@sjcrh/proteinpaint-client 2.76.2 → 2.77.1

package/dist/sampleScatter-55d9eb74.js

@@ -1 +0,0 @@
-import{h as t,M as e,a as s,d as a,y as o,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-6fb77603.js";import{c as b,f as v}from"./termsetting-492eefa7.js";import{controlsInit as x}from"./controls-268e40e6.js";import{d as S}from"./zoom-f445cfef.js";import{d as w}from"./lasso-1a02a545.js";import{c as C,g as j,r as T,a as k,b as D,d as A,e as _,f as L,h as M,o as O,i as W,j as z}from"./recover-299ffdb3.js";import{t as $}from"./downloadTextfile-5723af95.js";import{r as I}from"./table-0daf2b89.js";import{a as N,b as G,c as R}from"./FilterRxComp-02e68f1b.js";import{searchSampleInput as q}from"./sampleView-1dff3fca.js";import{s as V}from"./select2Terms-d48d037e.js";import{d as E}from"./svg.download-f4aa48e4.js";import{s as P}from"./sampleScatter.rendererThree-ef289434.js";import{a as F,b as H,c as U}from"./axis-747c801e.js";import{l as B}from"./line-264f8f9e.js";class K{constructor(t){this.type="search";J(this);X(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 Y=t(K);function J(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=a(this);const o=s.append("td").text(e.name);if(e.type){o.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{o.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 X(t){t.onInput=async()=>{const e=t.dom.input.property("value");try{await t.doSearch(e)}catch(e){t.clear();o(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-bbfad00d.js");case"../plots/Disco.js":return import("./Disco-b7c9bf72.js");case"../plots/DziViewer.js":return import("./DziViewer-28915c11.js");case"../plots/WSIViewer.js":return import("./WSIViewer-957695a8.js");case"../plots/barchart.data.js":return import("./FilterRxComp-02e68f1b.js").then((function(t){return t.j}));case"../plots/barchart.events.js":return import("./barchart.events-426d737a.js");case"../plots/barchart.js":return import("./barchart-2898d229.js");case"../plots/bars.renderer.js":return import("./bars.renderer-71935d34.js");case"../plots/bars.settings.js":return import("./bars.settings-64bb4642.js");case"../plots/boxplot.js":return import("./boxplot-4c9a5479.js");case"../plots/brainImaging.js":return import("./brainImaging-7716bc66.js");case"../plots/controls.btns.js":return import("./controls.btns-5bf9e7d7.js");case"../plots/controls.config.js":return import("./controls.config-2f0fa061.js");case"../plots/controls.js":return import("./controls-268e40e6.js");case"../plots/cuminc.js":return import("./cuminc-8dffb765.js");case"../plots/dataDownload.js":return import("./dataDownload-452ae3cd.js");case"../plots/dictionary.js":return import("./dictionary-a132a3cc.js");case"../plots/facet.js":return import("./facet-fa4fe49c.js");case"../plots/geneExpression.js":return import("./geneExpression-66208299.js");case"../plots/geneORA.js":return import("./geneORA-9456872c.js");case"../plots/geneset.js":return import("./geneset-0315daf8.js");case"../plots/genomeBrowser.controls.js":return import("./genomeBrowser.controls-2601cab5.js");case"../plots/genomeBrowser.js":return import("./genomeBrowser-608b924e.js");case"../plots/gsea.js":return import("./gsea-0c0cf8de.js");case"../plots/hierCluster.config.js":return import("./hierCluster.config-f4daaf92.js");case"../plots/hierCluster.interactivity.js":return import("./hierCluster.interactivity-7f475259.js").then((function(t){return t.i}));case"../plots/hierCluster.js":return import("./hierCluster-7ab62ca5.js");case"../plots/hierCluster.renderers.js":return import("./hierCluster.renderers-19b79639.js").then((function(t){return t.r}));case"../plots/imagePlot.js":return import("./imagePlot-1ef24562.js");case"../plots/matrix.cells.js":return import("./matrix.cells-a018d731.js");case"../plots/matrix.cluster.js":return import("./matrix.cluster-a6e713e8.js");case"../plots/matrix.config.js":return import("./matrix.config-2c550b5d.js");case"../plots/matrix.controls.js":return import("./matrix.controls-42ad4912.js");case"../plots/matrix.data.js":return import("./matrix.data-2b814c9f.js").then((function(t){return t.m}));case"../plots/matrix.dom.js":return import("./matrix.dom-1e0da5b3.js");case"../plots/matrix.groups.js":return import("./matrix.groups-824a7244.js").then((function(t){return t.m}));case"../plots/matrix.interactivity.js":return import("./matrix.interactivity-1cb56534.js");case"../plots/matrix.js":return import("./matrix-38cd47c3.js");case"../plots/matrix.layout.js":return import("./matrix.layout-47e44357.js").then((function(t){return t.m}));case"../plots/matrix.legend.js":return import("./matrix.legend-9af0c757.js").then((function(t){return t.m}));case"../plots/matrix.renderers.js":return import("./matrix.renderers-337ce240.js");case"../plots/matrix.serieses.js":return import("./matrix.serieses-7b7184c9.js").then((function(t){return t.m}));case"../plots/matrix.sort.js":return import("./matrix.sort-1ac05842.js");case"../plots/matrix.sorterUi.js":return import("./matrix.sorterUi-1c60c145.js");case"../plots/plot.app.js":return import("./plot.app-2a805759.js");case"../plots/plot.brainImaging.js":return import("./plot.brainImaging-32a484b6.js");case"../plots/plot.disco.js":return import("./plot.disco-1fdfee3c.js");case"../plots/plot.ssgq.js":return import("./plot.ssgq-d33113d5.js");case"../plots/profileBarchart.js":return import("./profileBarchart-58f0a8c0.js");case"../plots/profilePlot.js":return import("./profilePlot-4db8ca78.js");case"../plots/profilePolar.js":return import("./profilePolar-50b8e40e.js");case"../plots/profileRadar.js":return import("./profileRadar-fff0b004.js");case"../plots/profileRadarFacility.js":return import("./profileRadarFacility-d6d34c15.js");case"../plots/profileSummary.js":return import("./profileSummary-04b8b15b.js");case"../plots/regression.inputs.js":return import("./regression.inputs-14df7c31.js").then((function(t){return t.b}));case"../plots/regression.inputs.term.js":return import("./regression.inputs-14df7c31.js").then((function(t){return t.a}));case"../plots/regression.inputs.values.table.js":return import("./regression.inputs.values.table-d79efa9e.js");case"../plots/regression.js":return import("./regression.inputs-14df7c31.js").then((function(t){return t.r}));case"../plots/regression.results.js":return import("./regression.results-4767144e.js").then((function(t){return t.r}));case"../plots/sampleScatter.interactivity.js":return Promise.resolve().then((function(){return It}));case"../plots/sampleScatter.js":return Promise.resolve().then((function(){return Xt}));case"../plots/sampleScatter.renderer.js":return Promise.resolve().then((function(){return Wt}));case"../plots/sampleScatter.rendererThree.js":return import("./sampleScatter.rendererThree-ef289434.js").then((function(t){return t.c}));case"../plots/sampleView.js":return import("./sampleView-1dff3fca.js");case"../plots/scatter.js":return import("./scatter-f8285107.js");case"../plots/singleCellPlot.js":return import("./singleCellPlot-eff5760b.js");case"../plots/stattable.js":return import("./stattable-46cde32c.js");case"../plots/summary.js":return import("./summary-a6c15c9e.js");case"../plots/survival.js":return import("./survival-52714cd3.js");case"../plots/table.js":return import("./table-bf40249b.js");case"../plots/variantBrowser.js":return import("./variantBrowser-14d5c3f6.js");case"../plots/violin.interactivity.js":return import("./violin.interactivity-bf40ddde.js");case"../plots/violin.js":return import("./violin-74d26b75.js");case"../plots/violin.renderer.js":return import("./violin.renderer-469fa0ff.js");default:return new Promise((function(e,s){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(s.bind(null,new Error("Unknown variable dynamic import: "+t)))}))}}class Q{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='${t}' value='current' checked=checked style='margin-right: 0; vertical-align: bottom'/>\n\t\t\t\t<span>current tab</span>\n\t\t\t</label>\n\t\t`);const e=await this.listSessions({trClickHandler:async(e,s)=>{const{loc:a,id:o}=s;if(!o)return;if(a.includes("browser")){this.sessionName=o;const e=this.savedSessions[o];await tt(e,this.app);const s=this.dom.tip.d.node().querySelector(`[name="${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=${o}&src=browser`)}else{if(e.embedder)i({state:e});else{const{protocol:t,host:s,search:a,origin:o,href:n}=window.location;const r={protocol:t,host:s,search:a,origin:o,href:n};i({state:Object.assign({embedder:r},e)})}}this.dom.tip.hide()}else if(a=="server"){const e=this.app.vocabApi.mayGetAuthHeaders(this.route);const s={id:o,route:this.route,dslabel:this.dslabel,embedder:window.location.hostname};const a=await n(`/massSession?