacing","5px").style("border-collapse","separate");e.legend.table=o;K(e,s);Q(e);X(e);J(e);nt(e);lt(e);dt(e)}function K(t,e){if(!t.legend.mclass)t.legend.mclass={};if(!t.legend.mclass.hiddenvalues)t.legend.mclass.hiddenvalues=new Set;t.legend.mclass.row=t.legend.table.append("tr");t.legend.mclass.row.append("td").style("text-align","right").style("opacity",.7).text(e.mclassOverride?e.mclassOverride.className||"Mutation":"Mutation");t.legend.mclass.holder=t.legend.mclass.row.append("td")}function Q(t){if(!t.variantShapeName)return;const e=t.legend.table.append("tr").append("td").attr("colspan",2);const s=t.legend.variantShapeName={};{const a=e.append("div");a.append("span").html(`<svg style="display:inline-block" width=12 height=12>\n\t\t\t<circle cx=6 cy=6 r=6 fill=gray></circle></svg> n=`);s.dotCount=a.append("span");if(t.variantShapeName.dot)a.append("span").text(", "+t.variantShapeName.dot);s.dotDiv=a}{const a=e.append("div");a.append("span").html(`<svg style="display:inline-block" width=12 height=12>\n\t\t\t<path d="M 6 0 L 0 12 h 12 Z" fill=gray></path></svg> n=`);s.triangleCount=a.append("span");if(t.variantShapeName.triangle)a.append("span").text(", "+t.variantShapeName.triangle);s.triangleDiv=a}{const a=e.append("div");a.append("span").html(`<svg style="display:inline-block" width=13 height=13>\n\t\t\t<circle cx=6.5 cy=6.5 r=6 stroke=gray fill=none></circle></svg> n=`);s.circleCount=a.append("span");if(t.variantShapeName.circle)a.append("span").text(", "+t.variantShapeName.circle);s.circleDiv=a}}function X(t){if(!t.mds.bcf?.info)return;const e=[];for(const s in t.mds.bcf.info){const a=t.mds.bcf.info[s];if(a.categories){e.push(s)}}if(!e.length)return;if(!t.legend.bcfInfo)t.legend.bcfInfo={};for(const s of e){const e=t.legend.table.append("tr");e.append("td").style("text-align","right").style("opacity",.7).text(t.mds.bcf.info[s].name||s);t.legend.bcfInfo[s]={hiddenvalues:new Set,row:e,holder:e.append("td")}}}function J(t){if(!t.mds.bcf?.format)return;const e=[];for(const s in t.mds.bcf.format){if(t.mds.bcf.format[s].isFilter)e.push(s)}if(!e.length)return;if(!t.legend.formatFilter)t.legend.formatFilter={};for(const s of e){const e=t.legend.table.append("tr");e.append("td").style("text-align","right").style("opacity",.7).text(t.mds.bcf.format[s].Description);t.legend.formatFilter[s]={hiddenvalues:new Set,row:e,holder:e.append("td")}}}function Y(t,e){if(!e.legend.formatFilter)return;if(!t.skewer){console.log("data.skewer[] is not present and cannot show INFO legend");return}for(const s in e.legend.formatFilter){e.legend.formatFilter[s].holder.selectAll("*").remove();const a=new Map;let n=0;for(const e of t.skewer){if(!e.formatK2count?.[s])continue;for(const t in e.formatK2count[s].v2c){a.set(t,e.formatK2count[s].v2c[t]+(a.get(t)||0))}n+=e.formatK2count[s].unannotatedCount||0}const i=[...a];i.sort(((t,e)=>e[1]-t[1]));if(n){i.push([V,n])}for(const[t,a]of i){const n=e.legend.formatFilter[s].holder.append("div").attr("class","sja_clb").style("display","inline-block").on("click",(()=>{e.legend.tip.clear().showunder(n.node()).d.append("div").attr("class","sja_menuoption").text("Hide").on("click",(()=>{e.legend.formatFilter[s].hiddenvalues.add(t);Z(e)}));e.legend.tip.d.append("div").attr("class","sja_menuoption").text("Show only").on("click",(()=>{for(const t of i){e.legend.formatFilter[s].hiddenvalues.add(t[0])}e.legend.formatFilter[s].hiddenvalues.delete(t);Z(e)}));if(e.legend.formatFilter[s].hiddenvalues.size){e.legend.tip.d.append("div").attr("class","sja_menuoption").text("Show all").on("click",(()=>{e.legend.formatFilter[s].hiddenvalues.clear();Z(e)}))}}));n.append("div").style("display","inline-block").attr("class","sja_mcdot").style("background","#aaa").style("margin-right","5px").html(a>1?a:"&nbsp;");n.append("div").style("display","inline-block").text(t)}for(const t of e.legend.formatFilter[s].hiddenvalues){let a=false;e.legend.formatFilter[s].holder.append("div").style("display","inline-block").attr("class","sja_clb").style("text-decoration","line-through").style("opacity",.7).text(t).on("click",(async()=>{if(a)return;a=true;e.legend.formatFilter[s].hiddenvalues.delete(t);Z(e)}))}}}function Z(t){t.legend.tip.hide();t.load()}function tt(t,e,s){if(!e.legend){return}e.legend.mclass.currentData=t.mclass2variantcount;at(e);et(t,e);st(t,e);Y(t,e);ot(t,e);ct(e);ft(e)}function et(t,e){if(!e.variantShapeName)return;let s=0,a=0,n=0;for(const e of t.skewer){if(e.shapeTriangle)a++;else if(e.shapeCircle)n++;else s++}const i=e.legend.variantShapeName;i.dotDiv.style("display",s?"block":"none");i.triangleDiv.style("display",a?"block":"none");i.circleDiv.style("display",n?"block":"none");i.dotCount.text(s);i.triangleCount.text(a);i.circleCount.text(n)}function st(t,e){if(!e.legend.bcfInfo)return;if(!t.skewer){console.log("data.skewer[] is not present and cannot show INFO legend");return}for(const s in e.legend.bcfInfo){e.legend.bcfInfo[s].holder.selectAll("*").remove();if(e.mds.bcf.info[s].Type=="String"){const a=new Map;for(const e of t.skewer){const t=s in e.info?e.info[s]:V;if(Array.isArray(t)){for(const e of t){a.set(e,1+(a.get(e)||0))}}else{a.set(t,1+(a.get(t)||0))}}const n=[...a].sort(((t,e)=>e[1]-t[1]));for(const[t,a]of n){const i=e.legend.bcfInfo[s].holder.append("div").attr("class","sja_clb").style("display","inline-block").on("click",(()=>{e.legend.tip.clear().showunder(i.node()).d.append("div").attr("class","sja_menuoption").text("Hide").on("click",(()=>{e.legend.bcfInfo[s].hiddenvalues.add(t);Z(e)}));e.legend.tip.d.append("div").attr("class","sja_menuoption").text("Show only").on("click",(()=>{for(const t of n){e.legend.bcfInfo[s].hiddenvalues.add(t[0])}e.legend.bcfInfo[s].hiddenvalues.delete(t);Z(e)}));if(e.legend.bcfInfo[s].hiddenvalues.size){e.legend.tip.d.append("div").attr("class","sja_menuoption").text("Show all").on("click",(()=>{e.legend.bcfInfo[s].hiddenvalues.clear();Z(e)}))}const a=e.mds.bcf.info[s].categories?.[t]?.desc;if(a){e.legend.tip.d.append("div").style("padding","10px").style("font-size",".8em").style("width","150px").html(a)}}));i.append("div").style("display","inline-block").attr("class","sja_mcdot").style("background",e.mds.bcf.info[s].categories?.[t]?.color||E).html(a>1?a:"&nbsp;");i.append("div").style("display","inline-block").style("color",e.mds.bcf.info[s].categories?.