@sjcrh/proteinpaint-client 2.77.0 → 2.78.0

package/dist/sampleScatter-f6c04130.js

@@ -0,0 +1 @@
+import{h as t,M as e,a as s,d as o,y as a,J as i,b as n,K as r,I as l,r as c,L as p,N as d,O as h,B as m,z as f,n as u,P as g,Q as y}from"./app-488d9fd6.js";import{c as b,f as v}from"./termsetting-c12f1c69.js";import{controlsInit as x}from"./controls-f4648f7f.js";import{d as S}from"./zoom-6a36fb2b.js";import{d as w}from"./lasso-48317f42.js";import{c as C,g as T,r as j,a as k,b as D,d as _,e as A,f as O,h as W,o as L,i as M,j as $}from"./recover-edcdde38.js";import{t as z,s as I}from"./shapes-21ebfec4.js";import{r as N}from"./table-10183501.js";import{a as G,b as R,c as q}from"./FilterRxComp-cb149666.js";import{searchSampleInput as V}from"./sampleView-0931e571.js";import{s as E}from"./select2Terms-480025f5.js";import{d as F}from"./svg.download-0dd56dfd.js";import{s as P}from"./sampleScatter.rendererThree-448689c6.js";import{a as B,b as U,c as H}from"./axis-747c801e.js";import{l as K}from"./line-264f8f9e.js";class Y{constructor(t){this.type="search";X(this);Q(this)}async init(t){this.dom={holder:this.opts.holder,holderNode:this.opts.holder.node(),tip:new e({padding:"5px"})};this.initUI()}reactsTo(t){return t.type.startsWith("search")||t.type.startsWith("cohort")}getState(t){return{cohortStr:t.activeCohort==-1||!t.termdbConfig.selectCohort?"":t.termdbConfig.selectCohort.values[t.activeCohort].keys.slice().sort().join(","),search:t.search,nav:t.nav}}async main(){this.dom.holder.style("display",this.state.search.isVisible&&this.state.nav.header_mode!="only_buttons"?"inline-block":"none")}async doSearch(t){if(!t){this.clear({hide:true});this.bus.emit("postSearch",[]);return}const e=await this.app.vocabApi.findTerm(t,this.state.cohortStr,this.opts.usecase,this.opts.targetType);if(!e.lst||e.lst.length==0){this.noResult()}else{this.showTerms(e)}this.bus.emit("postSearch",e)}}const J=t(Y);function X(t){t.initUI=()=>{t.dom.holder.style("display",t.search&&t.search.isVisible==false?"none":"inline-block");t.dom.input=t.dom.holder.style("text-align","center").append("input").attr("type","search").attr("class","tree_search").attr("placeholder","Search").style("width","180px").style("display","block").on("input",s.debounce(t.onInput,300));t.dom.resultDiv=t.dom.tip.d.style("border-left",t.opts.resultsHolder?"":"solid 1px rgb(133,182,225)").style("padding-left","5px")};t.noResult=()=>{t.clear();t.dom.resultDiv.append("div").text("No match").style("padding","3px 3px 3px 0px").style("opacity",.5)};t.showTerms=e=>{if(t.opts.disable_terms)e.lst.forEach((e=>{if(e.disabled)t.opts.disable_terms.push(e)}));t.clear({hide:!e.lst.length});if(e.lst.length){t.dom.resultDiv.append("table").selectAll().data(e.lst).enter().append("tr").each(t.showTerm)}};t.showTerm=function(e){const s=o(this);const a=s.append("td").text(e.name);if(e.type){a.style("cursor","pointer").attr("class","sja_menuoption").on("click",(()=>{t.app.dispatch({type:"plot_create",config:{chartType:e.type=="survival"?"survival":"summary",term:{term:e}}});t.clear({hide:true})}))}else{a.style("padding","5px 10px").style("opacity",.5)}s.append("td").text((e.__ancestorNames||[]).join(" > ")).style("opacity",.5).style("font-size",".7em")};t.clear=(e={})=>{t.dom.tip.clear();if(e.hide)t.dom.tip.hide();else t.dom.tip.showunder(t.dom.holderNode)}}function Q(t){t.onInput=async()=>{const e=t.dom.input.property("value");try{await t.doSearch(e)}catch(e){t.clear();a(t.dom.resultDiv,"Error: "+(e.message||e));if(e.stack)console.log(e.stack)}}}function Z(t){switch(t){case"../plots/DEanalysis.js":return import("./DEanalysis-417e1f88.js");case"../plots/Disco.js":return import("./Disco-30abd4cb.js");case"../plots/DziViewer.js":return import("./DziViewer-af3c5a76.js");case"../plots/WSIViewer.js":return import("./WSIViewer-64e55fb8.js");case"../plots/barchart.data.js":return import("./FilterRxComp-cb149666.js").then((function(t){return t.j}));case"../plots/barchart.events.js":return import("./barchart.events-9e2c1acf.js");case"../plots/barchart.js":return import("./barchart-687ae584.js");case"../plots/bars.renderer.js":return import("./bars.renderer-95f7250f.js");case"../plots/bars.settings.js":return import("./bars.settings-64bb4642.js");case"../plots/boxplot.js":return import("./boxplot-dbf30a19.js");case"../plots/brainImaging.js":return import("./brainImaging-b2865ba3.js");case"../plots/controls.btns.js":return import("./controls.btns-26bb6ef1.js");case"../plots/controls.config.js":return import("./controls.config-9870bdea.js");case"../plots/controls.js":return import("./controls-f4648f7f.js");case"../plots/cuminc.js":return import("./cuminc-2273cdd3.js");case"../plots/dataDownload.js":return import("./dataDownload-b94871d0.js");case"../plots/dictionary.js":return import("./dictionary-321e19f9.js");case"../plots/facet.js":return import("./facet-26292a3d.js");case"../plots/geneExpression.js":return import("./geneExpression-d1d5a7ca.js");case"../plots/geneORA.js":return import("./geneORA-248baba7.js");case"../plots/geneset.js":return import("./geneset-1f67d4c9.js");case"../plots/genomeBrowser.controls.js":return import("./genomeBrowser.controls-3a7a1c94.js");case"../plots/genomeBrowser.js":return import("./genomeBrowser-52c639b4.js");case"../plots/gsea.js":return import("./gsea-d3286c53.js");case"../plots/hierCluster.js":return import("./hierCluster-00268175.js");case"../plots/imagePlot.js":return import("./imagePlot-f6398b6e.js");case"../plots/matrix.js":return import("./matrix-1190d4b3.js");case"../plots/plot.app.js":return import("./plot.app-fc3608a9.js");case"../plots/plot.brainImaging.js":return import("./plot.brainImaging-a7bb79d6.js");case"../plots/plot.disco.js":return import("./plot.disco-ccdf741c.js");case"../plots/plot.ssgq.js":return import("./plot.ssgq-146075f5.js");case"../plots/profileBarchart.js":return import("./profileBarchart-46616916.js");case"../plots/profilePlot.js":return import("./profilePlot-a2591a28.js");case"../plots/profilePolar.js":return import("./profilePolar-006a56b1.js");case"../plots/profileRadar.js":return import("./profileRadar-3320d932.js");case"../plots/profileRadarFacility.js":return import("./profileRadarFacility-7a9cea80.js");case"../plots/profileSummary.js":return import("./profileSummary-7a747b4e.js");case"../plots/regression.inputs.js":return import("./regression.inputs-d5d44e49.js").then((function(t){return t.b}));case"../plots/regression.inputs.term.js":return import("./regression.inputs-d5d44e49.js").then((function(t){return t.a}));case"../plots/regression.inputs.values.table.js":return import("./regression.inputs.values.table-daf7bcda.js");case"../plots/regression.js":return import("./regression.inputs-d5d44e49.js").then((function(t){return t.r}));case"../plots/regression.results.js":return import("./regression.results-31a8884d.js").then((function(t){return t.r}));case"../plots/sampleScatter.interactivity.js":return