`,{headers:e,body:s});if(!a.state)throw a.error||"unable to get the cached session from the server";await tt(a.state,this.app);this.savedSessions[o]=a.state;const r=this.dom.tip.d.node().querySelector(`[name="${t}"]:checked`).value;if(r=="current"){this.app.dispatch({type:"app_refresh",state:a.state})}else if(window.location.origin==this.hostURL){window.open(`/?mass-session-id=${o}&src=cred&dslabel=${this.dslabel}&route=${this.route}`)}else{i(a)}this.dom.tip.hide()}}});e.headtr.select("th").html("Open from");const s=e.tbody.insert("tr","tr");s.append("td").style("text-align","center").style("padding","3px 9px").html("Local file");const a=s.append("td").style("text-align","left").append("label");a.append("span").style("padding","3px 9px").style("text-decoration","underline").style("cursor","pointer").html("Choose File");a.append("input").attr("type","file").attr("placeholder","file name").style("opacity",0).style("width","0.1px").style("height","0.1px").style("position","absolute").on("change",(async()=>{const e=event.target.files.item(0);const s=await e.text();let a=e.name;if(this.savedSessions[a]){a=prompt(`Leave as-is to overwrite a session with the same name, or enter a different session name.`,a)}this.sessionName=a;const o=JSON.parse(s);await tt(o,this.app);this.savedSessions[a]=o;localStorage.setItem("savedMassSessions",JSON.stringify(this.savedSessions));const n=this.dom.tip.d.node().querySelector(`[name="${t}"]:checked`).value;if(n=="current"){this.app.dispatch({type:"app_refresh",state:o})}else if(window.location.origin==this.hostURL){window.open(`/?mass-session-id=${a}&src=browser`)}else{if(o.embedder)i({state:o});else{const{protocol:t,host:e,search:s,origin:a,href:n}=window.location;const r={protocol:t,host:e,search:s,origin:a,href:n};i({state:Object.assign({embedder:r},o)})}}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 a=Object.keys(this.savedSessions).map((t=>({loc:"browser",id:t})));if(!this.serverCachedSessions)await this.setServerCachedSessions();a.push(...this.serverCachedSessions.map((t=>({loc:"server",id:t}))));const o=e.append("tbody");const i=o.selectAll("tr").data(a).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:o,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 a=await n("/sessionIds",{headers:e,body:s});this.serverCachedSessions=a.sessionIds||[]}async save(t){const e=this.dom.tip.d;const s=e.append("div");s.append("span").html("Save as");const a=Object.keys(this.savedSessions);if(!this.serverCachedSessions)await this.setServerCachedSessions();a.push(...this.serverCachedSessions.filter((t=>!a.includes(t))));const o=this.sessionName||"unnamed-session";const i=s.append("input").attr("type","text").attr("placeholder",o).style("width","220px").on("input",(()=>{n.selectAll("*").remove();const t=i.property("value");const e=a.filter((e=>e===t));const s=a.filter((e=>e.startsWith(t)));const o=a.filter((e=>e.includes(t)&&e!==t&&!s.includes(e)));n.selectAll("div").data([...e,...s,...o]).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")||o;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")||o;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")||o;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 a=`${e}${s}`;$(a,JSON.stringify(this.savedSessions[e]))}async getSessionUrl(t=""){const e=this.app.vocabApi.mayGetAuthHeaders("termdb");const s=structuredClone(this.app.getState());const{protocol:a,host:o,search:r,origin:l,href:c}=window.location;s.embedder={protocol:a,host:o,search:r,origin:l,href:c};if(t){s.__sessionFor__={route:this.route,filename:t,dslabel:this.dslabel,embedder:window.location.hostname}}const p=await n("/massSession",{headers:e,method:"POST",body:JSON.stringify(s)});if(t){return p}else{const t=`${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 a=e.append("a").attr("href",t).attr("target","_blank").html(p.id);if(this.hostURL!=window.location.origin){a.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 ${this.opts.massSessionDuration} days.</li>\n\t\t\t\t\t</ul>\n\t\t\t\t\t</div>`);setTimeout((()=>{this.dom.button.property("disabled",false)}),1e3)}}async delete(){const t=await this.listSessions({trClickHandler:function(s){const o=this.lastChild.querySelector("input");const i=s.target==o?o.checked:!o.checked;a(this).style("text-decoration",i?"line-through":"");if(s.target!=o)o.checked=i;const n=t.table.node().querySelectorAll("input:checked");e.property("disabled",n.length?false:true)}});t.headtr.append("th").html("Delete");t.trs.each((function(t){a(this).append("td").style("text-align","center").append("input").attr("type","checkbox").attr("value",t.id)}));const e=this.dom.tip.d.append("div").style("text-align","center").append("button").html("Delete selected sessions").property("disabled",true).on("click",(async()=>{const e=t.table.node().querySelectorAll("input");const s=[];for(const t of e){if(a(t).property("checked")){const e=t.parentNode.parentNode.__data__;if(e.loc=="browser"){delete this.savedSessions[t.value]}else if(e.loc=="server"){delete this.serverCachedSessions[t.value];s.push(t.value)}else throw`unknown cache location=${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 a=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 tt(t,e){if(t.plots){const s=[];for(const a of t.plots){s.push((async()=>{const t=await Z(`../plots/${a.chartType}.js`);return await t.getPlotConfig(a,e)})())}try{await Promise.all(s)}catch(t){console.log(t);e.printError(t)}}}const et=t(Q);class st{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 t=this.app.Inner.components.nav.Inner.tabs.findIndex((t=>t.subheader=="about"));const e=this.app.Inner.state.nav.activeTab==t;this.holder.style("display",e?"":"none")}}const at=t(st);let ot=0;const it="_MASS_AUTOID_"+Math.random().toString().slice(-6);let nt=(+new Date).toString().slice(-8);const rt=new e({padding:"0px",offsetX:0,offsetY:0});rt.d.style("z-index",5555);const lt={top:"CHARTS",mid:"NONE",btm:"",subheader:"charts"};const ct={top:"GROUPS",mid:"NONE",btm:"",subheader:"groups"};const pt={top:"FILTER",mid:"NONE",btm:"",subheader:"filter"};function dt(){return it+"_"+nt++}class ht{constructor(t){this.type="nav";this.instanceNum=ot++;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;ut(this);ft(this)}async init(t){try{this.cohortFilter=N(t.termfilter.filter,"cohortFilter");this.initUI(t);this.initCohort(t);this.components=await r({search:Y({app:this.app,holder:this.dom.searchDiv,usecase:{target:"summary",detail:"term"},targetType:"Dictionary Variables"}),filter:G({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:j({app:this.app,holder:this.dom.subheader.groups,vocab:this.opts.vocab}),recover:T({app:this.app,holder:this.dom.recoverDiv,getState:t=>t,reactsTo:t=>t.type!="plot_edit",maxHistoryLen:5}),sessionBtn:et({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=N(this.state.filter,"filterUiRoot");this.cohortFilter=N(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 mt=t(ht);function ft(t){t.initUI=s=>{const a=t.opts.holder.append("div").style("white-space","nowrap");let o=a.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=a.append("div").style("display","none").style("vertical-align","bottom");const n=a.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:a,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:o,tip:new e({padding:"5px"})};if(s.nav.header_mode=="only_buttons"){t.dom.tabDiv.style("display","none");t.dom.recoverDiv.style("display","none");o.style("margin-top","95px").style("font-size","0.9em");if(s.termdbConfig.title?.link)o.on("click",(()=>window.open(s.termdbConfig.title.link,"_blank"))).on("mouseover",(()=>o.style("cursor","pointer")))}if(t.opts.header_mode==="with_cohortHtmlSelect"){t.dom.cohortStandaloneDiv=a.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=[lt,ct,pt];if(s.termdbConfig?.selectCohort||s.termdbConfig?.about){const e=s.termdbConfig?.about?.tab||{};const a=s.termdbConfig.selectCohort?"COHORT":e.topLabel||"";const o=e.midLabel||(e?"ABOUT":"");const i=e.btmLabel||"";const n={top:a.toUpperCase(),mid:o.