[t]?.color||H).html("&nbsp;"+e.mds.bcf.info[s].categories?.[t]?.label||t)}for(const t of e.legend.bcfInfo[s].hiddenvalues){let a=false;e.legend.bcfInfo[s].holder.append("div").style("display","inline-block").attr("class","sja_clb").style("text-decoration","line-through").style("opacity",0).text(t).on("click",(async()=>{if(a)return;a=true;e.legend.bcfInfo[s].hiddenvalues.delete(t);Z(e)}))}}}}function at(t){if(!t.legend.mclass.currentData||t.legend.mclass.currentData.length==0)return;t.legend.mclass.holder.selectAll("*").remove();const c=[],d=[];for(const[e,s]of t.legend.mclass.currentData){const a={k:e,count:s};if(t.legend.mclass.hiddenvalues.has(e)){d.push(a)}else{c.push(a)}}c.sort(((t,e)=>e.count-t.count));d.sort(((t,e)=>e.count-t.count));for(const e of t.legend.mclass.hiddenvalues){if(!d.find((t=>t.k==e))){d.push({k:e})}}for(const f of c){let m,u,p="#858585";if(Number.isInteger(f.k)){m=e[f.k];if(f.k==s){u="Copy number variation."}else if(f.k==a){u="Loss of heterozygosity."}else if(f.k==n){p=i[o].color;u="Internal tandem duplication."}else if(f.k==r){u="Structural variation of DNA."}else if(f.k==l){u="Fusion gene from RNA-seq."}}else{m=i[f.k].label;p=i[f.k].color;u=i[f.k].desc}const h=t.legend.mclass.holder.append("div").attr("class","sja_clb").style("display","inline-block").on("click",(e=>{t.legend.tip.clear().showunder(e.target).d.append("div").attr("class","sja_menuoption").text("Hide").on("click",(()=>{t.legend.mclass.hiddenvalues.add(f.k);Z(t)}));t.legend.tip.d.append("div").attr("class","sja_menuoption").text("Show only").on("click",(()=>{for(const e of c){t.legend.mclass.hiddenvalues.add(e.k)}t.legend.mclass.hiddenvalues.delete(f.k);Z(t)}));if(d.length){t.legend.tip.d.append("div").attr("class","sja_menuoption").text("Show all").on("click",(()=>{t.legend.mclass.hiddenvalues.clear();Z(t)}))}t.legend.tip.d.append("div").style("padding","10px").style("font-size",".8em").style("width","150px").html(u)}));h.append("div").style("display","inline-block").attr("class","sja_mcdot").style("background",p).html(f.count>1?f.count:"&nbsp;");h.append("div").style("display","inline-block").style("color",p).html("&nbsp;"+m)}for(const s of d){let a=false;t.legend.mclass.holder.append("div").style("display","inline-block").attr("class","sja_clb").style("text-decoration","line-through").style("opacity",.7).text((s.count?"("+s.count+") ":"")+(Number.isInteger(s.k)?e[s.k]:i[s.k].label)).on("click",(async e=>{if(a)return;a=true;t.legend.mclass.hiddenvalues.delete(s.k);e.target.innerHTML="Updating...";await t.load()}))}}function nt(t,e){if(!t.mds.queries?.snvindel?.skewerRim)return;const s=t.legend.skewerRim={};if(!t.mds.queries.snvindel.skewerRim.hiddenvaluelst)t.mds.queries.snvindel.skewerRim.hiddenvaluelst=[];s.row=t.legend.table.append("tr");s.headerTd=s.row.append("td").style("text-align","right").style("opacity",.7);s.holder=s.row.append("td")}function it(t){const e=t.mds.queries.snvindel.skewerRim;if(e.type=="format"){if(!e.formatKey)throw"skewerRim.formatKey missing";return t.mds.bcf?.format?.[e.formatKey]?.Description||e.formatKey}return"unknown skewerRim.type"}function ot(t,e){const s=e.mds.queries?.snvindel?.skewerRim;if(!s)return;let a=0,n=0;for(const e of t.skewer){const t=e.rim1count||0;a+=t;n+=e.occurrence-t}const i=e.legend.skewerRim;i.headerTd.text(it(e));i.holder.selectAll("*").remove();if(a>0){i.holder.append("div").attr("class","sja_clb").style("display","inline-block").html(`${rt(1)}${s.rim1value}, n=${a}`).on("click",(t=>{e.legend.tip.clear().showunder(t.target).d.append("div").attr("class","sja_menuoption").text("Hide").on("click",(()=>{s.hiddenvaluelst.push(s.rim1value);Z(e)}))}))}if(n>0){i.holder.append("div").attr("class","sja_clb").style("display","inline-block").html(`${rt()}${s.noRimValue}, n=${n}`).on("click",(t=>{e.legend.tip.clear().showunder(t.target).d.append("div").attr("class","sja_menuoption").text("Hide").on("click",(()=>{s.hiddenvaluelst.push(s.noRimValue);Z(e)}))}))}for(const t of s.hiddenvaluelst){let a=false;i.holder.append("div").style("display","inline-block").attr("class","sja_clb").style("text-decoration","line-through").style("opacity",.7).text(t).on("click",(async n=>{if(a)return;a=true;s.hiddenvaluelst.splice(s.hiddenvaluelst.indexOf(t),1);n.target.innerHTML="Updating...";await e.load()}))}}function rt(t){return'<svg width="19" height="19" style="margin-right: 5px;">'+'<circle cx="7" cy="12" r="7" fill="#b1b1b1"></circle>'+(t==1?'<path d="M6.735557395310443e-16,-11A11,11 0 0,1 11,0L9,0A9,9 0 0,0 5.51091059616309e-16,-9Z" transform="translate(7,12)" fill="#858585" stroke="none"></path>':t==2?"":"")+"</svg>"}function lt(t,e){if(!t.mds.queries?.ld)return;t.mds.queries.ld.colorScale=c(t.mds.queries.ld.overlay.color_0,t.mds.queries.ld.overlay.color_1);const s=t.legend.ld={};s.row=t.legend.table.append("tr");s.headerTd=s.row.append("td").style("text-align","right").style("opacity",.7);s.holder=s.row.append("td");s.showHolder=s.holder.append("div").style("display","none");C(s.showHolder,t.mds.queries.ld.colorScale);s.showHolder.append("span").text("Cancel overlay").style("font-size",".7em").attr("class","sja_clbtext").on("click",(()=>{delete t.mds.queries.ld.mOverlay;if(t.skewer?.hlssmid)delete t.skewer.hlssmid;t.load()}))}function 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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-242f4615.js").then((function(t){return t.l}));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 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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; 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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-e49cb70b.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-e49cb70b.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-43e18d2f.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} 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qe(t){t.skewer.hlBoxG.selectAll("*").remove();if(!t.skewer.hlssmid)return;t.skewer.hlBoxG.filter((e=>{if(e.mlst){return e.mlst.find((e=>t.skewer.hlssmid.has(e.ssm_id)))}return t.skewer.hlssmid.has(e.ssm_id)})).append("rect").attr("x",(t=>-t.radius)).attr("y",(t=>-t.radius)).attr("width",(t=>t.radius*2)).attr("height",(t=>t.radius*2)).attr("stroke",t.skewer.hlBoxColor).attr("stroke-width",(t=>t.radius>10?1.5:1)).attr("fill","none").attr("class","sja_mds3_skewer_ssmhlbox")}const Ce=4;function ze(t,e,s){Le(e,t,s);const a=new Map;for(const t of e){if(t.