Promise.resolve().then((function(){return Nt}));case"../plots/sampleScatter.js":return Promise.resolve().then((function(){return Jt}));case"../plots/sampleScatter.renderer.js":return Promise.resolve().then((function(){return $t}));case"../plots/sampleScatter.rendererThree.js":return import("./sampleScatter.rendererThree-448689c6.js").then((function(t){return t.c}));case"../plots/sampleView.js":return import("./sampleView-0931e571.js");case"../plots/scatter.js":return import("./scatter-a8d7c2a0.js");case"../plots/singleCellPlot.js":return import("./singleCellPlot-2f5ad46a.js");case"../plots/stattable.js":return import("./stattable-7fa50fd2.js");case"../plots/summary.js":return import("./summary-54587ccf.js");case"../plots/survival.js":return import("./survival-21e6637b.js");case"../plots/table.js":return import("./table-bb97b5c9.js");case"../plots/variantBrowser.js":return import("./variantBrowser-2c465d02.js");case"../plots/violin.interactivity.js":return import("./violin.interactivity-57637244.js");case"../plots/violin.js":return import("./violin-edbe9a63.js");case"../plots/violin.renderer.js":return import("./violin.renderer-4cab7448.js");default:return new Promise((function(e,s){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(s.bind(null,new Error("Unknown variable dynamic import: "+t)))}))}}class tt{constructor(){this.type="sessionBtn";this.route="termdb";this.embedderOrigin=window.location.origin;this.hostURL=sessionStorage.getItem("hostURL")||this.embedderOrigin}async init(t){const s=new e({padding:"0px"});this.dom={button:this.opts.button,tip:s};this.dom.button.on("click",(()=>{this.dom.tip.clear();this.showMenu()}));this.dslabel=t.vocab.dslabel;this.savedSessions=JSON.parse(localStorage.getItem("savedMassSessions")||`{}`);this.requiredAuth=t.termdbConfig?.requiredAuth?.find((t=>t.route==this.route&&t.type=="jwt"))}async showMenu(){this.dom.tip.clear().d.style("padding",0);const t=[{label:`Open`,title:"Recover a saved session",callback:this.open},{label:`Save`,title:"Save the current view",callback:this.save},{label:`Share`,title:"Create a URL link to share this view",callback:this.getSessionUrl}];if(!this.serverCachedSessions)await this.setServerCachedSessions();if(Object.keys(this.savedSessions).length||Object.keys(this.serverCachedSessions).length){t.push({label:`Delete`,title:"Delete a saved session",callback:this.delete})}this.dom.tip.clear().d.selectAll(".sja_menuoption sja_sharp_border").data(t).enter().append("div").attr("class","sja_menuoption sja_sharp_border").attr("aria-label",(t=>t.title)).html((t=>t.label)).on("click",((t,e)=>{this.dom.tip.clear().d.style("padding","10px");this.showBackBtn();e.callback.call(this)}));this.dom.tip.showunder(this.dom.button.node())}async open(){const t=`sjpp-session-open-radio-`+Math.random().toString().slice(-6);this.dom.tip.d.append("div").style("display","none").style("padding","3px 9px").html(`\n\t\t\t<b>Open in</b>\n\t\t\t<label>\n\t\t\t\t<input type='radio' name='${t}' value='new' style='margin-right: 0; vertical-align: bottom'/>\n\t\t\t\t<span>a new tab</span>\n\t\t\t</label>\n\t\t\t<label style='margin-left: 5px'>\n\t\t\t\t<input type='radio' name='${t}' value='current' checked=checked style='margin-right: 0; vertical-align: bottom'/>\n\t\t\t\t<span>current tab</span>\n\t\t\t</label>\n\t\t`);const e=await this.listSessions({trClickHandler:async(e,s)=>{const{loc:o,id:a}=s;if(!a)return;if(o.includes("browser")){this.sessionName=a;const e=this.savedSessions[a];await et(e,this.app);const s=this.dom.tip.d.node().querySelector(`[name="${t}"]:checked`).value;if(s=="current"){this.app.dispatch({type:"app_refresh",state:e})}else if(window.location.origin==this.hostURL){window.open(`/?mass-session-id=${a}&src=browser`)}else{if(e.embedder)i({state:e});else{const{protocol:t,host:s,search:o,origin:a,href:n}=window.location;const r={protocol:t,host:s,search:o,origin:a,href:n};i({state:Object.assign({embedder:r},e)})}}this.dom.tip.hide()}else if(o=="server"){const e=this.app.vocabApi.mayGetAuthHeaders(this.route);const s={id:a,route:this.route,dslabel:this.dslabel,embedder:window.location.hostname};const o=await n(`/massSession?`,{headers:e,body:s});if(!o.state)throw o.error||"unable to get the cached session from the server";await et(o.state,this.app);this.savedSessions[a]=o.state;const r=this.dom.tip.d.node().querySelector(`[name="${t}"]:checked`).value;if(r=="current"){this.app.dispatch({type:"app_refresh",state:o.state})}else if(window.location.origin==this.hostURL){window.open(`/?mass-session-id=${a}&src=cred&dslabel=${this.dslabel}&route=${this.route}`)}else{i(o)}this.dom.tip.hide()}}});e.headtr.select("th").html("Open from");const s=e.tbody.insert("tr","tr");s.append("td").style("text-align","center").style("padding","3px 9px").html("Local file");const o=s.append("td").style("text-align","left").append("label");o.append("span").style("padding","3px 9px").style("text-decoration","underline").style("cursor","pointer").html("Choose File");o.append("input").attr("type","file").attr("placeholder","file name").style("opacity",0).style("width","0.1px").style("height","0.1px").style("position","absolute").on("change",(async()=>{const e=event.target.files.item(0);const s=await e.text();let o=e.name;if(this.savedSessions[o]){o=prompt(`Leave as-is to overwrite a session with the same name, or enter a different session name.`,o)}this.sessionName=o;const a=JSON.parse(s);await et(a,this.app);this.savedSessions[o]=a;localStorage.setItem("savedMassSessions",JSON.stringify(this.savedSessions));const n=this.dom.tip.d.node().querySelector(`[name="${t}"]:checked`).value;if(n=="current"){this.app.dispatch({type:"app_refresh",state:a})}else if(window.location.origin==this.hostURL){window.open(`/?mass-session-id=${o}&src=browser`)}else{if(a.embedder)i({state:a});else{const{protocol:t,host:e,search:s,origin:o,href:n}=window.location;const r={protocol:t,host:e,search:s,origin:o,href:n};i({state:Object.assign({embedder:r},a)})}}this.dom.tip.hide()}))}async listSessions(t={}){const e=this.dom.tip.d.append("table").attr("class","sjpp-controls-table");const s=e.append("thead").append("tr");s.selectAll("th").data(["Cache Location","Session ID"]).enter().append("th").style("text-align",((t,e)=>e===0?"center":"left")).style("padding","3px 9px").html((t=>t));const o=Object.keys(this.savedSessions).map((t=>({loc:"browser",id:t})));if(!this.serverCachedSessions)await this.setServerCachedSessions();o.push(...this.serverCachedSessions.map((t=>({loc:"server",id:t}))));const a=e.append("tbody");const i=a.selectAll("tr").data(o).enter().append("tr").on("click",t.trClickHandler||null);i.selectAll("td").data((t=>[t,t])).enter().append("td").style("text-align",((t,e)=>e===0?"center":"left")).style("padding","3px 9px").style("cursor","pointer").html(((t,e)=>e===0?t.loc:t.id));if(!this.serverCachedSessions.length&&this.requiredAuth&&!this.app.vocabApi.hasVerifiedToken()){e.append("tbody").append("tr").selectAll("td").data(["server","requires