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,a)=>({rowNum:s,key:e,colNum:a,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=rt.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"]?`${t.samplecounts["undefined"]}`:""}else{const a=t.samplecounts[t.filterJSON]!=undefined?""+t.samplecounts[t.filterJSON]:"";return e.key==="mid"?s.lst.length:a}}else{return e.key==="mid"?this.innerHTML:"&nbsp;"}}));for(const e in t.dom.subheader){t.dom.subheader[e].style("display",t.tabs[t.activeTab].subheader===e?"block":"none")}t.renderCohortsTable();if(t.opts.header_mode==="with_cohort_select"){t.dom.cohortSelect.selectAll("option").property("value",appState.activeCohort)}};t.renderCohortsTable=()=>{if(!t.dom.cohortTable)return;t.dom.cohortTable.selectAll("*").remove();const e=[{label:"Feature"}];const s=[];const a=t.cohortsData;if("error"in a)throw a.error;for(const t of a.features)s.push([{value:t.name}]);for(const t of a.cohorts){e.push({label:t.cohort?`${t.name} (${t.cohort})`:t.name});for(const[e,o]of a.features.entries()){const i=a.cfeatures.find((e=>e.idfeature===o.idfeature&&e.cohort===t.cohort));if(i)s[e].push({value:i.value})}}I({rows:s,columns:e,div:t.dom.cohortTable,showLines:false,maxHeight:"60vh"});t.dom.cohortTable.select("table").style("border-collapse","collapse");t.dom.cohortTable.selectAll(`tbody > tr > td`).style("background-color","transparent");const o=t.state.termdbConfig.selectCohort;const i=o.values[t.activeCohort].keys;let n=`tbody > tr > td:nth-child(${t.activeCohort+2})`;const r=i.length>1;if(r){n="";for(const t of i){const e=a.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 o=a(this);const i=o.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));o.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 ut(t){t.setTab=async(e,s)=>{if(s.colNum===t.activeTab&&!t.searching){t.prevCohort=t.activeCohort;await 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import("./app-6fb77603.js").then((function(t){return t.c3}));await o.default(a)};t.onLegendClick=function(s,a,o,i,n,r){const l=t.config[o];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(a,l,i,!p);d.hide();const e={};e[o]=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=o=="colorTW"?s.colorLegend:s.shapeLegend;for(const s of e.keys())t.hideCategory(a,l,s,l.term.type=="geneVariant"&&l.q.type=="values"?!s.startsWith(i):s!=i);d.hide();const n={};n[o]=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=o=="colorTW"?s.colorLegend:s.shapeLegend;for(const s of 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filter").on("click",(()=>{t.addToFilter(i);t.app.dispatch({type:"plot_edit",id:t.id,config:{groups:t.config.groups}})}));a.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 a=t.config.groups.findIndex((t=>t.name==s));if(a!=-1)alert(`Group named ${s} already exists`);else await t.app.dispatch({type:"rename_group",index:e.index,newName:s})};t.addCommonMenuItems=function(e,s){_(t.dom.tip,e,s,t.app,t.id,t.state);if(t.state.supportedChartTypes.includes("survival"))L("survival",e,"Compare survival",t.dom.tip,s,t.id,this);if(t.state.supportedChartTypes.includes("cuminc"))L("cuminc",e,"Compare cumulative incidence",t.dom.tip,s,t.id,this);const a=e.append("div").attr("class","sja_menuoption 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e=t.plots.find((t=>t.id===this.id));if(!e){throw`No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`}const s=W(t);return{config:e,termfilter:t.termfilter,supportedChartTypes:t.termdbConfig.supportedChartTypes[s],matrixplots:t.termdbConfig.matrixplots,vocab:t.vocab,termdbConfig:t.termdbConfig,groups:z(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,a]of Object.entries(e)){if(!Array.isArray(a.samples))throw"data.samples[] not array";if(a.isLast)this.createChart(t,a,s);else this.createChart(t,a,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 a=e.samples.filter((t=>"sampleId"in t));if(a.length>1e4)this.is2DLarge=true;const o=new Map(e.colorLegend);const i=new Map(e.shapeLegend);this.charts.splice(s,0,{id:t,data:e,cohortSamples:a,colorLegend:o,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,a,o,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=a;t.yMin=o;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,a,o,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=a;t.yMin=o;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 a={label:"Sample size",type:"number",chartType:"sampleScatter",settingsKey:"size",title:"Sample size, represents the factor used to scale the sample",min:0};const o=(qt-Rt)/10;const i={label:"Min size",type:"number",chartType:"sampleScatter",settingsKey:"minShapeSize",title:"Minimum sample size",min:Rt,max:qt,step:o};const n={label:"Max size",type:"number",chartType:"sampleScatter",settingsKey:"maxShapeSize",title:"Maximum sample size",min:Rt,max:qt,step:o};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 a=this.config.sampleCategory.order.indexOf(e.value);if(s<a)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 samples",label:"X",vocabApi:this.app.vocabApi,menuOptions:"!remove",numericEditMenuVersion:["continuous"]},{type:"term",configKey:"term2",chartType:"sampleScatter",usecase:{target:"sampleScatter",detail:"numeric"},title:"Y coordinate to plot the samples",label:"Y",vocabApi:this.app.vocabApi,menuOptions:"!remove",numericEditMenuVersion:["continuous"]}]);if(!this.is3D){p.splice(4,0,s);p.splice(5,0,e);if(this.config.scaleDotTW){p.splice(6,0,i);p.splice(7,0,n);p.splice(8,0,r);if(t)p.splice(9,0,l)}else{p.splice(6,0,a);if(t)p.splice(7,0,l)}p.push({label:"Show regression",type:"dropdown",chartType:"sampleScatter",settingsKey:"regression",options:[{label:"None",value:"None"},{label:"Lowess",value:"Lowess"},{label:"Polynomial",value:"Polynomial"}]})}else{p.push({label:"Chart depth",type:"number",chartType:"sampleScatter",settingsKey:"svgd"});p.push({label:"Field of vision",title:"Camera field of view, in 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,a);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)E(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 a=R(s);return a}}function Pt(t,e,s=null){let a={chartType:"sampleScatter",name:e.name,filter:s};if(e.sampleCategory)a.sampleCategory={tw:structuredClone(e.sampleCategory.tw),order:e.sampleCategory.order,defaultValue:e.sampleCategory.defaultValue};if(e.sampleType)a.sampleType=e.sampleType;if(e.colorTW)a.colorTW=structuredClone(e.colorTW);else if(e.colorColumn)a.colorColumn=structuredClone(e.colorColumn);if("shapeTW"in e)a.shapeTW=structuredClone(e.shapeTW);if(e.settings)a.settings=structuredClone(e.settings);t.dispatch({type:"plot_create",config:a})}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 Ht(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=Yt();if(t.settings)g(s,t.settings);if(!t.term&&!t.term2)s.showAxes=false;const a={groups:[],settings:{controls:{isOpen:false},sampleScatter:s},startColor:{},stopColor:{}};const o=g(a,t);if(o.term0?.q?.mode=="continuous"&&!e.hasWebGL())throw"Can not load Z/Divide by term in continuous mode as WebGL is not supported";return o}catch(t){console.log(t);throw`${t} [sampleScatter getPlotConfig()]`}}const Ut=t(Et);const Bt=Ut;function Kt(t,e){const s=t.append("div");if(e.state.termdbConfig.scatterplots)for(const t of e.state.termdbConfig.scatterplots){s.append("div").attr("class","sja_menuoption sja_sharp_border").text(t.name).on("click",(()=>{Pt(e.app,t);e.dom.tip.hide()}))}s.append("div");if(!e.state.termdbConfig.hiddenChartTypes?.includes("dynamicScatter")){const t=(t,s)=>{e.app.dispatch({type:"plot_create",config:{chartType:"sampleScatter",term:{term:t,q:{mode:"continuous"}},term2:{term:s,q:{mode:"continuous"}},name:`${t.name} vs ${s.name}`}})};V(e.dom.tip,e.app,"sampleScatter","numeric",t)}}function Yt(){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 Jt(t,e,s){const a={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 o=await import("./plot.app-2a805759.js");await o.appInit(a)}var Xt=Object.freeze({__proto__:null,minShapeSize:Rt,maxShapeSize:qt,shapes:Vt,openScatterPlot:Pt,downloadImage:Ft,getPlotConfig:Ht,scatterInit:Ut,componentInit:Bt,makeChartBtnMenu:Kt,getDefaultScatterSettings:Yt,renderScatter:Jt});export{It as a,Xt as b,Yt as g,mt as n,Wt as s};