__x==undefined)continue;if(!a.has(t.__x)){a.set(t.__x,[])}a.get(t.__x).push(t)}const n=[];if(s.exonsf>=Ce){for(const[t,e]of a){n.push({chr:e[0].chr,pos:e[0].pos,mlst:e,x:t})}}else{if(s.usegm&&s.usegm.coding&&s.gmmode!=x.genomic){const t=new Map;for(const[e,n]of a){if(n[0].chr!=s.usegm.chr){continue}let i=undefined;for(const t of n){if(Number.isFinite(t.aapos))i=t.aapos}if(i==undefined){i=v(n[0].pos,s.usegm).aapos}if(i==undefined){console.error("data item cannot map to aaposition");console.log(n[0]);continue}a.delete(e);if(!t.has(i)){t.set(i,[])}let o=true;for(const e of t.get(i)){if(Math.abs(e[0].__x-n[0].__x)<=s.exonsf*3){for(const t of n){e.push(t)}o=false;break}}if(o){t.get(i).push(n)}}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}n.push({chr:t[0].chr,pos:e.pos,mlst:t,x:t[0].__x})}}}const t=[];const e=2;for(const[s,n]of a){const a=Math.floor(s/e);if(!t[a]){t[a]=[]}t[a]=[...t[a],...n]}for(const e of t){if(!e)continue;const t=e.reduce(((t,e)=>t+e.__x),0);n.push({isbin:true,chr:e[0].chr,pos:e[0].pos,mlst:e,x:t/e.length})}}n.sort(((t,e)=>t.x-e.x));return n}function Le(t,e,s){let a=0,n=0;const i=[];const o=[];for(const e of t){delete 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Re(t,e){t.menutip.d.append("div").text("List").attr("class","sja_menuoption").attr("data-testid","sja_list_menuoption").style("border-radius","0px").on("click",(()=>{Oe(t,e)}));if(t.skewer){if(t.skewer.hlssmid){t.menutip.d.append("div").text("Cancel highlight").style("border-radius","0px").attr("class","sja_menuoption").on("click",(()=>{delete t.skewer.hlssmid;t.skewer.hlBoxG.selectAll("*").remove();const s=t.skewer.viewModes.find((t=>t.inuse));if(s.type=="skewer"){ye(t,e)}else if(s.type=="numeric");else{throw"unknown mode type"}t.menutip.hide()}))}const s=t.skewer.viewModes.find((t=>t.inuse));if(s.type=="skewer"){const s=t.skewer.data.reduce(((t,e)=>t+e.showmode),0);if(s>0){t.menutip.d.append("div").text("Collapse").attr("class","sja_menuoption").attr("data-testid","sja_collapse_menuoption").style("border-radius","0px").on("click",(()=>{Se(t.skewer.data,t);t.menutip.hide()}))}else 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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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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 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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 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$s=Object.freeze({__proto__:null,loadTk:As,rangequery_rglst:Cs});export{te as d,mt as g,Ee as m,$s as t};

package/dist/tp.ui-02911b56.js

@@ -1 +0,0 @@
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i)){i[s]={mcount:0,isoform:{}};c.push(s)}i[s].mcount+=t.dsset[e].bulkdata[s].length;for(const n of t.dsset[e].bulkdata[s]){const t=n.isoform;if(!t)continue;i[s].isoform[t]=1}}}let h=Math.min(100,c.length);const x=new Set(["Intron","P","S","E",g,y]);const w={};const k={};let v=true;n.html(c.length+' <span style="font-size:.8em">GENES</span>').attr("title","A summary table of gene by variant type, order by number of hits in descending order.");const j=o.append("div");const _=t=>{b(j,t)};const z=o.append("div").style("margin-bottom","8px");z.append("button").style("margin-right","10px").text("Configure").on("click",(()=>{if(R.style("display")=="block"){d(R)}else{f(R)}}));z.append("button").style("margin-right","10px").text("Download").on("click",(()=>{const t=G();m("Gene summary",[{text:t}])}));z.append("input").attr("type","text").attr("size",10).attr("placeholder","Find gene").style("margin","0px 20px 0px 5px").on("keyup",(e=>{let s=e.target.value;if(s==""){M.hide();return}if(t.geneToUpper){s=s.toUpperCase()}if(e.code=="Enter"){M.hide();e.target.value="";if(s in i){W(s)}return}const n=[];for(const t in i){if(t.indexOf(s)==0){n.push({name:t,count:i[t].mcount})}}if(n.length==0){M.hide();return}n.sort(((t,e)=>e.count-t.count));M.clear().showunder(e.target);for(let t=0;t<Math.min(30,n.length);t++){const e=n[t].name;const s=M.d.append("div").attr("class","sja_menuoption_y").on("click",(()=>{W(e)}));s.append("span").text(e);s.append("span").style("font-size",".7em").text(n[t].count)}}));z.append("a").attr("href","https://docs.google.com/document/d/1NrH1H-FUWJtEKLk69V-k8uaYHOr9YO2obM9ZLZslEQ0/edit?usp=sharing").attr("target","_blank").text("Help");const E=o.append("div").style("border","solid 1px #ccc").style("margin","10px 0px");const R=E.append("div").style("display","none").style("background-color","#f1f1f1");const S=140;const L=E.append("div").style("padding-top",S+"px").style("position","relative");const T=L.append("div").style("overflow-y","scroll").style("height","400px").style("resize","vertical");const N=T.append("table").style("border-spacing","1px").style("border-collapse","separate");const C=R.append("div").style("padding","10px").style("border-bottom","dashed 1px #ccc");const O=R.append("div").style("padding","10px").style("border-bottom","dashed 1px #ccc");const B=R.append("div").style("padding","10px").style("border-bottom","dashed 1px #ccc");const H=C.append("span").style("padding-right","10px").text("Showing "+(h<c.length?"top "+h+" genes":"all genes"));C.append("button").text("more").on("click",(()=>{h=Math.min(c.length,h+10);H.text("Showing "+(h<c.length?"top "+h:"all genes"));G()}));C.append("button").text("less").on("click",(()=>{h=Math.max(1,h-10);H.text("Showing "+(h<c.length?"top "+h:"all genes"));G()}));O.append("span").text("Show subset").style("padding-right","10px");const I=O.append("textarea").attr("rows",1).attr("cols",20).attr("placeholder","enter gene names").style("margin-right","10px");O.append("button").text("Submit").on("click",(()=>{const e=I.property("value").trim();if(e=="")return;const s=e.split(/[\s\t\n]+/),n=[],o=[];for(const e of s){if(e=="")continue;const s=t.geneToUpper?e.trim().toUpperCase():e.trim();if(s in i){n.push(s)}else{o.push(e)}}if(o.length){_("No match found for "+o.join(", "))}if(n.length==0)return;c=n;h=n.length;G()}));O.append("button").text("Use default").on("click",(()=>{c=[];for(const t in i){c.push(t)}h=Math.min(100,c.length);G()}));B.append("span").html("Noncoding mutation visibility:&nbsp;");const J=B.append("select").on("change",(()=>{v=!v;for(const t of F){if(!t.atlst){continue}for(const e of t.atlst){if(!e.ismclass)continue;if(v){e.hide=false;continue}e.hide=x.has(e.key)}}G()}));J.append("option").text("show").attr("value","y");J.append("option").text("hide").attr("value","n");B.append("p").style("font-size",".8em").style("color","#858585").text("Including: silent, splice_region, exon, UTR, and 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t=n.sample;if(t){if(!v&&x.has(n.class))continue;if(!