sign-in"]).enter().append("td").style("text-align",((t,e)=>e===0?"center":"left")).style("padding","3px 9px").html((t=>t))}return{table:e,headtr:s,tbody:a,trs:i}}async setServerCachedSessions(){const t=this.app.getState();this.requiredAuth=t.termdbConfig?.requiredAuth?.find((t=>t.route==this.route&&t.type=="jwt"));if(!this.requiredAuth){this.serverCachedSessions=[];return}const e=this.app.vocabApi.mayGetAuthHeaders(this.route);const s={route:this.route,dslabel:this.dslabel,embedder:window.location.hostname};const o=await n("/sessionIds",{headers:e,body:s});this.serverCachedSessions=o.sessionIds||[]}async save(t){const e=this.dom.tip.d;const s=e.append("div");s.append("span").html("Save as");const o=Object.keys(this.savedSessions);if(!this.serverCachedSessions)await this.setServerCachedSessions();o.push(...this.serverCachedSessions.filter((t=>!o.includes(t))));const a=this.sessionName||"unnamed-session";const i=s.append("input").attr("type","text").attr("placeholder",a).style("width","220px").on("input",(()=>{n.selectAll("*").remove();const t=i.property("value");const e=o.filter((e=>e===t));const s=o.filter((e=>e.startsWith(t)));const a=o.filter((e=>e.includes(t)&&e!==t&&!s.includes(e)));n.selectAll("div").data([...e,...s,...a]).enter().append("div").attr("class","sja_menuoption").html((t=>t)).on("click",((t,e)=>{i.property("value",e);n.selectAll("*").remove()}))}));const n=e.append("div");const r=e.append("div");r.append("span").html("Save to&nbsp;");r.append("button").style("min-width","80px").html("Browser").attr("title",`Save the session in your current browser's cache. The session can be easily recovered, but not shared among your other devices`).on("click",(()=>{this.sessionName=i.property("value")||a;this.savedSessions[this.sessionName]=this.app.getState();localStorage.setItem("savedMassSessions",JSON.stringify(this.savedSessions));this.confirmAction(`Cached '<b>${this.sessionName}</b>' in browser`)}));r.append("button").style("min-width","80px").html("File").attr("title",`Save the session into a local file. The session can be easily recoved using the 'Open from local file' option.`).on("click",(()=>{const t=i.property("value")||a;this.savedSessions[t]=this.app.getState();this.download(t);this.confirmAction(`Downloaded '<b>${t}</b>'`)}));if(this.requiredAuth){const t=this.app.vocabApi.hasVerifiedToken()?"":"Requires sign-in. ";r.append("button").style("min-width","80px").html("Server").attr("title",`${t}Save the session into a remote server. The session can be easily shared across your different devices and recovered using the 'Open from server' option.`).property("disabled",!this.app.vocabApi.hasVerifiedToken()).on("click",(async()=>{if(!this.app.vocabApi.hasVerifiedToken()){alert("Requires sign-in");return}const t=i.property("value")||a;this.savedSessions[t]=this.app.getState();const e=await this.getSessionUrl(t);if(e.id!=t)throw`error saving ${t}`;this.confirmAction(`Saved '<b>${t}</b>' on the server`)}))}}download(t=""){const e=t||this.sessionName;const s=e?.endsWith(".txt")?"":".txt";const o=`${e}${s}`;z(o,JSON.stringify(this.savedSessions[e]))}async getSessionUrl(t=""){const e=this.app.vocabApi.mayGetAuthHeaders("termdb");const s=structuredClone(this.app.getState());const{protocol:o,host:a,search:r,origin:l,href:c}=window.location;s.embedder={protocol:o,host:a,search:r,origin:l,href:c};if(t){s.__sessionFor__={route:this.route,filename:t,dslabel:this.dslabel,embedder:window.location.hostname}}const p=await n("/massSession",{headers:e,method:"POST",body:JSON.stringify(s)});if(t){return p}else{const t=`${this.hostURL}/?mass-session-id=${p.id}&noheader=1`;this.dom.tip.showunder(this.dom.button.node());const e=this.dom.tip.d.append("div").style("margin","10px");e.append("div").style("margin-bottom","12px").html(`Click the link to recover this session. Bookmark or share this link.`);const o=e.append("a").attr("href",t).attr("target","_blank").html(p.id);if(this.hostURL!=window.location.origin){o.on("click",(t=>{t.preventDefault();i({state:s},window.location.origin);return false}))}e.append("div").html(`\n\t\t\t\t\t<br>\n\t\t\t\t\t<div style="max-width: 400px; font-size: 1em; opacity:.6">\n\t\t\t\t\t<span>NOTES</span>\n\t\t\t\t\t<ul>\n\t\t\t\t\t<li>A recovered session may hide data or views to users that are not authorized to access the saved datasets or features.</li>\n\t\t\t\t\t<li>This session will be saved for ${this.opts.massSessionDuration} days.</li>\n\t\t\t\t\t</ul>\n\t\t\t\t\t</div>`);setTimeout((()=>{this.dom.button.property("disabled",false)}),1e3)}}async delete(){const t=await this.listSessions({trClickHandler:function(s){const a=this.lastChild.querySelector("input");const i=s.target==a?a.checked:!a.checked;o(this).style("text-decoration",i?"line-through":"");if(s.target!=a)a.checked=i;const n=t.table.node().querySelectorAll("input:checked");e.property("disabled",n.length?false:true)}});t.headtr.append("th").html("Delete");t.trs.each((function(t){o(this).append("td").style("text-align","center").append("input").attr("type","checkbox").attr("value",t.id)}));const e=this.dom.tip.d.append("div").style("text-align","center").append("button").html("Delete selected sessions").property("disabled",true).on("click",(async()=>{const e=t.table.node().querySelectorAll("input");const s=[];for(const t of e){if(o(t).property("checked")){const e=t.parentNode.parentNode.__data__;if(e.loc=="browser"){delete this.savedSessions[t.value]}else if(e.loc=="server"){delete this.serverCachedSessions[t.value];s.push(t.value)}else throw`unknown cache location=${e.loc}`}}localStorage.setItem("savedMassSessions",JSON.stringify(this.savedSessions));try{const t=this.app.vocabApi.mayGetAuthHeaders("termdb");const e={ids:s,route:this.route,dslabel:this.dslabel,embedder:window.location.hostname};const o=n(`/massSession?