package/dist/singleCellCellType-fd1606b8.js

@@ -1 +0,0 @@
-import{_ as t}from"./tslib.es6-c3c2d88f.js";import{s as e}from"./termsetting-492eefa7.js";import{getHandler as i}from"./categorical-1dea48ba.js";import{P as r}from"./app-6fb77603.js";import"path";import"./groupsetting-e3a4ecd5.js";function s(e){return t(this,void 0,void 0,(function*(){return i(e)}))}function o(t,i,s=null){var o,p;if(!((o=t.term)===null||o===void 0?void 0:o.sample))throw"missing term.sample";if(!((p=t.term)===null||p===void 0?void 0:p.plot))throw"missing term.plot";if(!Object.keys(t.q).includes("type"))t.q.type="values";if(!t.term.groupsetting)t.term.groupsetting={disabled:false};if(t.q.type=="predefined-groupset"){if(!Number.isInteger(t.q.predefined_groupset_idx))throw"predefined_groupset_idx is not an integer"}if(t.q.type=="custom-groupset"){if(!t.q.customset)throw"invalid customset"}if(s){s.isAtomic=true;r(t.q,s)}e(t.q,t.term)}export{o as fillTW,s as getHandler};

package/dist/singleCellPlot-eff5760b.js

@@ -1 +0,0 @@
-import{b as t,y as e,F as s,h as o,P as i,M as n,d as l,C as a,I as r,r as p,Q as c}from"./app-6fb77603.js";import{d}from"./zoom-f445cfef.js";import{r as h}from"./table-0daf2b89.js";import{controlsInit as g}from"./controls-268e40e6.js";import{d as m}from"./svg.download-f4aa48e4.js";import{a as f}from"./genesearch-ffd88bf2.js";import{T as y,c as u}from"./termsetting-492eefa7.js";import{a as b,b as v,c as x}from"./axis-747c801e.js";import"./pointer-c7475677.js";import"./nodrag-b2737073.js";import"./tslib.es6-c3c2d88f.js";import"./controls.btns-5bf9e7d7.js";import"./controls.config-2f0fa061.js";import"path";class C{constructor(){this.type="singleCellPlot";this.tip=new n({padding:"4px",offsetX:10,offsetY:0});this.tip.d.style("max-height","300px").style("overflow","scroll").style("font-size","0.9em");this.startGradient={};this.stopGradient={}}async init(e){const s=this.getState(e);const o=s.termdbConfig.queries;this.tableOnPlot=e.nav?.header_mode=="hidden";this.opts.holder.style("position","relative");this.showDivId=`${this.id}-sandbox`;const i=this.opts.holder.insert("div").style("display","inline-block").style("vertical-align","top");const a=i.append("div").style("padding","10px");const r=i.append("div");const p=a.append("div").attr("id",this.showDivId);const c=a.append("div").style("padding-top","10px").style("display","inline-block");if(this.tableOnPlot){p.append("input").attr("id",`showSamples`).attr("type","checkbox").property("checked",true).on("change",(t=>{this.app.dispatch({type:"plot_edit",id:this.id,config:{settings:{singleCellPlot:{showSamples:t.target.checked}}}})}));p.append("label").text("Show samples").attr("for",`showSamples`)}for(const t of s.config.plots){const e=t.name.replace(/\s+/g,"");p.append("input").attr("id",`show${e}`).attr("type","checkbox").property("checked",true).on("change",(t=>{this.app.dispatch({type:"plot_edit",id:this.id,config:{settings:{singleCellPlot:{[`show${e}`]:t.target.checked}}}})}));p.append("label").text(t.name).attr("for",`show${e}`)}if(o.singleCell?.geneExpression){c.append("label").html("Gene expression:");const t=f({tip:new n({padding:"0px"}),genome:this.app.opts.genome,row:c,searchOnly:"gene",placeholder:s.config.gene||"Gene",callback:()=>{o?.style("display","inline-block");e?.style("display","inline-block");const s=t.geneSymbol;this.app.dispatch({type:"plot_edit",id:this.id,config:{gene:s}})},emptyInputCallback:()=>{o.style("display","none");e.style("display","none");this.app.dispatch({type:"plot_edit",id:this.id,config:{gene:null}})},hideHelp:true,focusOff:true});const e=c.append("select").style("display",s.config.gene?"inline-block":"none");for(const t of s.termdbConfig?.queries.singleCell.data.plots){e.append("option").text(t.colorColumn)}e.on("change",(async()=>{const t=s.termdbConfig?.queries.singleCell.data.plots[0];const o=t.columnName;const i={sample:s.config.sample.sampleName,columnName:o,category:e.node().value};await this.app.vocabApi.getTopTermsByType(i)}));const o=c.append("button").text("Open violin").style("margin-left","2px").style("display",s.config.gene?"inline-block":"none");o.on("click",(()=>{const o=t.geneSymbol||s.config.gene;const i=this.state.config.plots.find((t=>t.colorColumn==e.node().value)).name;const n=this.plots.find((t=>t.name==i));const l={};for(const t of n.clusters){l[t]={key:t,value:t}}this.app.dispatch({type:"plot_create",config:{chartType:"violin",settings:{violin:{plotThickness:50}},term:{term:{type:y.SINGLECELL_GENE_EXPRESSION,id:o,gene:o,name:o,sample:s.config.sample}},term2:{term:{type:y.SINGLECELL_CELLTYPE,id:y.SINGLECELL_CELLTYPE,name:"Cell type",sample:s.config.sample,plot:n.name,values:l}}}})}))}const d=a.append("div").style("padding","10px").style("display","inline-block");const g=i.append("div").style("display","inline-block").attr("class","pp-termdb-plot-controls");const m=i.append("div").style("display","inline-block");const b=m.append("div").style("display","flex").style("flex-wrap","wrap").style("justify-content","flex-start").style("width","92vw");const v=this.opts.holder.append("div").style("position","absolute").style("top",0).style("left",0).style("width","100%").style("height","100%").style("background-color","rgba(255, 255, 255, 0.8)").style("text-align","center");v.append("div").attr("class","sjpp-spinner");this.dom={header:this.opts.header,mainDiv:i,loadingDiv:v,tip:new n({padding:"0px"}),tooltip:new n({padding:"2px",offsetX:10,offsetY:0}),controlsHolder:g,tableDiv:r,deDiv:d,plotsDiv:b,plotsDivParent:m};const x=80;this.axisOffset={x:x,y:30};if(o.singleCell?.DEgenes){this.dom.deDiv.append("label").html("View differentially expresed genes of a cluster vs rest of cells:&nbsp;");this.dom.deselect=this.dom.deDiv.append("select");if(this.app.opts.genome.termdbs)this.dom.GSEAbt=this.dom.deDiv.append("button").style("margin-left","5px").property("disabled",true).text("Gene set enrichment analysis").on("click",(t=>{const e={genes:this.genes,fold_change:this.fold_changes,genome:this.app.vocabApi.opts.state.vocab.genome};const s={chartType:"gsea",gsea_params:e,insertBefore:this.app.opts?.app?.getPlotHolder&&this.showDivId};this.app.dispatch({type:"plot_create",config:s})}));const e=this.dom.deDiv.append("div");this.dom.DETableDiv=e;this.dom.deselect.append("option").text("");this.dom.deselect.on("change",(async o=>{e.selectAll("*").remove();const i=this.dom.deselect.node().value.split(" ")?.[1];if(this.dom.GSEAbt)this.dom.GSEAbt.property("disabled",!i);if(!i)return;const n=s.termdbConfig.queries.singleCell.DEgenes.columnName;const l=this.state.config.experimentID||this.state.config.sample||this.samples[0]?.experiments[0]?.experimentID;const a={genome:s.genome,dslabel:s.dslabel,categoryName:i,sample:l,columnName:n};const r=await t("termdb/singlecellDEgenes",{body:a});const p=[{label:"Gene"},{label:"Log2FC"},{label:"Adjusted P-value"}];const c=[];this.genes=[];this.fold_changes=[];r.genes.sort(((t,e)=>e.avg_log2FC-t.avg_log2FC));for(const t of r.genes){const e=[{value:t.name},{value:u(t.avg_log2FC)},{value:u(t.p_val_adj)}];c.push(e);this.genes.push(t.name);this.fold_changes.push(t.avg_log2FC)}h({rows:c,columns:p,resize:true,div:e})}))}this.settings={};document.addEventListener("scroll",(t=>this?.tip?.hide()));l(".sjpp-output-sandbox-content").on("scroll",(t=>this.tip.hide()));await this.setControls(s)}async setControls(t){const e=[{label:"Chart width",type:"number",chartType:"singleCellPlot",settingsKey:"svgw",min:300,max:1e3},{label:"Chart height",type:"number",chartType:"singleCellPlot",settingsKey:"svgh",min:300,max:1e3},{label:"Show borders",type:"checkbox",chartType:"singleCellPlot",settingsKey:"showBorders",boxLabel:""}];if(this.tableOnPlot)e.push({label:"Show samples",type:"checkbox",chartType:"singleCellPlot",settingsKey:"showSamples",boxLabel:""});this.components={controls:await g({app:this.app,id:this.id,holder:this.dom.controlsHolder,inputs:e})};this.components.controls.on("downloadClick.singleCellPlot",(()=>{for(const t of this.plots)m(t.svg,"plot.svg",this.opts.holder.node())}))}getState(t){const e=t.plots.find((t=>t.id===this.id));if(!e){throw`No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`}this.prevFilter0=this.state?.termfilter.filter0;return{config:e,dslabel:t.vocab.dslabel,genome:t.vocab.genome,termdbConfig:t.termdbConfig,termfilter:t.termfilter}}async main(){this.config=structuredClone(this.state.config);i(this.settings,this.config.settings.singleCellPlot);this.dom.tableDiv.style("display",this.settings.showSamples?"block":"none");if(this.tableOnPlot){await D(this.dom.tableDiv,this,this.state);if(!this.samples?.length){this.showNoMatchingDataMessage();return}}this.dom.loadingDiv.selectAll("*").remove();this.dom.loadingDiv.style("display","").append("div").attr("class","sjpp-spinner");this.dom.mainDiv.style("opacity",1).style("display","");this.legendRendered=false;const t=await this.getData();this.dom.plotsDivParent.style("display","inline-block");this.renderPlots(t);this.dom.loadingDiv.style("display","none");if(this.dom.header)this.dom.header.html(`Single Cell Data`)}async getData(){const s=[];for(const t of this.config.plots){const e=t.name.replace(/\s+/g,"");const o=this.settings[`show${e}`];if(o)s.push(t.name)}const o={genome:this.state.genome,dslabel:this.state.dslabel,plots:s,filter0:this.state.termfilter.filter0};if(this.state.config.sample){this.state.config.sample;o.sample=this.state.config.experimentID||this.state.config.sample}else{this.samples[0].sample;o.sample=this.samples[0].experiments?.[0]?.experimentID||this.samples[0].sample}if(this.state.config.gene)o.gene=this.state.config.gene;try{const e=await t("termdb/singlecellData",{body:o});if(e.error)throw e.error;this.refName=e.refName;return e}catch(t){if(t.stack)console.log(t.stack);e(this.dom.plotsDiv,t);return}}showNoMatchingDataMessage(){this.dom.mainDiv.style("opacity",.001).style("display","none");this.dom.loadingDiv.style("display","").html("");this.dom.loadingDiv.append("div").style("display","inline-block").style("text-align","center").style("position","relative").style("left","-150px").style("font-size","1.2em").style("margin","2em 1em").html("No matching cohort data.")