(t in s)){s[t]=0}s[t]++}}}const n=[];for(const t in s){n.push({name:t,size:s[t]})}const o=e.target.getBoundingClientRect();A(n,"#76B38C","Mutation burden"+(v?"":", excluding noncoding mutations"),o)}))}}R.append("div").style("padding","10px").style("border-bottom","dashed 1px #ccc").text("Click on a column header to rank genes.");const F=[{label:"Name",isgenename:true}];let V=true;let q=0;for(const s in t.dsset){q++;const n={name:t.dsset[s].label,atlst:[{label:"# mutation",get:e=>{if(!(e in t.dsset[s].bulkdata))return 0;if(v){return t.dsset[s].bulkdata[e].length}let n=0;for(const o of t.dsset[s].bulkdata[e]){if(!x.has(o.class))n++}return n},rotate:true,descend:true,sort:V}]};V=false;if(t.dsset[s].hassample){n.atlst.push({label:"# sample",get:e=>{if(!(e in t.dsset[s].bulkdata))return 0;const n=new Set;for(const o of t.dsset[s].bulkdata[e]){if(!v&&x.has(o.class))continue;if(!o.sample)continue;n.add(o.sample)}return 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package/dist/tslib.es6-1f85f553.js

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package/dist/tvs.density-026fca97.js

@@ -1 +0,0 @@
-import{b as t}from"./brush-c386fe3d.js";import{c as n}from"./roundValue-b0d0517c.js";import{d as e}from"./app-a8c4854a.js";import"./pointer-c7475677.js";import"./nodrag-2c046d31.js";import"./tslib.es6-1f85f553.js";import"path";function s(t,n){const s=t.num_obj.brushes;const r=t.num_obj.density_data.maxvalue;const a=t.num_obj.density_data.minvalue;const u=(r-a)/10;const i=t.tvs.term.type=="integer"?Math.floor(u):u;for(const[e,o]of t.num_obj.ranges.entries()){const t=s.find((t=>t.orig===o));let e;if(!t){e={orig:o,range:JSON.parse(JSON.stringify(o))};s.push(e)}else{e=t}if(o.start===""){if(n=="center")e.range.start=a+i*4;else e.range.start=a+i*8}if(o.stop===""){if(n=="center")e.range.stop=a+i*6;else e.range.stop=Math.floor(r)}}const d=t.num_obj.brush_g.selectAll(".range_brush").data(s,(t=>s.indexOf(t)));d.exit().remove();d.each((function(t,n){e(this).selectAll(".overlay").style("pointer-events","all")}));d.enter().append("g").attr("class","range_brush").each((function(n,e){o(t,this,n)}))}function o(n,s,o){if(!o.elem)o.elem=e(s);const a=o.range;const u=n.num_obj.plot_size;const i=n.num_obj.xscale;const d=n.num_obj.density_data.maxvalue;const l=n.num_obj.density_data.minvalue;o.d3brush=t().extent([[0,0],[u.width,u.height]]).on("brush",(function(t,e){const s=t.selection;if(!s)return;const u=o.rangeInput.getRange();if(u.value!=undefined){o.range=u;return}r(i,s,a,u,l,d,n.tvs.term.type);const c=a.startunbounded?"":u.startinclusive?`${a.start} <=`:`${a.start} <`;const p=a.stopunbounded?"":u.stopinclusive?`<= ${a.stop}`:`< ${a.stop}`;o.rangeInput.getInput().node().value=`${c} x ${p}`})).on("end",(function(){o.elem.selectAll(".overlay").style("pointer-events","none")}));const c=a.startunbounded?l:a.start;const p=a.stopunbounded?d:a.stop;o.init=()=>{if(a.value==undefined)o.elem.call(o.d3brush).call(o.d3brush.move,[c,p].map(i))};if(a.startunbounded)delete a.start;if(a.stopunbounded)delete a.stop;o.elem.selectAll(".selection").style("fill",o.orig.start===""&&o.orig.stop===""||JSON.stringify(a)!=JSON.stringify(o.orig)?"#23cba7":"#777777")}function r(t,e,s,o,r,u,i){s.start=a(t,e[0]);s.stop=a(t,e[1]);const d=n(Number(r));const l=n(Number(u));s.startunbounded=d==s.start&&o.startunbounded;s.stopunbounded=l==s.stop&&o.stopunbounded;if(i=="integer"){s.start=s.startunbounded?"":Math.round(s.start);s.stop=s.stopunbounded?"":Math.round(s.stop)}}function a(t,e){let s=Number(t.invert(e));return n(s)}function u(t,n="end",e){const o={start:"",stop:"",index:t.tvs.ranges.length};t.num_obj.ranges.push(o);const r={orig:o,range:JSON.parse(JSON.stringify(o))};t.num_obj.brushes.push(r);s(t,n);if(e)e();r.init()}export{s as addBrushes,u as addNewBrush,r as updateTempRanges};

package/dist/tvs.numeric-3f3d9919.js

@@ -1 +0,0 @@
-import{V as t,I as e,d as n}from"./app-a8c4854a.js";import{addBrushes as s,addNewBrush as a}from"./tvs.density-026fca97.js";import{v as r}from"./violinRenderer-8215f40d.js";import{n as i}from"./niceNumLabels-6cfc1508.js";import"./brush-c386fe3d.js";import"./pointer-c7475677.js";import"./nodrag-2c046d31.js";import"./roundValue-b0d0517c.js";import"./tslib.es6-1f85f553.js";import"path";import"./axis-747c801e.js";import"./line-264f8f9e.js";import"./constant-426a1483.js";import"./basis-3870f5ba.js";class o{constructor(t,e,n){this.input=t.append("input").attr("name","rangeInput").attr("title",`leave blank for the allowed minimum value`).style("width","250px").style("margin","3px 5px").on("change",(()=>{try{this.parseRange()}catch(t){alert(t);this.setRange()}}));this.setRange(e);this.callback=n}getInput(){return this.input}parseRange(){const t=this.input.node().value;const e=l(t);if(this.range?.min!=undefined){if(!e.startunbounded&&this.range?.min>e.start)throw"Invalid start value < minimum allowed";if(!e.stopunbounded&&this.range?.min>=e.stop)throw"Invalid stop value >= minimum allowed"}if(this.range?.max!=undefined){if(!e.stopunbounded&&this.range?.max<e.stop)throw"Invalid stop value > maximum allowed";if(!e.startunbounded&&e.start>=this.range?.max)throw"Invalid start value >= maximum allowed"}this.range=e;this.callback(e);return e}getRange(){return this.range}setRange(t){if(!t)t=this.range;else this.range=t;const e=t.start!=undefined?`${t.start} <=`:"";const n=t.stop!=undefined?`<= ${t.stop}`:"";this.input.node().value=t.value!=undefined?` x=${t.value} `:`${e} x ${n}`}}function l(t){if(!t)throw"Empty range";const e=t.replace(/\s/g,"").split("x");let n,s,a,r,i;if(e[0])p(e[0]);if(e[1])p(e[1]);if(i!=undefined)return{value:i,label:`x = ${i}`};const o=n===undefined;const l=s===undefined;if(!o&&!l&&n>s)throw"start must be lower than stop";return{start:n,stop:s,value:i,startinclusive:a,stopinclusive:r,startunbounded:o,stopunbounded:l};function p(t){const e="[+-]?