`,{method:"DELETE",headers:t,body:e})}catch(t){throw t}this.dom.tip.hide()}))}showBackBtn(){this.dom.tip.d.append("div").attr("class","sja_clbtext2").style("margin-bottom","10px").style("cursor","pointer").html(`&lt; Session Menu`).on("click",(()=>this.showMenu()))}confirmAction(t){this.dom.tip.clear().d.append("div").html(t).transition().delay(3e3).duration(1e3).style("opacity",0);setTimeout((()=>{this.dom.tip.hide()}),3500)}}async function et(t,e){if(t.plots){const s=[];for(const o of t.plots){s.push((async()=>{const t=await Z(`../plots/${o.chartType}.js`);return await t.getPlotConfig(o,e)})())}try{await Promise.all(s)}catch(t){console.log(t);e.printError(t)}}}const st=t(tt);class ot{constructor(t){this.type="about";this.app=t.app;this.holder=t.holder;this.features=t.features}init(){this.holder.append("div").style("padding","10px").html(this.features.html)}main(){}}const at=t(ot);let it=0;const nt="_MASS_AUTOID_"+Math.random().toString().slice(-6);let rt=(+new Date).toString().slice(-8);const lt=new e({padding:"0px",offsetX:0,offsetY:0});lt.d.style("z-index",5555);const ct={top:"CHARTS",mid:"NONE",btm:"",subheader:"charts"};const pt={top:"GROUPS",mid:"NONE",btm:"",subheader:"groups"};const dt={top:"FILTER",mid:"NONE",btm:"",subheader:"filter"};function ht(){return nt+"_"+rt++}class mt{constructor(t){this.type="nav";this.instanceNum=it++;this.activeTab=0;this.activeCohort=0;this.searching=false;this.samplecounts={};this.massSessionDuration=t.massSessionDuration;this.sessionDaysLeft=t.app.opts.sessionDaysLeft||null;this.sessionId=t.app.opts.sessionId||null;gt(this);ut(this)}async init(t){try{this.cohortFilter=G(t.termfilter.filter,"cohortFilter");this.initUI(t);this.initCohort(t);this.components=await r({search:J({app:this.app,holder:this.dom.searchDiv,usecase:{target:"summary",detail:"term"},targetType:"Dictionary Variables"}),filter:R({app:this.app,vocabApi:this.app.vocabApi,holder:this.dom.subheader.filter.append("div"),hideLabel:this.opts.header_mode==="with_tabs",emptyLabel:"+Add new filter",callback:t=>{this.app.dispatch({type:"filter_replace",filter:t})}}),charts:C({app:this.app,holder:this.dom.subheader.charts,vocab:this.opts.vocab}),groups:T({app:this.app,holder:this.dom.subheader.groups,vocab:this.opts.vocab}),recover:j({app:this.app,holder:this.dom.recoverDiv,getState:t=>t,reactsTo:t=>t.type!="plot_edit",maxHistoryLen:5}),sessionBtn:st({app:this.app,button:this.dom.saveBtn,massSessionDuration:this.opts.massSessionDuration,sessionDaysLeft:this.app.opts.sessionDaysLeft||null}),about:t.termdbConfig.about?at({app:this.app,holder:this.dom.subheader.about,features:t.termdbConfig.about}):[]});this.mayShowMessage_sessionDaysLeft()}catch(t){throw t}}reactsTo(t){if(t.type.includes("cache_termq"))return true;if(t.type.startsWith("filter"))return true;if(t.type.startsWith("cohort"))return true;if(t.type.startsWith("tab"))return true;if(t.type=="plot_create")return true;if(t.type=="plot_delete")return true;if(t.type=="app_refresh")return true;if(t.type.endsWith("_customTerm"))return true;if(t.type.endsWith("_group"))return true}getState(t){return{searching:this.searching,nav:t.nav,activeCohort:t.activeCohort,termdbConfig:t.termdbConfig,filter:t.termfilter.filter,plots:t.plots,groups:t.groups}}async main(){if(this.state.termdbConfig.selectCohort&&this.state.termdbConfig.about){console.error("Cohort(s) and an About tab are defined. Only one can be used.");return}this.dom.tabDiv.style("display",this.state.nav.header_mode==="with_tabs"?"inline-block":"none");this.dom.tip.hide();this.activeTab=this.state.nav.activeTab;this.prevCohort=this.activeCohort;this.activeCohort=+this.state.activeCohort;this.filterUiRoot=G(this.state.filter,"filterUiRoot");this.cohortFilter=G(this.state.filter,"cohortFilter");if(this.cohortNames){this.activeCohortName=this.cohortNames[this.activeCohort];if(this.activeCohort!==-1)this.activeCohortLabel=this.state.termdbConfig.selectCohort.values[this.activeCohort].shortLabel}this.filterJSON=JSON.stringify(this.state.filter);this.cohortsData=await this.app.vocabApi.getCohortsData();if(this.state.termdbConfig.about)this.about=this.state.termdbConfig.about;if(this.state.nav.header_mode==="with_tabs"){if(!(this.activeCohortName in this.samplecounts)){const t=await this.app.vocabApi.getCohortSampleCount(this.activeCohortName);this.samplecounts[this.activeCohortName]=t}if(!(this.filterJSON in this.samplecounts)){if(!this.filterUiRoot||!this.filterUiRoot.lst.length){this.samplecounts[this.filterJSON]=this.samplecounts[this.activeCohortName]}else{const t=await this.app.vocabApi.getFilteredSampleCount(this.filterJSON);this.samplecounts[this.filterJSON]=t}}}this.updateUI()}}const ft=t(mt);function ut(t){t.initUI=s=>{const o=t.opts.holder.append("div").style("white-space","nowrap");let a=o.append("div").style("display","inline-block").style("float","right").style("font-size","1.1em").style("margin-top","50px").text(s.termdbConfig?.title?.text||"");const i=o.append("div").style("display","none").style("vertical-align","bottom");const n=o.append("div").style("vertical-align","top").style("margin","10px").style("display","inline-block");t.opts.holder.attr("class","sjpp-nav");t.dom={holder:t.opts.holder,header:o,tabDiv:i,controlsDiv:n,searchDiv:n.append("div").style("margin","10px"),sessionDiv:n.append("div").style("display","inline-block"),recoverDiv:n.append("div").style("display","inline-block"),helpDiv:n.append("div").style("display","none"),sessionElapsedMessageDiv:n.append("div").style("display","none"),subheaderDiv:t.opts.holder.append("div").style("display","block").style("padding-top","5px").style("border-bottom","1px solid #000"),messageDiv:t.opts.holder.append("div").style("margin","30px").style("display","none"),titleDiv:a,tip:new e({padding:"5px"})};if(s.nav.header_mode=="only_buttons"){t.dom.tabDiv.style("display","none");t.dom.recoverDiv.style("display","none");a.style("margin-top","95px").style("font-size","0.9em");if(s.termdbConfig.title?.link)a.on("click",(()=>window.open(s.termdbConfig.title.link,"_blank"))).on("mouseover",(()=>a.style("cursor","pointer")))}if(t.opts.header_mode==="with_cohortHtmlSelect"){t.dom.cohortStandaloneDiv=o.append("div").style("display","inline-block").style("margin","10px").style("vertical-align","top");t.dom.cohortStandaloneDiv.append("label").html("Cohort: ");t.dom.cohortSelect=t.dom.cohortStandaloneDiv.append("select").on("change",(function(){t.app.dispatch({type:"cohort_set",activeCohort:+this.value})}));t.dom.cohortSelect.selectAll("option").data(s.termdbConfig.selectCohort.values).enter().append("option").attr("value",((t,e)=>e)).property("selected",((t,e)=>e===s.activeCohort)).html((t=>t.shortLabel))}t.dom.subheader=Object.freeze({search:t.dom.subheaderDiv.append("div").style("display","none"),groups:t.dom.subheaderDiv.append("div").style("display","none"),charts:t.dom.subheaderDiv.append("div").style("display","none"),filter:t.dom.subheaderDiv.append("div").style("display","none"),cart:t.dom.subheaderDiv.append("div").style("display","none").html("<br/>Cart feature under construction - work in progress<br/>&nbsp;<br/>"),about:t.dom.subheaderDiv.append("div").style("display","none").attr("data-testid","sjpp-mass-about")});t.tabs=[ct,pt,dt];if(s.termdbConfig.hideGroupsTab)t.tabs.splice(1,1);if(s.termdbConfig?.selectCohort||s.termdbConfig?.about){const e=s.termdbConfig?.about?.tab||{};const o=s.termdbConfig.selectCohort?"COHORT":e.topLabel||"";const a=e.midLabel||(e?"ABOUT":"");const i=e.btmLabel||"";const n={top:o.toUpperCase(),mid:a.toUpperCase(),btm:i,subheader:"about"};const r=s.termdbConfig?.selectCohort?0:e.order||0;t.tabs.splice(r,0,n)}const r=t.dom.tabDiv.append("table").style("border-collapse","collapse");r.selectAll("tr").data(["top","mid","btm"]).enter().append("tr").style("font-size",((t,e)=>e==1?"20px":"12px")).selectAll("td").data(((e,s)=>t.tabs.map(((t,o)=>({rowNum:s,key:e,colNum:o,label:t[e],subheader:t.subheader}))))).enter().append("td").style("display","none").style("width","100px").style("padding",(t=>t.rowNum===0?"12px 12px 3px 12px":"3px 12px")).style("text-align","center").style("border-left","1px solid #ccc").style("border-right","1px solid #ccc").style("color","#aaa").style("cursor","pointer").html((t=>t.label)).on("click",((e,s)=>{t.setTab(e,s)}));t.dom.trs=r.selectAll("tr");t.dom.tds=r.selectAll("td");t.subheaderKeys=t.tabs.map((t=>t.subheader));t.dom.saveBtn=t.dom.sessionDiv.append("button").style("margin","10px").text("Session ▼");if(t.sessionDaysLeft!