}renderPlots(t){this.dom.plotsDiv.selectAll("*").remove();this.plots=[];for(const e of t.plots){e.id=e.name.replace(/\s+/g,"");this.renderPlot(e)}}renderPlot(t){const e={};let s=new Set(t.cells.map((t=>t.category)));t.clusters=Array.from(s).sort(((t,e)=>{const s=parseInt(t.split(" ")[1]);const o=parseInt(e.split(" ")[1]);return s-o}));if(this.dom.deselect&&!this.legendRendered){this.dom.deselect.selectAll("*").remove();this.dom.deselect.append("option").text("");for(const e of t.clusters)this.dom.deselect.append("option").text(e)}const o=a(t.clusters.length+2);for(const s of t.clusters)e[s]=s=="ref"||s=="No"?"#F2F2F2":t.colorMap?.[s]?t.colorMap[s]:o(s);t.colorMap=e;this.plots.push(t);this.initAxes(t);t.plotDiv=this.dom.plotsDiv.append("div").style("overflow","hidden").style("display","inline-block").style("padding","10px").style("flex-grow",1);if(this.state.config.settings.singleCellPlot.showBorders)t.plotDiv.style("border","1px solid #aaa");this.renderLegend(t);const i=t.plotDiv.append("svg").attr("width",this.settings.svgw).attr("height",this.settings.svgh+40).on("mouseover",(e=>{if(this.state.config.gene&&!this.onClick)this.showTooltip(e,t)})).on("click",(e=>this.showTooltip(e,t)));i.append("text").attr("transform",`translate(20, 30)`).style("font-weight","bold").text(`${t.name}`);t.svg=i;const n=d().scaleExtent([.5,5]).on("zoom",(e=>this.handleZoom(e,t))).filter((t=>{if(t.type==="wheel")return t.ctrlKey;return true}));i.call(n);const l=i.selectAll("g").data(t.cells);l.enter().append("g").attr("transform",(e=>`translate(${t.xAxisScale(e.x)}, ${t.yAxisScale(e.y)+40})`)).append("circle").attr("r",1.5).attr("fill",(e=>this.getColor(e,t))).style("fill-opacity",(t=>this.getOpacity(t)))}getOpacity(t){if(this.config.hiddenClusters.includes(t.category))return 0;return.7}getColor(t,e){const s="#FAFAFA";if(this.state.config.gene){if(!t.geneExp)return s;if(e.colorGenerator)return e.colorGenerator(t.geneExp);return s}return e.colorMap[t.category]}handleZoom(t,e){e.svg.attr("transform",t.transform);e.zoom=t.transform.scale(1).k}initAxes(t){if(!t.cells.length)return;const e=t.cells[0];const[s,o,i,n]=t.cells.reduce(((t,e)=>[e.x<t[0]?e.x:t[0],e.x>t[1]?e.x:t[1],e.y<t[2]?e.y:t[2],e.y>t[3]?e.y:t[3]]),[e.x,e.x,e.y,e.y]);const l=5;t.xAxisScale=r().domain([s,o]).range([0+l,this.settings.svgh+l]);t.axisBottom=b(t.xAxisScale);t.yAxisScale=r().domain([n,i]).range([0+l,this.settings.svgh+l]);t.axisLeft=v(t.yAxisScale);t.zoom=1}renderLegend(t){const e=t.colorMap;let s=t.legendSVG;if(!t.legendSVG){s=t.plotDiv.append("svg").attr("width",250).attr("height",this.settings.svgh).style("vertical-align","top");t.legendSVG=s}s.selectAll("*").remove();if(this.state.termdbConfig.queries.singleCell.data.sameLegend&&this.legendRendered)return;this.legendRendered=true;const o=s.append("g").attr("transform",`translate(25, 50)`).style("font-size","0.8em");if(this.state.config.gene){this.renderColorGradient(t,o);return}o.append("text").attr("transform",`translate(${0}, ${25})`).style("font-weight","bold").text(`${t.colorBy}`);const i=20;let n=50;let l=0;for(const s in e){const r=t.cells.filter((t=>t.category==s));const p=this.config.hiddenClusters.includes(s);const c=r.length;const d=e[s];const h=o.append("g").attr("transform",(t=>`translate(${l}, ${n})`));h.append("circle").attr("r",3).attr("fill",d);h.append("g").attr("transform",`translate(${l+10}, ${5})`).append("text").text(`${s=="ref"?this.state.termdbConfig.queries.singleCell.data.refName:s=="query"?this.state.config.sample:s} n=${c}`).style("text-decoration",p?"line-through":"none").on("click",(t=>a(this,t,s)));n+=i}function a(t,e,s,o){const i=e.target;const n=i.style["text-decoration"]=="line-through";i.style["text-decoration"]=n?"none":"line-through";let l=t.config.hiddenClusters;if(!n)l.push(s);else l.splice(l.indexOf(s),1);t.app.dispatch({type:"plot_edit",id:t.id,config:{hiddenClusters:l}})}}renderColorGradient(t,e){if(t.cells.length==0)return;const s=p(c);if(!this.config.startColor[t.name])this.config.startColor[t.name]=s.brighter(1).toString();if(!this.config.stopColor[t.name])this.config.stopColor[t.name]=s.darker(3).toString();const o=this.config.startColor[t.name];const i=this.config.stopColor[t.name];const n=e.append("defs").append("linearGradient").attr("id",`linear-gradient-${t.id}`).attr("x1","0%").attr("y1","0%").attr("x2","100%").attr("y2","0%");this.startGradient[t.name]=n.append("stop").attr("offset","0%").attr("stop-color",o);this.stopGradient[t.name]=n.append("stop").attr("offset","100%").attr("stop-color",i);let l,a;const d=t.cells[0]?.geneExp==undefined?[]:t.cells.map((t=>t.geneExp));if(d.length==0){t.colorGenerator=null;return}else[l,a]=d.reduce(((t,e)=>[e<t[0]?e:t[0],e>t[1]?e:t[1]]),[d[0],d[0]]);t.colorGenerator=r().domain([l,a]).range([o,i]);const h=100;const g=r().domain([l,a]).range([0,h]);const m=(a-l)/4;const f=[l,l+m,l+2*m,l+3*m,a];const y=x(g).tickValues(f);e.append("g").attr("transform",`translate(0, 100)`).call(y);t.startRect=e.append("rect").attr("x",-25).attr("y",100).attr("width",20).attr("height",20).style("fill",o).on("click",(e=>this.editColor(t,"startColor",t.startRect)));t.stopRect=e.append("rect").attr("x",h+5).attr("y",100).attr("width",20).attr("height",20).style("fill",i).on("click",(e=>this.editColor(t,"stopColor",t.stopRect)));e.append("rect").attr("x",0).attr("y",100).attr("width",h).attr("height",20).style("fill",`url(#linear-gradient-${t.id})`)}editColor(t,e,s){const o=this.config[e][t.name];const i=new n({padding:"3px"});const l=i.clear().d.append("Label").text("Color:").append("input").attr("type","color").attr("value",p(o).formatHex()).on("change",(()=>{const o=l.node().value;this.changeGradientColor(t,e,s,o);i.hide()}));i.showunder(s.node(),false)}changeGradientColor=function(t,e,s,o){this.config[e][t.name]=o;this.app.dispatch({type:"plot_edit",id:this.id,config:this.config})};distance(t,e,s,o,i){const n=i.xAxisScale(s)-i.xAxisScale(t);const l=i.yAxisScale(o)-i.yAxisScale(e);const a=Math.sqrt(Math.pow(n,2)+Math.pow(l,2));return a}showTooltip(t,e){if(this.onClick&&t.type=="click"){this.onClick=false;this.tip.hide();return}if(t.target.tagName=="circle"){this.onClick=t.type=="click";const s=t.target.__data__;const o=this.tip.clear();const i=o.d.append("table");let n=i.append("tr");n.append("td").style("color","#aaa").text(e.colorBy);const l=n.append("td");const a=l.append("svg").attr("width",150).attr("height",20);const r=10;const p=12;const c=a.append("g").attr("transform",`translate(${r}, ${p})`);c.append("circle").attr("fill",this.getColor(s,e)).attr("r",4);a.append("g").attr("transform",`translate(${r+15}, ${p+4})`).append("text").text(s.category);if("geneExp"in s){n=i.append("tr");n.append("td").style("color","#aaa").text("Gene expression");n.append("td").text(u(s.geneExp))}o.show(t.clientX,t.clientY,true,true)}else this.onMouseOut(t)}onMouseOut(t){this.tip.hide()}}async function w(t,e){const s=t.append("div").style("padding","5px");D(s,e,e.state)}async function D(o,i,n){const l={genome:n.genome,dslabel:n.dslabel,filter0:n.termfilter.filter0||null};let a;try{a=await t("termdb/singlecellSamples",{body:l});if(a.error)throw a.error}catch(t){e(o,t);return}const r=a.samples;i.samples=r;if(i.tableOnPlot){if(r.length==0){i.dom.plotsDiv.selectAll("*").remove();return}if(i.table&&s(i.state.termfilter.filter0,i.prevFilter0))return}o.selectAll("*").remove();r.sort(((t,e)=>{const s=t.primarySite?.localeCompare(e.primarySite);if(s==1||s==-1)return s;else return t.sample.localeCompare(e.sample)}));const[p,c]=await k(i,r,n);const d=[];let g="40vh";if(i.tableOnPlot){const t=i.config.sample;const e=i.samples.findIndex((e=>e.sample==t));const s=e==-1?0:e;d.push(s);g="30vh"}i.table=h({rows:p,columns:c,resize:true,singleMode:true,div:o,maxHeight:g,noButtonCallback:t=>{if(i.dom.DETableDiv){i.dom.deselect.node().value="";i.dom.DETableDiv.selectAll("*").remove();if(i.dom.GSEAbt)i.dom.GSEAbt.property("disabled",true)}const e=p[t][0].value;const s={chartType:"singleCellPlot",sample:e};if(p[t][0].__experimentID){s.experimentID=p[t][0].__experimentID}if(i.tableOnPlot){i.app.dispatch({type:"plot_edit",id:i.id,config:s})}else{i.dom.tip.hide();i.app.dispatch({type:"plot_create",config:s})}},selectedRows:d})}async function k(t,e,s){const o=[];for(const t of e){if(t.experiments)for(const e of t.experiments){const i=[{value:t.sample,__experimentID:e.experimentID}];for(const e of s.termdbConfig.queries.singleCell.samples.sampleColumns||[]){i.push({value:t[e.termid]})}for(const e of s.termdbConfig.queries.singleCell.samples.experimentColumns||[]){i.push({value:t[e.label]})}i.push({value:e.experimentID});o.push(i)}else{const e=[{value:t.sample}];for(const o of s.termdbConfig.queries.singleCell.samples.sampleColumns||[]){e.push({value:t[o.termid]})}o.push(e)}}const i=[{label:s.termdbConfig.queries.singleCell.samples.firstColumnName||"Sample"}];for(const e of s.termdbConfig.queries.singleCell.samples.sampleColumns||[]){i.push({label:(await t.app.vocabApi.getterm(e.termid)).name,width:"15vw"})}for(const t of s.termdbConfig.queries.singleCell.samples.experimentColumns||[]){i.push({label:t.label,width:"20vw"})}if(e.some((t=>t.experiments))){i.push({label:"Experiment"})}return[o,i]}const S=o(C);const A=S;async function _(t,e){try{const s=e.vocabApi.termdbConfig?.queries?.singleCell.data.plots;const o=E();for(const t of s){const e=t.name.replace(/\s+/g,"");const s=`show${e}`;o[s]=true}const n={hiddenClusters:[],settings:{singleCellPlot:o},startColor:{},stopColor:{},plots:s};const l=i(n,t);return l}catch(t){console.log(t);throw`${t} [singleCellPlot getPlotConfig()]`}}function E(){return{svgw:420,svgh:420,showBorders:false,showSamples:true}}export{A as componentInit,E as getDefaultSingleCellSettings,_ as getPlotConfig,w as makeChartBtnMenu,S as scatterInit};