\\d+(\\.\\d+)?";if(new RegExp(`^${e}<$`).test(t)||new RegExp(`^>${e}$`).test(t)){n=parseFloat(t.match(e));a=false}else if(new RegExp(`^${e}<=$`).test(t)||new RegExp(`^>=${e}$`).test(t)){n=parseFloat(t.match(e));a=true}else if(new RegExp(`^${e}>$`).test(t)||new RegExp(`^<${e}$`).test(t)){s=parseFloat(t.match(e));r=false}else if(new RegExp(`^${e}>=$`).test(t)||new RegExp(`^<=${e}$`).test(t)){s=parseFloat(t.match(e));r=true}else if(new RegExp(`^${e}=$`).test(t)||new RegExp(`^=${e}$`).test(t)){i=parseFloat(t.match(e));r=true;a=true}else throw`Could not parse expression '${t}'`}}const p={type:"numeric",term_name_gen:u,get_pill_label:d,getSelectRemovePos:c,fillMenu:f,setTvsDefaults:b};function u(t){const e=t.term.name;return e.length<26?e:'<label title="'+e+'">'+e.substring(0,24)+"..."+"</label>"}function d(t){if(t.ranges.length==1){const e=t.ranges[0];if("value"in e){if(e.label)return{txt:e.label};if(t.term.values&&t.term.values[e.value]&&t.term.values[e.value].label)return{txt:t.term.values[e.value].label};console.error(`key "${e.value}" not found in values{} of ${t.term.name}`);return{txt:e.value}}return{txt:m(e,t.term)}}return{txt:t.ranges.length+" intervals"}}function m(e,n){const s='<span style="font-family:Times;font-style:italic;font-size:1em; vertical-align:top">x</span>';if(e.startunbounded&&e.stopunbounded){const t=(t="")=>`<span style='vertical-align: middle; font-size:1.1em; line-height: 0.9em'>${t}∞</span>`;const e=`<span style='vertical-align: top; font-size: 0.9em'>&lt;</span>`;return`<span>${t("﹣")} ${e} ${s} ${e} ${t("﹢")}</span>`}const a=n.valueConversion;if(e.startunbounded)return`${s} ${e.stopinclusive?"&le;":"&lt;"} ${a?t(e.stop,a.fromUnit,a.toUnit,a.scaleFactor):e.stop}`;if(e.stopunbounded)return`${s} ${e.startinclusive?"&ge;":"&gt;"} ${a?t(e.start,a.fromUnit,a.toUnit,a.scaleFactor):e.start}`;let r,o;if(a){r=t(e.start,a.fromUnit,a.toUnit,a.scaleFactor);o=t(e.stop,a.fromUnit,a.toUnit,a.scaleFactor)}else{[r,o]=i([e.start,e.stop])}return`${r} \n\t\t\t${e.startinclusive?"&le;":"&lt;"}\n\t\t\t${s}\n\t\t\t${e.stopinclusive?"&le;":"&lt;"}\n\t\t\t${o}`}function c(t,e){return t-e.ranges.slice(0,t).filter((t=>t.start||t.stop)).length}async function f(t,n,i){const o=n.append("div");t.num_obj={};t.num_obj.num_div=o.append("div").attr("class","num_div").style("padding","5px").style("color","#000");t.num_obj.plot_size={width:500,height:100,xpad:10,ypad:20};if(typeof t.opts.vocabApi.getViolinPlotData=="function"){try{const e=await t.opts.vocabApi.getViolinPlotData({tw:{term:i.term,q:{mode:"continuous"}},filter:t.filter,svgw:t.num_obj.plot_size.width/window.devicePixelRatio},t.opts.getCategoriesArguments);if(e.error)throw e.error;t.num_obj.density_data=g(e)}catch(t){throw t}}else{t.num_obj.density_data={}}if(t.num_obj.density_data.error)throw t.num_obj.density_data.error;if(!t.num_obj.density_data.density||!t.num_obj.density_data.density.length){y(t,i);return}t.vr=new r(t.num_obj.num_div,t.num_obj.density_data,t.num_obj.xpad,t.num_obj.ypad);t.vr.render();t.num_obj.svg=t.vr.svg;t.num_obj.range_table=t.num_obj.num_div.append("table").style("table-layout","fixed").style("border-collapse","collapse");const l=[];for(const[t,e]of i.ranges.entries()){e.index=t;l.push(e)}t.num_obj.brush_g=t.num_obj.svg.append("g").attr("transform",`translate(${t.num_obj.plot_size.xpad}, ${t.num_obj.plot_size.ypad})`).attr("class","brush_g");const p=t.num_obj.density_data.maxvalue;const u=t.num_obj.density_data.minvalue;t.num_obj.xscale=e().domain([u,p]).range([t.num_obj.plot_size.xpad,t.num_obj.plot_size.width+t.num_obj.plot_size.xpad]);t.num_obj.ranges=l;t.num_obj.brushes=[];s(t);_(t);t.num_obj.num_div.append("div").style("width","100px").attr("class","add_range_btn sja_menuoption").style("border-radius","13px").style("padding","7px 6px").style("margin","5px").style("margin-left","20px").style("text-align","center").style("font-size",".8em").text("Add a Range").on("click",(()=>{const e=()=>_(t);a(t,l.length?"end":"center",e)}));if(!l.length){const e=()=>_(t);a(t,"center",e)}t.num_obj.brushes.forEach((t=>t.init()));await x(t,i,n)}function g(t){const e=t.plots[0]||{plotValueCount:0,biggestBin:0};const n={minvalue:t.min,maxvalue:t.max,samplecount:e.plotValueCount,densityMax:e.density.densityMax,densityMin:e.density.densityMin,density:e.density.bins,valuesImg:e.src};return n}function b(t){if(!t.ranges)t.ranges=[]}function y(t,e){const n=e.term.range||{};const s=e.ranges&&e.ranges[0]?e.ranges[0]:n;const a=t.num_obj.num_div;a.selectAll("*").remove();a.append("div").style("padding","5px").style("font-weight",600).html(e.term.name);const r={};const i=a.append("table");const l=i.append("tr");l.append("td").html("Range");r.equation_td=l.append("td");s.min="min"in e.term?e.term.min:null;s.max="max"in e.term?e.term.max:null;r.rangeInput=new o(r.equation_td,s,p);r.apply_btn=l.append("td").attr("class","sja_filter_tag_btn sjpp_apply_btn").style("border-radius","13px").style("margin","5px").style("margin-left","10px").style("text-align","center").style("font-size",".8em").style("text-transform","uppercase").text("apply").on("click",(async()=>{r.rangeInput.parseRange()}));function p(){t.dom.tip.hide();t.opts.callback({term:e.term,ranges:[r.rangeInput.getRange()]})}}function _(t){const e=t.num_obj.brushes;const s=t.num_obj.range_table.selectAll(".range_div").data(e);s.exit().each((function(){n(this).style("opacity",1).transition().duration(100).style("opacity",0).remove()}));s.enter().append("tr").attr("class","range_div").style("white-space","nowrap").style("padding","2px").transition().duration(200).each((function(e,n){h(t,this,e,n)}))}function h(t,e,a,r){if(!a.range_tr)a.range_tr=n(e);const i=a.range_tr;const l=t.num_obj.xscale;i.append("td").append("td").style("display","inline-block").style("margin-left","10px").style("padding","3px 10px").style("font-size",".9em").text("Range "+(r+1)+": ");a.equation_td=i.append("td").style("width","150px");a.rangeInput=new o(a.equation_td,a.range,p);u(t,a);if(r==0){t.num_obj.range_table.append("tr").attr("class","note_tr").append("td").attr("colspan","3").append("div").style("font-size",".8em").style("margin-left","20px").style("font-style","italic").style("color","#888").html("Option 1: Drag the rectangle to select a range. Overlapping ranges will be merged")}if(r==0){t.num_obj.range_table.append("tr").attr("class","note_tr").append("td").attr("colspan","3").append("div").style("font-size",".8em").style("margin-left","20px").style("font-style","italic").style("color","#888").html(`Option 2: Type in values to select a range. ${t.tvs.term.valueConversion?