=null){t.dom.fileBtn=t.dom.sessionDiv.append("button").style("margin","10px").text("Export Session").on("click",(e=>{t.getSessionFile(e)}))}const l=s.termdbConfig.helpPages;if(l){t.dom.helpBtn=t.dom.helpDiv.style("display","inline-block").append("button").style("margin","10px").html("Help &#9660;").on("click",(t=>{const e=t.target.getBoundingClientRect();const s=lt.clear().show(e.left-0,e.top+e.height+5).d.append("div");for(const t of l){s.append("div").style("margin","15px").append("a").attr("href",t.url).attr("target","_blank").text(t.label)}}))}};t.mayShowMessage_sessionDaysLeft=()=>{if(!Number.isFinite(t.sessionDaysLeft)){return}t.dom.sessionElapsedMessageDiv.style("display","block");t.dom.remainingDaysMessage=t.dom.sessionElapsedMessageDiv.append("div").style("display","block").style("opacity","0.65").html(`<u>${t.sessionDaysLeft} days</u> left until this session is removed. Click the "Save Session" button to create a new one.`)};t.updateUI=async(e=false)=>{if(!t.dom.subheaderDiv)return;if(t.activeTab&&t.state.termdbConfig.selectCohort&&t.activeCohort==-1){t.dom.subheaderDiv.style("display","none");t.dom.messageDiv.selectAll("text").remove();t.dom.messageDiv.style("display","").text('No cohort selected. Please select a cohort in the "COHORT" tab.')}else{let s="block";if(e){s=t.dom.subheaderDiv.style("display")=="none"?"block":"none"}if(t.dom.subheaderDiv)t.dom.subheaderDiv.style("display",s);if(t.dom.messageDiv)t.dom.messageDiv.style("display","none")}const s=t.state.termdbConfig.selectCohort;t.dom.searchDiv.style("display",s&&t.activeCohort==-1||t.state.nav.header_mode=="only_buttons"?"none":"inline-block");t.dom.header.style("border-bottom",t.state.nav.header_mode==="with_tabs"?"1px solid #000":"");t.dom.tds.style("display","").style("color",(e=>e.colNum==t.activeTab?"#000":"#aaa")).style("background-color",(e=>e.colNum==t.activeTab&&t.dom.subheaderDiv.style("display")!="none"?"#ececec":"transparent")).html((function(e,s){if(e.key=="top")return this.innerHTML;if(e.subheader=="groups"){if(e.key=="mid")return t.state.groups.length||"NONE";return""}if(e.subheader==="charts"){const s=t.state.plots.length;if(e.key=="mid")return!s?"NONE":s;else return""}else if(e.subheader==="about"){if(t.activeCohortName&&t.activeCohortName in t.samplecounts){const s={top:this.innerHTML,mid:t.activeCohortLabel,btm:t.samplecounts[t.activeCohortName]};return s[e.key]||""}else if(t.about){const s={top:t.about?.tab?.topLabel?t.about.tab.topLabel.toUpperCase():this.innerHTML,mid:t.about?.tab?.midLabel?t.about.tab.midLabel.toUpperCase():"ABOUT",btm:t.about?.tab?.btmLabel||this.innerHTML};return s[e.key]||""}else{return e.key==="mid"?"NONE":this.innerHTML}}else if(e.subheader==="filter"){const s=t.filterUiRoot?t.filterUiRoot:{lst:[]};if(s.lst.length===0){return e.key==="mid"?"NONE":t.samplecounts["undefined"]?`${t.samplecounts["undefined"]}`:""}else{const o=t.samplecounts[t.filterJSON]!=undefined?""+t.samplecounts[t.filterJSON]:"";return e.key==="mid"?s.lst.length:o}}else{return e.key==="mid"?this.innerHTML:"&nbsp;"}}));for(const e in t.dom.subheader){t.dom.subheader[e].style("display",t.tabs[t.activeTab].subheader===e?"block":"none")}t.renderCohortsTable();if(t.opts.header_mode==="with_cohort_select"){t.dom.cohortSelect.selectAll("option").property("value",appState.activeCohort)}};t.renderCohortsTable=()=>{if(!t.dom.cohortTable)return;t.dom.cohortTable.selectAll("*").remove();const e=[{label:"Feature"}];const s=[];const o=t.cohortsData;if("error"in o)throw o.error;for(const t of o.features)s.push([{value:t.name}]);for(const t of o.cohorts){e.push({label:t.cohort?`${t.name} (${t.cohort})`:t.name});for(const[e,a]of o.features.entries()){const i=o.cfeatures.find((e=>e.idfeature===a.idfeature&&e.cohort===t.cohort));if(i)s[e].push({value:i.value})}}N({rows:s,columns:e,div:t.dom.cohortTable,showLines:false,maxHeight:"60vh"});t.dom.cohortTable.select("table").style("border-collapse","collapse");t.dom.cohortTable.selectAll(`tbody > tr > td`).style("background-color","transparent");const a=t.state.termdbConfig.selectCohort;const i=a.values[t.activeCohort].keys;let n=`tbody > tr > td:nth-child(${t.activeCohort+2})`;const r=i.length>1;if(r){n="";for(const t of i){const e=o.cohorts.map((t=>t.cohort)).indexOf(t);if(n!=="")n+=",";n+=`tbody > tr > td:nth-child(${e+2})`}}const l=t.dom.cohortTable.selectAll(n);l.style("background-color","yellow");t.dom.cohortInputs.property("checked",((e,s)=>s===t.activeCohort))};t.initCohort=async e=>{const s=e.termdbConfig.selectCohort;if(!s)return;t.dom.tds.filter((t=>t.colNum===0)).style("display","");t.cohortNames=s.values.map((t=>t.keys.slice().sort().join(",")));if(s.title){t.dom.cohortTitle=t.dom.subheader.about.append("h2").style("margin-left","10px").text(s.title)}if(s.description){t.dom.cohortDescription=t.dom.subheader.about.append("div").style("margin-left","10px").html(s.description)}if(s.prompt){t.dom.cohortPrompt=t.dom.subheader.about.append("div").style("margin-left","10px").style("padding-top","30px").style("padding-bottom","10px").style("font-weight","bold").text(s.prompt)}t.dom.cohortOpts=t.dom.subheader.about.append("div").style("margin-bottom","30px").style("margin-left","10px");t.dom.cohortOpts.append("table").selectAll("tr").data(s.values).enter().append("tr").each((function(e,s){const a=o(this);const i=a.append("td");const n="sja-termdb-cohort-"+t.instanceNum;const r=n+"-"+s;i.append("input").attr("type","radio").attr("name",n).attr("id",r).attr("value",s).property("checked",s===t.activeCohort).style("margin-right","5px").style("margin-left","0px").on("click",(()=>{t.app.dispatch({type:"cohort_set",activeCohort:s})}));i.append("label").attr("for",r).attr("colspan",2).style("cursor","pointer").html((t=>t.label));a.selectAll("td").style("max-width","600px").style("padding-bottom","10px").style("padding-right","20px").style("vertical-align","top")}));t.dom.cohortInputs=t.dom.cohortOpts.selectAll("input");t.dom.cohortTable=t.dom.subheader.about.append("div");if(s.asterisk){t.dom.cohortAsterisk=t.dom.subheader.about.append("div").style("margin-left","10px").style("padding-top","20px").style("padding-bottom","20px").style("font-size","small").text(s.asterisk)}}}function gt(t){t.setTab=async(e,s)=>{if(s.colNum===t.activeTab&&!t.searching){t.prevCohort=t.activeCohort;await 