package/dist/snp-f6123244.js

@@ -1 +0,0 @@
-import{_ as s}from"./tslib.es6-c3c2d88f.js";import{M as t}from"./app-6fb77603.js";import{a as o}from"./genesearch-ffd88bf2.js";class r{init(s){this.callback=s.callback;const r=o({tip:new t({padding:"0px"}),genome:s.genomeObj,row:s.holder,searchOnly:"snp",allowVariant:true,callback:()=>this.selectSnp(r)})}selectSnp(t){return s(this,void 0,void 0,(function*(){const{chr:s,ref:o,alt:r,fromWhat:a}=t;if(!s||!o||!r||!a)throw"missing chr, ref, alt, or fromWhat of snp";let e,i;if(!t.start&&!t.stop){if(t.pos){e=t.pos-1;i=t.pos}else{throw"missing coordinate of snp"}}else{e=t.start;i=t.stop}const n={id:a,chr:s,start:e,stop:i,name:a,ref:o,alt:typeof r=="string"?[r]:r,type:"snp"};this.callback(n)}))}}export{r as SearchHandler};

package/dist/snplocus-acafb1ba.js

@@ -1 +0,0 @@
-import{_ as t}from"./tslib.es6-c3c2d88f.js";import{mayRestrictAncestry as e,makeSnpSelect as i}from"./snplst-6865d7c7.js";import{f as r}from"./FilterStateless-16a33070.js";import{g as n}from"./FilterRxComp-02e68f1b.js";import"./termsetting-492eefa7.js";import"./app-6fb77603.js";import{a as s}from"./genesearch-ffd88bf2.js";import"./snplst.sampleSum-e47d05f0.js";import"./table-0daf2b89.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-39d11f24.js";import"path";const a="Variants in a locus";function o(e){return{getPillName(){return e.term.name},getPillStatus(){if(!e.term||!e.q)return;if(!e.term.snps)throw`Missing term.snps [snplocs.ts getPillStatus()]`;let t=`${e.q.chr}:${e.q.start}-${e.q.stop}, ${e.term.snps.length} variant${e.term.snps.length>1?"s":""}`;if(e.term.reachedVariantLimit){t+='<span style="margin-left: 6px; background:#aaa; font-size:1em;font-style: normal; border-radius: 7px;color:white;padding:0px 5px;">&#9888;<span>'}return{text:t}},validateQ(t){d(t)},showEditMenu(i){return t(this,void 0,void 0,(function*(){yield l(e,i)}))}}}function l(r,o){var l;return t(this,void 0,void 0,(function*(){const d=o.append("div").style("margin","15px");const c=yield e(r,d);const u=s({genome:r.opts.genomeObj,tip:r.dom.tip2,row:d.append("div").style("margin-top","20px"),defaultCoord:r.q&&r.q.chr?{chr:r.q.chr,start:r.q.start,stop:r.q.stop}:undefined});d.select(".sja_genesearchinput").style("margin","0px");d.append("span").style("margin","5px 0px").style("display","inline-block").style("opacity",.4).style("font-size",".7em").html('"Gene": Gene name (e.g. AKT1)</br>"Position": chr:start-stop (e.g. chr1:5000-6000)</br>"dbSNP": dbSNP accession (e.g. rs1042522)');yield f(r,(l=r.q)===null||l===void 0?void 0:l.variant_filter,d);const[v,h,y]=i(d.append("div").attr("class","sjpp-snp-select").style("margin-top","15px"),r,"snplocus");if(r.usecase.target=="dataDownload")d.select(".sjpp-snp-select").style("display","none");const g=d.append("div").style("margin-top","15px");g.append("button").style("margin-top","15px").text("Submit").on("click",(e=>t(this,void 0,void 0,(function*(){if(!u.chr)return window.alert("Invalid coordinate");e.target.disabled=true;e.target.innerHTML="Validating input...";if(r.term);else{r.term={id:m()}}if(!r.q)r.q={};r.term.type="snplocus";r.q.chr=u.chr;r.q.start=u.start;r.q.stop=u.stop;r.term.name=a;delete r.term.snps;r.q.variant_filter=n(r.variantFilter.active);yield p(r);{const t=Number(v.property("value"));r.q.AFcutoff=t<0||t>=100?5:t}r.q.alleleType=h.property("selectedIndex");r.q.geneticModel=y.property("selectedIndex");if(c){r.q.restrictAncestry=c.node().options[c.property("selectedIndex")].__ancestry_obj}r.runCallback()}))));g.append("span").style("padding-left","15px").style("opacity",.8).style("font-size",".8em").text(r.usecase.target=="dataDownload"?"":"Variants will be treated individually in separate regression models")}))}function p(e){return t(this,void 0,void 0,(function*(){const t=yield e.vocabApi.validateSnps(e.q);if(t.error)throw t.error;e.q.cacheid=t.cacheid;e.term.snps=t.snps;e.term.reachedVariantLimit=t.reachedVariantLimit}))}function d(t){const e=t.q;if(!Number.isFinite(e.AFcutoff))throw"AFcutoff is not number";if(e.AFcutoff<0||e.AFcutoff>100)throw"AFcutoff is not within 0 to 100";if(![0,1].includes(e.alleleType))throw"alleleType value is not one of 0/1";if(![0,1,2,3].includes(e.geneticModel))throw"geneticModel value is not one of 0/1";if(!e.chr)throw"chr missing";if(!Number.isInteger(e.start))throw"start coordinate is not integer";if(!Number.isInteger(e.stop))throw"stop coordinate is not integer";if(e.start<0)throw"start < 0";if(e.stop<=e.start)throw"stop <= start"}function c(e,i){return t(this,void 0,void 0,(function*(){try{d(e)}catch(t){throw"snplocus validateQ(): "+t}if(!e.term.name)e.term.name=a;if(e.id==undefined||e.id==""){if(e.term.id==undefined||e.term.id==""){e.term.id=m()}e.id=e.term.id}else{if(e.term.id==undefined||e.term.id==""){e.term.id=e.id}}yield p({term:e.term,q:e.q,vocabApi:i})}))}function m(){return"snplocus"+Math.random()}function f(e,i,n,s){return t(this,void 0,void 0,(function*(){if(!e.variantFilter){e.variantFilter=yield e.vocabApi.get_variantFilter()}if(!e.variantFilter.terms){return}if(!e.variantFilter.opts)throw"variantFilter.opts{} missing";if(!e.variantFilter.filter)throw".filter missing from variantFilter{}";if(!Array.isArray(e.variantFilter.terms)||e.variantFilter.terms.length==0)throw"variantFilter.terms[] is not non-empty array";if(i){e.variantFilter.active=JSON.parse(JSON.stringify(i))}else{e.variantFilter.active=JSON.parse(JSON.stringify(e.variantFilter.filter))}const a=n.append("div").style("margin-top","15px");a.append("span").text("VARIANT FILTERS").style("font-size",".8em").style("opacity",.5);const o=a.append("div");r({joinWith:e.variantFilter.opts.joinWith,emptyLabel:"+Variant Filter",holder:o,vocab:{terms:e.variantFilter.terms},callback:i=>t(this,void 0,void 0,(function*(){e.variantFilter.active=i;if(s)yield s()}))}).main(e.variantFilter.active)}))}export{c as fillTW,o as getHandler};