`Values are in the unit of ${t.tvs.term.valueConversion.fromUnit}`:""}.`)}async function p(e){try{a.range=e;const n=t.num_obj.density_data.minvalue;const s=t.num_obj.density_data.maxvalue;const r=e.value!=undefined?e.value:e.start!=undefined?e.start:n;const i=e.value!=undefined?e.value:e.stop!=undefined?e.stop:s;a.elem.call(a.d3brush).call(a.d3brush.move,[r,i].map(l))}catch(t){window.alert(t)}}function u(t,e){const n=e.range_tr.append("td");const a=e.range;e.apply_btn=n.append("td").attr("class","sja_filter_tag_btn sjpp_apply_btn").style("border-radius","13px").style("margin","5px").style("margin-left","10px").style("text-align","center").style("font-size",".8em").style("text-transform","uppercase").text("apply").on("click",(async()=>{t.dom.tip.hide();const n=e.rangeInput.parseRange();const s=JSON.parse(JSON.stringify(t.tvs));delete s.groupset_label;if(t.num_obj.ranges.length>1)s.ranges=v(t,n);else s.ranges[a.index]=n;try{w(s);t.opts.callback(s)}catch(t){alert(t)}}));n.append("td").attr("class","sja_filter_tag_btn sjpp_delete_btn").style("border-radius","13px").style("display",t.num_obj.ranges.length>1?"inline-block":"none").style("margin","5px").style("margin-left","10px").style("text-align","center").style("font-size",".8em").style("text-transform","uppercase").text("Delete").on("click",(async()=>{const e=JSON.parse(JSON.stringify(t.tvs));e.ranges.splice(a.index,1);t.num_obj.ranges.pop();t.num_obj.brushes.pop();t.num_obj.num_div.select(".note_tr").remove();s(t);_(t);if(e.ranges.length)t.opts.callback(e)}))}}function v(t,e){let n=JSON.parse(JSON.stringify(t.tvs.ranges));let s=false;for(const[t,a]of n.entries()){if(!a.value&&e.index!=t){if(e.start<=a.start&&e.stop>=a.stop){a.start=e.start;a.stop=e.stop;s=true}else if(e.start<=a.stop&&e.stop>=a.stop){a.stop=e.stop;s=true}else if(e.stop>=a.start&&e.start<=a.start){a.start=e.start;s=true}else if(e.start>=a.start&&e.stop<=a.stop){s=true}else if(e.startunbounded){if(e.stop>a.stop){a.stop=e.stop}delete a.start;a.startunbounded=true;s=true}else if(e.stopunbounded){if(e.start<a.start){a.start=e.start}delete a.stop;a.stopunbounded=true;s=true}}}if(s){if(e.index<=n.length-1)n.splice(e.index,1)}else{n=JSON.parse(JSON.stringify(t.tvs.ranges));if(e.index)n[e.index]=e;else n.push(e)}return n}async function x(t,e,n){if(!e.term.values){return}const s=await t.opts.vocabApi.getNumericUncomputableCategories(e.term,t.filter);const a=[];const r=s.lst?s.lst:s;for(const t of r){const n="key"in t?t.key:t.value;if(!("key"in t))t.key=n;if(!("value"in t))t.value=n;if(n in e.term.values){t.label=e.term.values[n].label;a.push(t)}}const i=a.sort(((t,e)=>e.samplecount-t.samplecount));const o=n.append("div").style("padding","5px").style("color","#000");const l=n=>{try{const s=JSON.parse(JSON.stringify(e));delete s.groupset_label;s.ranges=[...s.ranges.filter((t=>!("value"in t))),...n.map((t=>({value:i[t].value,label:i[t].label})))];t.dom.tip.hide();if(s.ranges.length==0)throw"select at least one range or category";if(JSON.parse(JSON.stringify(e)!=s)){try{w(s)}catch(t){window.alert(t);return}t.opts.callback(s)}}catch(t){window.alert(t)}};t.makeValueTable(o,e,i,l).node()}function w(t){if(!t.term)throw"tvs.term is not defined";if(!t.ranges)throw`.values[] missing for a term ${t.term.name}`;if(!Array.isArray(t.ranges))throw`.values[] is not an array for a term ${t.term.name}`;if(!t.ranges.length)throw`no categories selected for ${t.term.name}`;for(const e of t.ranges){if(e.value!=undefined){if(!e.label)throw`.label missing for special category for a term ${t.term.name}`}else{if(e.startunbounded){if(e.stopunbounded)throw`both start & stop are unbounded for a term ${t.term.name}`;if(!Number.isFinite(e.stop))throw`.stop undefined when start is unbounded for a term ${t.term.name}`}else if(e.stopunbounded){if(!Number.isFinite(e.start))throw`.start undefined when stop is unbounded for a term ${t.term.name}`}else{if(!Number.isFinite(e.start))throw`.start undefined when start is not unbounded for a term ${t.term.name}`;if(!Number.isFinite(e.stop))throw`.stop undefined when stop is not unbounded for a term ${t.term.name}`;if(e.start>=e.stop)throw`.start is not lower than stop for a term ${t.term.name}`}}}}export{g as convertViolinData,p as handler};

package/dist/violin-1515c3e6.js

@@ -1 +0,0 @@
-import{h as t,P as i,Q as e}from"./app-a8c4854a.js";import{controlsInit as s}from"./controls-0bacec22.js";import o from"./violin.renderer-dafd89fa.js";import{h as n}from"./html.legend-abb5452e.js";import{f as a,i as l}from"./roundValue-b0d0517c.js";import{setInteractivity as r}from"./violin.interactivity-8e2f480d.js";import"./controls.btns-1cb2bfab.js";import"./controls.config-0ccc9d79.js";import"./controls.overlay-fe20d41d.js";import"./FilterRxComp-242f4615.js";import"./table-79e3e776.js";import"./tslib.es6-1f85f553.js";import"./termdb.bins-9faa5170.js";import"./controls.term1-faa2efcf.js";import"./controls.divide-a9fe9466.js";import"./brush-c386fe3d.js";import"./pointer-c7475677.js";import"./nodrag-2c046d31.js";import"./axis-747c801e.js";import"./line-264f8f9e.js";import"./constant-426a1483.js";import"./basis-3870f5ba.js";import"./log-cf45fcf2.js";import"path";import"./niceNumLabels-6cfc1508.js";class p{constructor(t){this.type="violin"}async init(t){const i=this.opts.holder.append("div").attr("class","sjpp-plot-controls").style("display","inline-block");t.plots.find((t=>t.id===this.id));const e=this.opts.holder.append("div").style("display","inline-block").style("padding",this.opts.mode!="minimal"?"5px":"0px").style("padding-left",this.opts.mode!="minimal"?"45px":"0px").attr("id","sjpp-vp-holder");this.dom={header:this.opts.header,loadingDiv:this.opts.holder.append("div").style("position","absolute").style("display",this.opts.mode!="minimal"?"inline-block":"none").style("padding-left","10px").style("padding-top","20px").text("Loading ..."),controls:i,violinDiv:e.append("div").attr("class","sjpp-vp-violinDiv").style("padding-left",this.opts.mode!