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o=u(t.opts.plotDiv);o.header.text(e.sample_id);const a=await import("./plot.ssgq-146075f5.js");await a.plotSingleSampleGenomeQuantification(t.state.termdbConfig,t.state.vocab.dslabel,s,e,o.body.append("div").style("margin","20px"),t.app.opts.genome)}t.dom.tip.hide()};t.openDiscoPlot=async function(e){t.dom.tooltip.hide();t.onClick=false;e.sample_id=e.sample;const s=u(t.opts.plotDiv);s.header.text(e.sample_id);const o=await import("./plot.disco-ccdf741c.js");o.default(t.state.termdbConfig,t.state.vocab.dslabel,e,s.body,t.app.opts.genome)};t.openLollipop=async function(e){t.dom.tooltip.hide();t.onClick=false;const s=u(t.opts.plotDiv||select(t.opts.holder.node().parentNode));s.header.text(e);const o={holder:s.body.append("div").style("margin","20px"),genome:t.app.opts.genome,nobox:true,query:e,tklst:[{type:"mds3",dslabel:t.app.opts.state.vocab.dslabel,filter0:t.state.termfilter.filter0,filterObj:structuredClone(t.state.termfilter.filter)}]};const a=await import("./app-488d9fd6.js").then((function(t){return t.c3}));await a.default(o)};t.onLegendClick=function(s,o,a,i,n,r){const l=t.config[a];const p=l.q.hiddenValues?i in l.q.hiddenValues:false;const d=new e({padding:"0px"});const h=d.d.append("div");h.append("div").attr("class","sja_menuoption sja_sharp_border").text(p?"Show":"Hide").on("click",(()=>{t.hideCategory(o,l,i,!p);d.hide();const e={};e[a]=l;t.app.dispatch({type:"plot_edit",id:t.id,config:e})}));h.append("div").attr("class","sja_menuoption sja_sharp_border").text("Show only").on("click",(()=>{const e=a=="colorTW"?s.colorLegend:s.shapeLegend;for(const s of e.keys())t.hideCategory(o,l,s,l.term.type=="geneVariant"&&l.q.type=="values"?!s.startsWith(i):s!=i);d.hide();const n={};n[a]=l;t.app.dispatch({type:"plot_edit",id:t.id,config:n})}));h.append("div").attr("class","sja_menuoption sja_sharp_border").text("Show all").on("click",(()=>{d.hide();const e=a=="colorTW"?s.colorLegend:s.shapeLegend;for(const s of e.keys())t.hideCategory(o,l,s,false);const i={};i[a]=l;t.app.dispatch({type:"plot_edit",id:t.id,config:i})}));if(r.color){const e=c(r.color).formatHex();const s=h.append("div").attr("class","sja_sharp_border").style("padding","0px 10px").text("Color:").append("input").attr("type","color").attr("value",e).on("change",(()=>{t.changeColor(i,s.node().value);d.hide()}))}d.showunder(n.target)};t.hideCategory=function(e,s,o,a){if(o=="Ref"){t.settings.showRef=!a;t.app.dispatch({type:"plot_edit",id:t.id,config:{settings:{sampleScatter:t.settings}}})}if(!s.q.hiddenValues)s.q.hiddenValues={};const i=!(s.term.type=="geneVariant"&&s.q.type=="values")&&s.term.values[o]?s.term.values[o]:{key:o,label:o};const n=e.selectAll(`text[name="sjpp-scatter-legend-label"]`).nodes();const r=n.find((t=>o.startsWith(t.innerHTML)))?.parentElement;if(r)r.style["text-decoration"]=a?"line-through":"none";if(!a)delete s.q.hiddenValues[o];else s.q.hiddenValues[o]=i};t.changeColor=async function(e,s){const o=t.config.colorTW;if(!(o.term.type=="geneVariant"&&o.q.type=="values")&&o.term.values[e])o.term.values[e].color=s;else{if(!o.term.values)o.term.values={};o.term.values[e]={key:e,label:e,color:s}}await t.app.dispatch({type:"plot_edit",id:t.id,config:{colorTW:o}})};t.searchSample=async function(s){if(!this.searchMenu){this.searchMenu=new e({padding:"3px"});this.samplesData=await this.app.vocabApi.getSamplesByName({filter:t.state.termfilter.filter});const s=t=>{};V(this.searchMenu.d,this.samplesData,s,(e=>t.filterSamples(e)))}this.searchMenu.show(s.clientX,s.clientY,false)};t.filterSamples=function(e){this.filterSampleStr=e;t.render()};t.getCategoryInfo=function(t,e){if(!(e in t))return"";return t[e]};t.addToFilter=function(e){const s=G(t.state.termfilter.filter,"filterUiRoot");const o=q([s,D(e)]);o.tag="filterUiRoot";t.app.dispatch({type:"filter_replace",filter:o})};t.showTable=function(e,s,o,a){let i=[];const n=[];const r=e.items[0];if("sample"in r)n.push(f("Sample","label"));if(t.config.colorTW)n.push(f(t.config.colorTW.term.name,"label"));if(t.config.shapeTW)n.push(f(t.config.shapeTW.term.name,"label"));let l=false;for(const s of e.items){const e=[];if("sample"in s)e.push(f(s.sample));if(t.config.colorTW)e.push(f(t.getCategoryInfo(s,"category")));if(t.config.shapeTW)e.push(f(t.getCategoryInfo(s,"shape")));if("info"in s){l=true;const t=[];for(const[e,o]of Object.entries(s.info))t.push(`${e}: ${o}`);e.push(f(t.join(", ")))}i.push(e)}if(l)n.push(f("Info","label"));t.dom.tip.clear();const c=t.dom.tip.d.append("div").style("padding","5px");const p=c.append("div").style("margin-top","5px");const d=p.append("div").html("&nbsp;"+e.name).style("font-size","0.9rem").on("click",(()=>{const s=d.select("input").empty();if(!s)return;d.html("");const o=d.append("input").attr("value",e.name).on("change",(async()=>{const s=o.node().value;if(s)t.renameGroup(e,s);else o.node().value=e.name;d.html("&nbsp;"+e.name)}));o.node().focus();o.node().select()}));const h=c.append("div");const m=[];if(a){const e={text:"Add to a group",callback:e=>{const s=[];for(const o of e)s.push(t.selectedItems[o].__data__);const o={name:`Group ${t.config.groups.length+1}`,items:s,index:t.config.groups.length};const a=D(k([o]));_(t.app,a,t.state.groups)}};m.push(e)}else{const i={text:"Delete samples",callback:i=>{e.items=e.items.filter(((t,e,s)=>!(e in i)));t.showTable(e,s,o,a)}};m.push(i)}N({rows:i,columns:n,div:h,showLines:true,maxWidth:n.length*"15"+"vw",maxHeight:"35vh",buttons:m,selectAll:true});t.dom.tip.show(s,o,false,false);function f(t,e="value"){let s={};s[e]=t;return s}};t.showGroupMenu=function(e,s){t.dom.tip.clear();t.dom.tip.show(e.clientX,e.clientY,false,true);const o=t.dom.tip.d.append("div");const a=t.config.name?t.config.name:"Summary scatter";const i=k([s],a+" groups");const n=o.append("div").attr("name","sjpp-group-input-div").html("&nbsp;"+s.name).style("font-size","0.9rem").on("click",(()=>{const e=n.select("input").empty();if(!e)return;n.html("");const o=n.append("input").attr("value",s.name).on("change",(async()=>{const e=o.node().value;if(e)t.renameGroup(s,e);else o.node().value=s.name;n.html("&nbsp;"+s.name)}));o.node().focus();o.node().select()}));o.append("div").attr("class","sja_menuoption sja_sharp_border").text(`Edit ${s.items.length} samples`).on("click",(o=>{t.dom.tip.hide();t.showTable(s,e.clientX,e.clientY,false)}));t.addCommonMenuItems(o,i);o.append("div").attr("class","sja_menuoption sja_sharp_border").text(`Delete group`).on("click",(async e=>{await t.app.vocabApi.deleteGroup(s.name);t.dom.tip.hide()}));o.append("div").attr("class","sja_menuoption sja_sharp_border").text("Add to filter").on("click",(()=>{t.addToFilter(i);t.app.dispatch({type:"plot_edit",id:t.id,config:{groups:t.config.groups}})}));o.append("div").attr("class","sja_menuoption sja_sharp_border").text(s.showOnly?"Show All":"Show Only").on("click",(()=>{s.showOnly=!s.showOnly;t.app.dispatch({type:"plot_edit",id:t.id,config:{groups:t.config.groups}})}))};t.renameGroup=async function(e,s){const o=t.config.groups.findIndex((t=>t.name==s));if(o!