package/dist/spliceevent.exonskip.getdefault-237c481c.js

@@ -1 +0,0 @@
-import{bX as e,bV as n}from"./app-6fb77603.js";function o(o){let t=0;for(let f=1;f<o.length;f++){const i=o[f];const r=o[t];if(i.isskipexon&&r.isaltexon){t=f;continue}if(i.frame==e&&r.framenocheck){t=f;continue}if(i.frame==n&&r.frame!=n){t=f;continue}}return t}export{o as e};

package/dist/summary-a6c15c9e.js

@@ -1 +0,0 @@
-import{h as t,P as e,M as i}from"./app-6fb77603.js";import{f as o,i as s}from"./termsetting-492eefa7.js";import{r}from"./recover-299ffdb3.js";import{getDefaultViolinSettings as a}from"./violin-74d26b75.js";import{getDefaultBarSettings as n}from"./barchart-2898d229.js";import{g as l}from"./sampleScatter-55d9eb74.js";import{T as p}from"./toggleButtons-c4d6f260.js";import"./tslib.es6-c3c2d88f.js";import"path";import"./FilterRxComp-02e68f1b.js";import"./table-0daf2b89.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-39d11f24.js";import"./FilterStateless-16a33070.js";import"./app-d215327f.js";import"./termInfo-491b10af.js";import"./genesearch-ffd88bf2.js";import"./checkbox-96437f4d.js";import"./rehydrateFilter-12d118cb.js";import"./controls-268e40e6.js";import"./controls.btns-5bf9e7d7.js";import"./controls.config-2f0fa061.js";import"./violin.renderer-469fa0ff.js";import"./brush-9faa7ae7.js";import"./pointer-c7475677.js";import"./nodrag-b2737073.js";import"./axis-747c801e.js";import"./line-264f8f9e.js";import"./constant-426a1483.js";import"./basis-3870f5ba.js";import"./log-c26b6cfd.js";import"./html.legend-80b2b3ec.js";import"./violin.interactivity-bf40ddde.js";import"./niceNumLabels-29a7c6ca.js";import"./bars.settings-64bb4642.js";import"./bars.renderer-71935d34.js";import"./svg.legend-749348e0.js";import"./barchart.events-426d737a.js";import"./zoom-f445cfef.js";import"./lasso-1a02a545.js";import"./drag-2e9c80bb.js";import"./downloadTextfile-5723af95.js";import"./sampleView-1dff3fca.js";import"./select2Terms-d48d037e.js";import"./svg.download-f4aa48e4.js";import"./sampleScatter.rendererThree-ef289434.js";class c{constructor(t){this.type="summary";this.components={recover:{},plots:{}};this.chartsByType={}}async init(t){const e=this.getState(t);const i=structuredClone(e.config);m(this);this.initUi(this.opts,i);this.components.recover=await r({app:this.app,holder:this.dom.localRecoverDiv,getState:t=>this.getState(t),reactsTo:t=>t.id==this.id&&t.type=="plot_edit"&&t._scope_!="none",plot_id:this.id,maxHistoryLen:10,margin:"5px 10px"})}reactsTo(t){if(t.type.includes("cache_termq"))return true;if(t.type.startsWith("plot_")){return t.id===this.id}if(t.type.startsWith("filter"))return true;if(t.type.startsWith("cohort"))return true;if(t.type=="app_refresh")return true}getState(t){const e=t.plots.find((t=>t.id===this.id));if(!e){throw`No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`}return{config:e,_scope_:t._scope_}}async main(){this.dom.errdiv.style("display","none");this.config=structuredClone(this.state.config);if(!this.components.plots[this.config.childType]){await this.setComponent(this.config)}for(const t in this.components.plots){this.components.plots[t]}this.render();const t=this.tabsData.findIndex((t=>t.childType==this.config.childType));this.chartToggles.update(t,this.config);const e=this.tabsData.filter((t=>t.isVisible())).length;if(e>1)this.dom.chartToggles.style("display","inline-block");else this.dom.chartToggles.style("display","none")}async setComponent(t){let e;if(t.childType=="barchart")e=await import("./barchart-2898d229.js");else if(t.childType=="violin")e=await import("./violin-74d26b75.js");else if(t.childType=="table")e=await import("./table-bf40249b.js");else if(t.childType=="boxplot")e=await import("./boxplot-4c9a5479.js");else if(t.childType=="sampleScatter")e=await import("./sampleScatter-55d9eb74.js").then((function(t){return t.b}));else throw`unsupported childType='${t.childType}'`;this.dom.plotDivs[t.childType]=this.dom.viz.append("div");this.components.plots[t.childType]=await e.componentInit({app:this.app,holder:this.dom.plotDivs[t.childType],id:this.id,parent:this.api})}destroy(){this.dom.holder.app_div.selectAll("*").remove();this.dom.holder.app_div.remove();for(const t in this.dom){delete this.dom[t]}}}const d=t(c);function m(t){t.initUi=function(e,o){const r=e.holder;try{t.dom={tip:new i({padding:"0px"}),holder:r,body:r.body.style("white-space","nowrap").style("overflow-x","auto"),errdiv:r.body.append("div").style("display","none").style("padding","5px").style("background-color","rgba(255,100,100,0.2)"),viz:r.body.append("div"),plotDivs:{}};r.header.style("padding",0);t.dom.paneTitleDiv=t.dom.holder.header.append("div").style("display","inline-block").style("color","#999").style("padding-left","7px");t.dom.paneTitleDiv.append("div").classed("sjpp-term-header",true).style("display","inline-block").style("vertical-align","sub").html(o.term.term.name);t.tabsData=[{childType:"barchart",label:"Barchart",isVisible:()=>true,disabled:t=>false,getConfig:async()=>{if(!t.config)return;const e={id:t.id,childType:"barchart"};const i=t.config?.term;const o=t.config?.term2;if(i){const o=s(i?.term)?"discrete":i?.q.mode||"discrete";e.term=await t.getWrappedTermCopy(i,o)}if(o){const i=s(o.term)?"discrete":o.q.mode||"discrete";e.term2=await t.getWrappedTermCopy(o,i)}return e},active:true,callback:t.tabClickCallback},{childType:"violin",label:"Violin",disabled:t=>false,isVisible:()=>s(t.config?.term?.term)||s(t.config?.term2?.term),getConfig:async()=>{const e=t.config?.term;const i=t.config.term2;let o,r;s(e?.term)?t.violinContTerm="term":t.violinContTerm="term2";if(t.violinContTerm&&t.violinContTerm==="term"||e.q?.mode=="continuous"){o=await t.getWrappedTermCopy(e,"continuous");r=await t.getWrappedTermCopy(i,"discrete");t.violinContTerm="term"}else if(t.violinContTerm&&t.violinContTerm==="term2"||i?.q?.mode=="continuous"){o=await t.getWrappedTermCopy(e,"discrete");r=await t.getWrappedTermCopy(i,"continuous");t.violinContTerm="term2"}else if(i?.q?.mode=="discrete"){o=await t.getWrappedTermCopy(e,"discrete");r=await t.getWrappedTermCopy(i,"continuous");t.violinContTerm="term2"}else{o=await t.getWrappedTermCopy(e,"continuous");r=await t.getWrappedTermCopy(i,"discrete");t.violinContTerm="term"}const a={childType:"violin",term:o,term2:r};return a},active:false,callback:t.tabClickCallback},{childType:"table",label:"Crosstab - in development",disabled:t=>true,isVisible:()=>false,active:false,callback:t.tabClickCallback},{childType:"boxplot",label:"Boxplot - TODO",disabled:t=>true,isVisible:()=>false,active:false,callback:t.tabClickCallback},{childType:"sampleScatter",label:"Scatter",disabled:t=>false,isVisible:()=>s(t.config?.term.term)&&s(t.config?.term2?.term),getConfig:async()=>{const e=await t.getWrappedTermCopy(t.config?.term,"continuous");const i=await t.getWrappedTermCopy(t.config?.term2,"continuous");let o={childType:"sampleScatter",term:e,term2:i,groups:[],term0:t.config.term0};return o},active:false,callback:t.tabClickCallback}];t.dom.chartToggles=t.dom.paneTitleDiv.append("div").style("display","inline-block").style("margin-left","10px");t.chartToggles=new p({holder:t.dom.chartToggles,tabs:t.tabsData,noContent:true});t.chartToggles.main();t.dom.localRecoverDiv=t.dom.paneTitleDiv.append("div").style("display","inline-block")}catch(t){throw t}};t.tabClickCallback=async(e,i)=>{if(!i||!i.getConfig)return;const o=await i.getConfig();if(o)t.app.dispatch({type:"plot_edit",id:t.id,config:o})};t.getWrappedTermCopy=async function(e,i){if(!e)return;const s=structuredClone(e);s.q.mode=i;await o(s,t.app.vocabApi);return s};t.render=function(){for(const e in t.components.plots){const i=t.components.plots[e];if(i.type!=t.config.childType){t.dom.plotDivs[i.type].style("display","none")}}t.dom.plotDivs[t.config.childType].style("display","")}}async function f(t,i){if(!t.term)throw"summary getPlotConfig: opts.term{} missing";try{await o(t.term,i.vocabApi);if(t.term2)await o(t.term2,i.vocabApi);if(t.term0)await o(t.term0,i.vocabApi)}catch(t){throw`${t} [summary getPlotConfig()]`}const s={chartType:"summary",childType:"barchart",term:t.term,groups:[],settings:{controls:{isOpen:false},common:{use_logscale:false,use_percentage:false,barheight:300,barwidth:20,barspace:2},barchart:n(i),violin:a(),sampleScatter:l()},mayAdjustConfig(t,e={}){if(!e.childType){if(t.term?.q?.mode=="continuous"&&t.term2?.q?.mode=="continuous"){t.childType="sampleScatter"}else if(t.term?.q?.mode=="continuous"||t.term2?.q?.mode=="continuous")t.childType="violin";else t.childType="barchart"}}};return e(s,t)}export{f as getPlotConfig,d as summaryInit};