="minimal"?"10px":"0px"),legendDiv:e.append("div").classed("sjpp-vp-legend",true).style("padding-left","5px"),tableHolder:this.opts.holder.append("div").classed("sjpp-tableHolder",true).style("display","inline-block").style("padding","10px").style("vertical-align","top").style("margin-left","0px").style("margin-top","30px").style("margin-right","30px")};o(this);r(this);if(this.opts.mode!="minimal"){this.legendRenderer=n(this.dom.legendDiv,{settings:{legendOrientation:"vertical"},handlers:{}})}await this.setControls()}async setControls(){this.components={};if(this.opts.mode=="minimal")return;const t=[{type:"term1",usecase:{target:"violin",detail:"term"}},{type:"overlay",title:"Overlay data",usecase:{target:"violin",detail:"term2"},callback:t=>this.settings.plotThickness=undefined},{label:"Orientation",title:"Orientation of the chart",type:"radio",chartType:"violin",settingsKey:"orientation",options:[{label:"Vertical",value:"vertical"},{label:"Horizontal",value:"horizontal"}]},{label:"Method",title:`If selected uses the KDE method, otherwise uses a histogram`,type:"radio",chartType:"violin",settingsKey:"method",options:[{label:"KDE",value:0},{label:"Histogram",value:1}]},{label:"Data symbol",title:"Symbol type",type:"radio",chartType:"violin",settingsKey:"datasymbol",options:[{label:"Ticks",value:"rug"},{label:"Circles",value:"bean"},{label:"Off",value:"none"}]},{label:"Scale",title:"Axis scale",type:"radio",chartType:"violin",settingsKey:"unit",options:[{label:"Linear",value:"abs"},{label:"Log",value:"log"}]},{label:"Symbol size",type:"number",chartType:"violin",settingsKey:"radius",step:1,max:15,min:3},{label:"Stroke width",title:"Size of Symbol stroke",type:"number",chartType:"violin",settingsKey:"strokeWidth",step:.1,max:2,min:.1},{label:"Bins",type:"number",chartType:"violin",settingsKey:"ticks",title:"Number of bins used to build the plot",min:1,max:50},{label:"Plot length",title:"Length of the plot",type:"number",chartType:"violin",settingsKey:"svgw",step:10,max:1e3,min:500,debounceInterval:1e3},{label:"Plot thickness",title:"Thickness of plots, can be between 40 and 200",type:"number",chartType:"violin",settingsKey:"plotThickness",step:10,max:500,min:40,debounceInterval:1e3},{label:"Median length",title:"Length of median",type:"number",chartType:"violin",settingsKey:"medianLength",step:1,max:15,min:3,debounceInterval:1e3},{label:"Median thickness",title:"Width of median",type:"number",chartType:"violin",settingsKey:"medianThickness",step:1,max:10,min:3,debounceInterval:100},{label:"Default color",type:"color",chartType:"violin",settingsKey:"defaultColor"}];this.components.controls=await s({app:this.app,id:this.id,holder:this.dom.controls,inputs:t});this.components.controls.on("downloadClick.violin",this.download)}reactsTo(t){if(t.type.startsWith("plot_")){return t.id===this.id&&(!t.config.childType||t.config.childType==this.type)}return true}getState(t){const i=t.plots.find((t=>t.id===this.id));if(!i){throw`No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`}return{termfilter:t.termfilter,config:i,displaySampleIds:t.termdbConfig.displaySampleIds,hasVerifiedToken:this.app.vocabApi.hasVerifiedToken()}}async main(){this.config=structuredClone(this.state.config);this.settings=this.config.settings.violin;if(this.config.chartType!=this.type&&this.config.childType!=this.type)return;if(this.dom.header)this.dom.header.html(this.config.term.term.name+` <span style="opacity:.6;font-size:1em;margin-left:10px;">Violin Plot</span>`);await this.getDescrStats();const t=this.validateArgs();this.data=await this.app.vocabApi.getViolinPlotData(t);if(this.settings.plotThickness==undefined){const t=this.data.plots.length==1?200:150;this.settings.plotThickness=Math.min(1400/this.data.plots.length,t)}if(this.data.error)throw this.data.error;this.toggleLoadingDiv(this.opts.mode=="minimal"?"none":"");setTimeout((()=>{this.render();this.renderPvalueTable()}),this.opts.mode=="minimal"?0:500);this.toggleLoadingDiv("none")}async getDescrStats(){const t=[this.config.term];if(this.config.term2)t.push(this.config.term2);if(this.config.term0)t.push(this.config.term0);for(const i of t){if(l(i.term)){const t=await this.app.vocabApi.getDescrStats(i,this.state.termfilter,this.config.settings?.violin?.unit=="log");if(t.error)throw t.error;i.q.descrStats=t.values}}}validateArgs(){const{term:t,term2:i,settings:e}=this.config;const s=this.settings;const o={filter:this.state.termfilter.filter,filter0:this.state.termfilter.filter0,svgw:s.svgw/window.devicePixelRatio,orientation:s.orientation,devicePixelRatio:window.devicePixelRatio,datasymbol:s.datasymbol,radius:s.radius,strokeWidth:s.strokeWidth,axisHeight:s.axisHeight,rightMargin:s.rightMargin,unit:s.unit,isKDE:s.method==0,ticks:s.ticks};if(this.opts.mode=="minimal"){o.tw=t;if(i)throw"only a single term allowed for minimal plot";if(t.q.mode=="spline"){s.lines=t.q.knots.map((t=>Number(t.value)))}else{s.lines=[]}if(t.q.scale){o.scale=t.q.scale}}else if(l(t.term)&&t.q.mode==="continuous"){o.tw=t;if(i)o.divideTw=i}else if(l(i?.term)&&i.q.mode==="continuous"){o.tw=i;o.divideTw=t}else{throw"both term1 and term2 are not numeric/continuous"}return o}}const d=t(p);const h=d;function m(t,i={}){const s={orientation:"horizontal",rowlabelw:250,brushRange:null,svgw:500,datasymbol:"rug",radius:3,strokeWidth:.2,axisHeight:60,rightMargin:50,lines:[],unit:"abs",plotThickness:undefined,medianLength:7,medianThickness:3,ticks:20,defaultColor:e,method:0};return Object.assign(s,i)}async function c(t,e){if(!t.term)throw"violin getPlotConfig: opts.term{} missing";try{await a(t.term,e.vocabApi);if(t.term2)await a(t.term2,e.vocabApi);if(t.term0)await a(t.term0,e.vocabApi)}catch(t){throw`${t} [violin getPlotConfig()]`}const s={id:t.term.term.id,settings:{controls:{term2:null,term0:null},violin:m()}};return i(s,t)}export{h as componentInit,m as getDefaultViolinSettings,c as getPlotConfig,d as violinInit};

package/dist/violin.interactivity-8e2f480d.js

@@ -1 +0,0 @@