=-1)alert(`Group named ${s} already exists`);else await t.app.dispatch({type:"rename_group",index:e.index,newName:s})};t.addCommonMenuItems=function(e,s){A(t.dom.tip,e,s,t.app,t.id,t.state);if(t.state.supportedChartTypes.includes("survival"))O("survival",e,"Compare survival",t.dom.tip,s,t.id,this);if(t.state.supportedChartTypes.includes("cuminc"))O("cuminc",e,"Compare cumulative incidence",t.dom.tip,s,t.id,this);const o=e.append("div").attr("class","sja_menuoption sja_sharp_border").html("Summarize");o.insert("div").html("›").style("float","right");o.on("click",(async e=>{W(o,(e=>{L(e,s,t.app,t.id)}),t.app,t.dom.tip)}))};t.showGroupsMenu=function(e){t.dom.tip.clear();t.dom.tip.show(e.clientX,e.clientY,false,true);const s=t.dom.tip.d.append("div");const o=t.config.name?t.config.name:"Summary scatter";const a=k(t.config.groups,o+" groups");let i=s.append("div");for(const[o,a]of t.config.groups.entries()){i=s.append("div").attr("class","sja_menuoption sja_sharp_border");i.insert("div").style("display","inline-block").text(` ${a.name}: ${a.items.length} `);i.append("div").style("display","inline-block").style("float","right").html("&nbsp;&nbsp;›");i.on("click",(s=>{t.dom.tip.clear().hide();t.showGroupMenu(e,a)}))}t.addCommonMenuItems(s,a);i=s.append("div").attr("class","sja_menuoption sja_sharp_border").text("Delete groups").on("click",(async e=>{for(const e of t.config.groups)await t.app.vocabApi.deleteGroup(e.name);t.app.dispatch({type:"plot_edit",id:t.id,config:{groups:[]}})}))}}function It(t,e,s,o,a){const i=a.xAxisScale(s)-a.xAxisScale(t);const n=a.yAxisScale(o)-a.yAxisScale(e);const r=Math.sqrt(Math.pow(i,2)+Math.pow(n,2));return r}var Nt=Object.freeze({__proto__:null,setInteractivity:zt});const Gt=.2;const Rt=4;const qt=I;class Vt{constructor(){this.type="sampleScatter";this.lassoOn=false;this.zoom=1;this.startGradient={};this.stopGradient={}}async init(t){const s=this.opts.holder.insert("div").style("display","inline-block");const a=s.insert("div").style("display","inline-block").attr("class","pp-termdb-plot-controls");this.mainDiv=this.opts.holder.insert("div").style("display","inline-block").style("vertical-align","top");const i=80;this.axisOffset={x:i,y:30};this.dom={header:this.opts.header,loadingDiv:this.opts.holder.append("div").style("position","absolute").style("left","45%").style("top","60%"),tip:new e({padding:"0px"}),tooltip:new e({padding:"2px",offsetX:10,offsetY:0}),controlsHolder:a,toolsDiv:s.insert("div")};this.settings={};if(this.dom.header)this.dom.header.html("Scatter Plot");zt(this);Mt(this);document.addEventListener("scroll",(t=>this?.dom?.tooltip?.hide()));o(".sjpp-output-sandbox-content").on("scroll",(t=>this.dom.tooltip.hide()))}getState(t){const e=t.plots.find((t=>t.id===this.id));if(!e){throw`No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`}const s=M(t);return{config:e,termfilter:t.termfilter,supportedChartTypes:t.termdbConfig.supportedChartTypes[s],matrixplots:t.termdbConfig.matrixplots,vocab:t.vocab,termdbConfig:t.termdbConfig,groups:$(t)}}getDataRequestOpts(){const t=this.config;const e=[];if(t.term)e.push(t.term);if(t.term2)e.push(t.term2);const s={name:t.name,colorTW:t.colorTW,filter:this.getFilter(),coordTWs:e};if(this.state.termfilter.filter0)s.filter0=this.state.termfilter.filter0;if(t.colorColumn)s.colorColumn=t.colorColumn;if(t.shapeTW)s.shapeTW=t.shapeTW;if(t.scaleDotTW){if(!t.scaleDotTW.q)t.scaleDotTW.q={};t.scaleDotTW.q.mode="continuous";s.scaleDotTW=t.scaleDotTW}if(t.term0)s.divideByTW=t.term0;return s}async main(){this.config=structuredClone(this.state.config);if(this.config.settings.sampleScatter.regression!=="None"&&this.config.term0){if(this.charts)for(const t of this.charts)t.chartDiv.selectAll("*").remove();this.dom.loadingDiv.style("display","block").html("Processing data...")}if(this.dom.header)this.dom.header.html(this.config.name+` <span style="opacity:.6;font-size:.7em;margin-left:10px;">SCATTER PLOT</span>`);g(this.settings,this.config.settings.sampleScatter);const t=this.getDataRequestOpts();if(t.coordTWs.length==1)return;const e=await this.app.vocabApi.getScatterData(t);if(e.error)throw e.error;this.charts=[];let s=0;for(const[t,o]of Object.entries(e)){if(!Array.isArray(o.samples))throw"data.samples[] not array";if(o.isLast)this.createChart(t,o,s);else this.createChart(t,o,0)}this.initRanges();this.is3D=this.config.term&&this.config.term0?.q.mode=="continuous";if(!this.config.colorColumn)await this.setControls();await this.processData();this.render();this.dom.loadingDiv.style("display","none");if(!this.is3D)this.setTools();this.dom.tip.hide()}createChart(t,e,s){const o=e.samples.filter((t=>"sampleId"in t));if(o.length>1e4)this.is2DLarge=true;const a=new Map(e.colorLegend);const i=new Map(e.shapeLegend);this.charts.splice(s,0,{id:t,data:e,cohortSamples:o,colorLegend:a,shapeLegend:i})}initRanges(){if(this.charts.length>1){const t=[];for(const e of this.charts)t.push(...e.data.samples);const e=t[0];const[s,o,a,i,n,r,l,c]=t.reduce(((t,e)=>[e.x<t[0]?e.x:t[0],e.x>t[1]?e.x:t[1],e.y<t[2]?e.y:t[2],e.y>t[3]?e.y:t[3],e.z<t[4]?e.z:t[4],e.z>t[5]?e.z:t[5],"scale"in e?e.scale<t[6]?e.scale:t[6]:Number.POSITIVE_INFINITY,"scale"in e?e.scale>t[7]?e.scale:t[7]:Number.NEGATIVE_INFINITY]),[e.x,e.x,e.y,e.y,e.z,e.z,e.scale,e.scale]);for(const t of this.charts){t.xMin=s;t.xMax=o;t.yMin=a;t.yMax=i;t.zMin=n;t.zMax=r;t.scaleMin=l;t.scaleMax=c}}else for(const t of this.charts){if(t.data.samples.length==0)return;const e=t.data.samples[0];const[s,o,a,i,n,r,l,c]=t.data.samples.reduce(((t,e)=>[e.x<t[0]?e.x:t[0],e.x>t[1]?e.x:t[1],e.y<t[2]?e.y:t[2],e.y>t[3]?e.y:t[3],e.z<t[4]?e.z:t[4],e.z>t[5]?e.z:t[5],"scale"in e?e.scale<t[6]?e.scale:t[6]:Number.POSITIVE_INFINITY,"scale"in e?e.scale>t[7]?e.scale:t[7]:Number.NEGATIVE_INFINITY]),[e.x,e.x,e.y,e.y,e.z,e.z,e.scale,e.scale]);t.xMin=s;t.xMax=o;t.yMin=a;t.yMax=i;t.zMin=n;t.zMax=r;t.scaleMin=l;t.scaleMax=c}}async setControls(){this.dom.controlsHolder.selectAll("*").remove();const t=this.charts[0]?.data.samples.find((t=>!("sampleId"in t)))||false;const e={type:"term",configKey:"scaleDotTW",chartType:"sampleScatter",usecase:{target:"sampleScatter",detail:"numeric"},title:"Scale sample by term value",label:"Scale by",vocabApi:this.app.vocabApi,numericEditMenuVersion:["continuous"]};const s={type:"term",configKey:"shapeTW",chartType:"sampleScatter",usecase:{target:"sampleScatter",detail:"shapeTW"},title:"Categories to assign a shape",label:"Shape",vocabApi:this.app.vocabApi};const o={label:"Sample size",type:"number",chartType:"sampleScatter",settingsKey:"size",title:"Sample size, represents the factor used to scale the sample",min:0};const a=(Rt-Gt)/10;const i={label:"Min size",type:"number",chartType:"sampleScatter",settingsKey:"minShapeSize",title:"Minimum sample size",min:Gt,max:Rt,step:a};const n={label:"Max size",type:"number",chartType:"sampleScatter",settingsKey:"maxShapeSize",title:"Maximum sample size",min:Gt,max:Rt,step:a};const r={label:"Scale order",type:"radio",chartType:"sampleScatter",settingsKey:"scaleDotOrder",options:[{label:"Ascending",value:"Ascending"},{label:"Descending",value:"Descending"}]};const l={label:"Reference size",type:"number",chartType:"sampleScatter",settingsKey:"refSize",title:"It represents the area of the reference symbol in square pixels",min:0};const c={boxLabel:"Visible",label:"Show axes",type:"checkbox",chartType:"sampleScatter",settingsKey:"showAxes",title:`Option to show/hide plot axes`};const p=[{type:"term",configKey:"colorTW",chartType:"sampleScatter",usecase:{target:"sampleScatter",detail:"colorTW"},title:"Categories to color the samples",label:"Color",vocabApi:this.app.vocabApi,numericEditMenuVersion:["continuous","discrete"]},{label:"Opacity",type:"number",chartType:"sampleScatter",settingsKey:"opacity",title:"It represents the opacity of the elements",min:0,max:1,step:.1},{label:"Chart width",type:"number",chartType:"sampleScatter",settingsKey:"svgw"},{label:"Chart height",type:"number",chartType:"sampleScatter",settingsKey:"svgh"}];if(this.config.sampleCategory){const t=Object.values(this.config.sampleCategory.tw.term.values).map((t=>({label:t.label||t.key,value:t.key})));if(this.config.sampleCategory.order)t.sort(((t,e)=>{const s=this.config.sampleCategory.order.indexOf(t.value);const o=this.config.sampleCategory.order.indexOf(e.value);if(s<o)return-1;return 1}));if(!this.settings.sampleCategory)this.settings.sampleCategory=this.config.sampleCategory.defaultValue||"";t.push({label:"All",value:""});const e={label:"Sample type",type:"dropdown",chartType:"sampleScatter",settingsKey:"sampleCategory",options:t};p.push(e)}if(!this.is2DLarge){p.unshift({type:"term",configKey:"term0",chartType:"sampleScatter",usecase:{target:"sampleScatter",detail:"term0"},title:"Categories to divide by",label:this.config.term0?.q?.mode=="continuous"?"Z":"Divide by",vocabApi:this.app.vocabApi,numericEditMenuVersion:this.app.hasWebGL?.()?["discrete","continuous"]:["discrete"],processInput:t=>{if(t?.term.type=="integer"||t?.term.type=="float")t.q={mode:"continuous"}}})}else{p.push({label:"Sample size",type:"number",chartType:"sampleScatter",settingsKey:"threeSize",title:"Sample size",min:0,max:1,step:.001}),p.push({label:"Field of Vision",type:"number",chartType:"sampleScatter",settingsKey:"threeFOV",title:"Field of Vision",min:50,max:90,step:1})}if(this.config.term){p.unshift(...[{type:"term",configKey:"term",chartType:"sampleScatter",usecase:{target:"sampleScatter",detail:"numeric"},title:"X coordinate to plot the 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degrees",type:"number",chartType:"sampleScatter",settingsKey:"fov"})}p.push(c);p.push({label:"Default color",type:"color",chartType:"sampleScatter",settingsKey:"defaultColor"})}else if(!this.is2DLarge){p.splice(2,0,s);p.splice(3,0,e);if(this.config.scaleDotTW){p.splice(4,0,i);p.splice(5,0,n);p.splice(6,0,r);if(t)p.splice(7,0,l)}else{p.splice(4,0,o);if(t)p.splice(5,0,l)}p.push(c)}this.components={controls:await x({app:this.app,id:this.id,holder:this.dom.controlsHolder,inputs:p})};this.components.controls.on("downloadClick.scatter",(()=>{if(this.is2DLarge||this.is3D){const t=this.canvas.toDataURL("image/png");Ft(t)}else for(const t of this.charts)F(t.svg,"scatter.svg",this.opts.holder.node())}))}getFilter(){const t={type:"tvslst",in:true,join:"and",lst:[]};const e="sampleCategory"in this.settings?this.settings.sampleCategory:this.config.sampleCategory?.defaultValue;if(e){const s=this.config.sampleCategory.tw;t.lst.push({type:"tvs",tvs:{term:s.term,values:[{key:e}]}})}const s=[this.state.termfilter.filter,t];if(this.config.filter)s.push(this.config.filter);const o=q(s);return o}}function Et(t,e,s=null){let o={chartType:"sampleScatter",name:e.name,filter:s};if(e.sampleCategory)o.sampleCategory={tw:structuredClone(e.sampleCategory.tw),order:e.sampleCategory.order,defaultValue:e.sampleCategory.defaultValue};if(e.sampleType)o.sampleType=e.sampleType;if(e.colorTW)o.colorTW=structuredClone(e.colorTW);else if(e.colorColumn)o.colorColumn=structuredClone(e.colorColumn);if("shapeTW"in e)o.shapeTW=structuredClone(e.shapeTW);if(e.settings)o.settings=structuredClone(e.settings);t.dispatch({type:"plot_create",config:o})}function Ft(t){const e=document.createElement("a");e.setAttribute("download","image");document.body.appendChild(e);e.click();e.remove();e.href=t;e.click();e.remove()}async function Pt(t,e){try{if(t.colorTW)await v(t.colorTW,e.vocabApi);if(t.shapeTW)await v(t.shapeTW,e.vocabApi);if(t.term)await v(t.term,e.vocabApi);if(t.term2)await v(t.term2,e.vocabApi);if(t.term0)await v(t.term0,e.vocabApi);if(t.scaleDotTW)await v(t.scaleDotTW,e.vocabApi);if(t.sampleCategory)await v(t.sampleCategory.tw,e.vocabApi);let s=Kt();if(t.settings)g(s,t.settings);if(!t.term&&!t.term2)s.showAxes=false;const o={groups:[],settings:{controls:{isOpen:false},sampleScatter:s},startColor:{},stopColor:{}};const a=g(o,t);if(a.term0?.q?.mode=="continuous"&&!e.hasWebGL())throw"Can not load Z/Divide by term in continuous mode as WebGL is not supported";return a}catch(t){console.log(t);throw`${t} [sampleScatter getPlotConfig()]`}}const Bt=t(Vt);const Ut=Bt;function Ht(t,e){const s=t.append("div");if(e.state.termdbConfig.scatterplots)for(const t of e.state.termdbConfig.scatterplots){s.append("div").attr("class","sja_menuoption sja_sharp_border").text(t.name).on("click",(()=>{Et(e.app,t);e.dom.tip.hide()}))}s.append("div");if(!e.state.termdbConfig.hiddenChartTypes?.includes("dynamicScatter")){const t=(t,s)=>{e.app.dispatch({type:"plot_create",config:{chartType:"sampleScatter",term:{term:t,q:{mode:"continuous"}},term2:{term:s,q:{mode:"continuous"}},name:`${t.name} vs ${s.name}`}})};E(e.dom.tip,e.app,"sampleScatter","numeric",t)}}function Kt(){return{size:1,minShapeSize:.5,maxShapeSize:4,scaleDotOrder:"Ascending",refSize:.8,svgw:500,svgh:500,svgd:500,axisTitleFontSize:16,showAxes:true,showRef:true,opacity:.8,defaultColor:y,regression:"None",fov:50,threeSize:.002,threeFOV:70}}async function Yt(t,e,s){const o={holder:t,state:{vocab:e.vocab,plots:[{chartType:"sampleScatter",subfolder:"plots",name:s.name,colorTW:s.colorTW,sampleType:s.sampleType,sampleCategory:{tw:structuredClone(s.sampleCategory.tw),order:s.sampleCategory.order,defaultValue:s.sampleCategory.defaultValue}}]}};const a=await import("./plot.app-fc3608a9.js");await a.appInit(o)}var Jt=Object.freeze({__proto__:null,minShapeSize:Gt,maxShapeSize:Rt,shapes:qt,openScatterPlot:Et,downloadImage:Ft,getPlotConfig:Pt,scatterInit:Bt,componentInit:Ut,makeChartBtnMenu:Ht,getDefaultScatterSettings:Kt,renderScatter:Yt});export{Nt as a,Jt as b,Kt as g,ft as n,$t as s};