-import{r as t}from"./table-79e3e776.js";import{c as e}from"./roundValue-b0d0517c.js";import{a as s,c as i}from"./FilterRxComp-242f4615.js";import{U as n,r as a}from"./app-a8c4854a.js";import{n as l}from"./niceNumLabels-6cfc1508.js";import"./tslib.es6-1f85f553.js";import"path";import"./termdb.bins-9faa5170.js";function o(s){s.download=()=>{if(!s.state)return;s.dom.violinDiv.selectAll(".sjpp-violin-plot").each((function(){n(this,"violin",{apply_dom_styles:true})}))};s.displayLabelClickMenu=function(t,e,i,n){if(!e||s.data.plots.length===1){return}const a=t.q.mode==="continuous"?"term2":"term";const l=[{label:`Add filter: ${i.label.split(",")[0]}`,callback:d(t,e,s,i,a,false)},{label:`Hide: ${i.label}`,callback:()=>{const t=s.config[a];const e=true;s.app.dispatch({type:"plot_edit",id:s.id,config:{[a]:{isAtomic:true,term:t.term,q:r(i,t,e)}}})}}];if(s.state.displaySampleIds&&s.state.hasVerifiedToken){l.push({label:`List samples`,callback:async()=>{const[a,l]=[s.data.min,s.data.max*2];await s.listSamples(n,t,e,i,a,l)}})}s.displayMenu(n,l,i)};s.displayBrushMenu=function(t,e,s,i,n,a,l){const[o,r]=l?[a.invert(n[0]),a.invert(n[1])]:[a.invert(n[1]),a.invert(n[0])];const p=[{label:`Add filter`,callback:d(t,e,s,i,o,r,true)}];if(s.state.displaySampleIds&&s.state.hasVerifiedToken){p.push({label:`List samples`,callback:async()=>s.listSamples(event,t,e,i,o,r)})}s.displayMenu(event,p,i,o,r)};s.displayMenu=function(t,e,i,n,a){s.app.tip.d.selectAll("*").remove();s.app.tip.d.classed("sjpp-violin-brush-tip",true);const o=n!=null&&a!=null;if(o){const[t,e]=s.config.term.term.type=="integer"?[Math.round(n),Math.round(a)]:l([n,a]);s.app.tip.d.append("div").text(`From ${t} to ${e}`)}s.app.tip.d.append("div").selectAll("div").data(e).enter().append("div").attr("class","sja_menuoption").text((t=>t.label)).on("click",((t,e)=>{s.app.tip.hide();e.callback();s.dom.tableHolder.style("display","none")}));s.app.tip.show(t.clientX,t.clientY)};s.addEditColorToMenu=function(t){const e=a(t.color).formatHex();const i=s.app.tip.d.append("div").attr("class","sja_sharp_border").style("padding","0px 10px").text("Color:").append("input").attr("type","color").attr("value",e).on("change",(()=>{const e=i.node().value;const n=s.config.term2;let a;for(const s in n.term.values)if(n.term.values[s].label==t.label){n.term.values[s].color=e;a=s}if(!a)n.term.values={[t.label]:{label:t.label,color:e}};s.app.dispatch({type:"plot_edit",id:s.id,config:{term2:{isAtomic:true,term:s.config.term2.term,q:r(t,s.config.term2,false)}}});s.app.tip.hide()}))};s.listSamples=async function(t,e,i,n,a,l){const o=s.getTvsLst(e,i,n,a,l);const d=e.q?.mode==="continuous"?e:i;const r={type:"tvslst",join:"and",lst:[s.state.termfilter.filter,o],in:true};const p={terms:[d],filter:r};const c=await s.app.vocabApi.getAnnotatedSampleData(p);s.displaySampleIds(t,d,c)};s.displaySampleIds=function(i,n,a){s.app.tip.clear();if(!a?.samples)return;const l=[];for(const[t,s]of Object.entries(a.samples))l.push([{value:a.refs.bySampleId[t].label},{value:e(s[n.$id].value)}]);const o=s.app.tip.d.append("div");const d=[{label:"Sample"},{label:"Value"}];const r=l;t({rows:r,columns:d,div:o,maxWidth:"30vw",maxHeight:"25vh",resize:true,showLines:true});s.app.tip.show(i.clientX,i.clientY)};s.labelHideLegendClicking=function(t,e){s.dom.legendDiv.selectAll(".sjpp-htmlLegend").on("click",(i=>{i.stopPropagation();const n=i.target.__data__;const a=t?.term.type==="condition"||t?.term.type==="samplelst"||t?.term.type==="categorical"||(t?.term.type==="float"||t?.term.type==="integer")&&s.config.term?.q.mode==="continuous"?"term2":"term";const l=s.config[a];if(t){for(const t of Object.keys(l?.q?.hiddenValues)){if(n.text===t){delete l.q.hiddenValues[t]}}const t=false;s.app.dispatch({type:"plot_edit",id:s.id,config:{[a]:{isAtomic:true,term:l.term,q:r(e,l,t)}}})}})).on("mouseover",(t=>{const e=t.target.__data__;if(e===undefined)return;if(e.isHidden===true){s.dom.tip.d.html("Click to unhide plot");s.dom.tip.show(t.clientX,t.clientY)}})).on("mouseout",(function(){s.dom.tip.hide()}))};s.createTvsLstRanges=function(t,e,s,i,n){c(t,e);e.lst[n].tvs.ranges=[{start:t.term.type=="integer"?Math.round(s):s,stop:t.term.type=="integer"?Math.round(i):i,startinclusive:true,stopinclusive:true,startunbounded:false,stopunbounded:false}]};s.getTvsLst=function(t,e,i,n,a){const l={type:"tvslst",in:true,join:"and",lst:[]};if(e){if(t.term.type==="categorical"||t.term.type==="condition"){p(t,i,l,0);s.createTvsLstRanges(e,l,n,a,1)}else if(e.q?.mode==="continuous"||(e.term?.type==="float"||e.term?.type==="integer")&&i.divideTwBins!=null){c(e,l);l.lst[0].tvs.ranges=[{start:i.divideTwBins?.start||null,stop:i.divideTwBins?.stop||null,startinclusive:i.divideTwBins?.startinclusive||true,stopinclusive:i.divideTwBins?.stopinclusive||false,startunbounded:i.divideTwBins?.startunbounded?i.divideTwBins?.startunbounded:null,stopunbounded:i.divideTwBins?.stopunbounded?i.divideTwBins?.stopunbounded:null}];s.createTvsLstRanges(t,l,n,a,1)}else{p(e,i,l,0);s.createTvsLstRanges(t,l,n,a,1)}}else s.createTvsLstRanges(t,l,n,a,0);return l}}function d(t,e,n,a,l,o,d){const r={type:"tvslst",in:true,join:"and",lst:[]};if(e){if(t.term.type==="categorical"||t.term.type==="condition"){p(t,a,r,0);if(d){n.createTvsLstRanges(e,r,l,o,1)}}else if(e.q?.mode==="continuous"||(e.term?.type==="float"||e.term?.type==="integer")&&a.divideTwBins!=null){c(e,r);r.lst[0].tvs.ranges=[{start:a.divideTwBins?.start||null,stop:a.divideTwBins?.stop||null,startinclusive:a.divideTwBins?.startinclusive||true,stopinclusive:a.divideTwBins?.stopinclusive||false,startunbounded:a.divideTwBins?.startunbounded?a.divideTwBins?.startunbounded:null,stopunbounded:a.divideTwBins?.stopunbounded?a.divideTwBins?.stopunbounded:null}];if(d){n.createTvsLstRanges(t,r,l,o,1)}}else{p(e,a,r,0);if(d){n.createTvsLstRanges(t,r,l,o,1)}}}else{if(d){n.createTvsLstRanges(t,r,l,o,0)}}return()=>{const t=s(n.state.termfilter.filter,"filterUiRoot");const e=i([t,r]);e.tag="filterUiRoot";n.app.dispatch({type:"filter_replace",filter:e})}}function r(t,e,s=false){const i=t.label;const n=e?.term?.values?e?.term?.values?.[i]?.label:i;const a=!n?i:n;const l=e.q;if(!l.hiddenValues)l.hiddenValues={};if(s)l.hiddenValues[a]=1;else delete l.hiddenValues[a];return l}function p(t,e,s,i){c(t,s);s.lst[i].tvs.values=[{key:e.seriesId,label:e.label}];if(t.term.type==="condition"){s.lst[i].tvs.bar_by_grade=t.q.bar_by_grade;s.lst[i].tvs.value_by_max_grade=t.q.value_by_max_grade}if(t.term.type==="samplelst"){s.lst[i].tvs.values=t.term.values[e.label].list}}function c(t,e){e.lst.push({type:"tvs",tvs:{term:t.term}})}export{o as setInteractivity};