package/dist/termdb.bins-39d11f24.js

@@ -1 +0,0 @@
-import{V as t,C as s,H as e,W as n}from"./app-6fb77603.js";function i(t){const s=t;if(!s||typeof s!=="object")throw"bin schema must be an object";if(!("type"in s))s.type="regular-bin";if(s.type=="custom-bin"){if(!Array.isArray(s.lst))throw"binconfig.lst must be an array";if(!s.lst.length)throw"binconfig.lst must have entries";const t=s.lst[0];const n=s.lst[s.lst.length-1];for(const i of s.lst){if(!("startinclusive"in i)&&!("stopinclusive"in i)){throw"custom bin.startinclusive and/or bin.stopinclusive must be defined"}if(i==t){if("startunbounded"in i&&!i.startunbounded){throw`a custom first bin must not set bin.startunbounded to false`}i.startunbounded=true;if("start"in i){throw"a custom first bin must not set a bin.start value"}if("start_percentile"in i){throw"the first bin must not set a bin.start_percentile value"}if(!("stop"in i)){throw`a custom first bin must define a bin.stop value`}if(!e(i.stop)){throw`a custom first bin.stop value should be numeric`}}else if(i==n){if(!("start"in i)){throw`a custom last bin must define a bin.start value`}if(!e(i.start)){throw`a custom last bin.start must be numeric`}if("stopunbounded"in i&&!i.stopunbounded){throw"a custom last bin must not set bin.stopunbounded to false"}i.stopunbounded=true;if("stop"in i){throw"a custom last bin must not set a bin.stop value"}}else{if(!e(i.start))throw"bin.start must be numeric for a non-first bin";if(!e(i.stop))throw"bin.stop must be numeric for a non-last bin"}}}else if(s.type=="regular-bin"){if(!Number.isFinite(s.bin_size))throw"non-numeric bin_size";if(s.bin_size<=0)throw"bin_size must be greater than 0";if(!s.startinclusive&&!s.stopinclusive){s.startinclusive=1;s.stopinclusive=0}if(!s.first_bin)throw"first_bin{} missing";if(typeof s.first_bin!="object")throw"first_bin{} is not an object";if(!Object.keys(s.first_bin).length)throw"first_bin is an empty object";{const t=s.first_bin;t.startunbounded=true;if(t.stop_percentile){if(!Number.isInteger(t.stop_percentile))throw"first_bin.stop_percentile should be integer";if(t.stop_percentile<=0||t.stop_percentile>=100)throw"first_bin.stop_percentile out of bound (0-100)"}else if(!Number.isFinite(t.stop)){throw"first_bin.stop not a number when stop_percentile is not set"}}if(s.last_bin){const t=s.last_bin;if(t.start_percentile){if(!Number.isInteger(t.start_percentile))throw"last_bin.start_percentile should be integer";if(t.start_percentile<=0||t.start_percentile>=100)throw"last_bin.start_percentile out of bound (0-100)"}else if(!Number.isFinite(t.start)){throw"last_bin.start not a number when start_percentile is not set"}t.stopunbounded=true;if("stop"in t){throw"a regular last bin must not set a bin.stop value"}}}else{throw`invalid binconfig.type="${s.type}"`}}function o(t,n,o){const l=t;i(l);if(l.lst){const t=s(l.lst.length);for(const s of l.lst)s.color=t(s.label)}if(l.type=="custom-bin")return JSON.parse(JSON.stringify(l.lst));if(typeof n!="function")throw"summaryfxn required for modules/termdb.bins.js compute_bins()";const b=u(l);const c=n(b);if(!c||typeof c!=="object")throw"invalid returned value by summaryfxn";l.results={summary:c};if(!l.binLabelFormatter)l.binLabelFormatter=r(l);const f=Math.floor(c.min*100)/100;const p=Math.ceil(c.max*100)/100;const _=l.first_bin.startunbounded?f:l.first_bin.start_percentile?c["p"+l.first_bin.start_percentile]:l.first_bin.start;let d=p,m,h;if(l.last_bin){d=l.last_bin.stopunbounded?p:l.last_bin.stop_percentile?c["p"+l.last_bin.stop_percentile]:e(l.last_bin.stop)&&l.last_bin.stop<=c.max?l.last_bin.stop:p;m=e(l.last_bin.start_percentile)?c["p"+l.last_bin.start_percentile]:e(l.last_bin.start)?l.last_bin.start:undefined;h=l.last_bin.stopunbounded?null:l.last_bin.stop_percentile?c["p"+l.last_bin.stop_percentile]:e(l.last_bin.stop)?l.last_bin.stop:null}else if(l.lst){const t=l.lst[l.lst.length-1];m=t.start;h="stop"in t&&!t.stopunbounded?t.stop:p;d=h}else{m=p;h=p}const v=e(d);const g=e(m);const w=e(h);if(!v&&!g)return[];const y=[];let F={startunbounded:l.first_bin.startunbounded,start:l.first_bin.startunbounded?undefined:_,stop:e(l.first_bin.stop_percentile)?+c["p"+l.first_bin.stop_percentile]:e(l.first_bin.stop)?+l.first_bin.stop:_+l.bin_size,startinclusive:l.startinclusive,stopinclusive:l.stopinclusive};if(!e(F.stop))throw"the computed first_bin.stop is non-numeric"+F.stop;const U=100;while(v&&F.stop<=d||F.startunbounded&&!y.length||F.stopunbounded){y.push(F);if(F.stop>=d){F.stopunbounded=true;if(y.length>1){delete F.stop}}F.label=a(F,l,o);if(F.stopunbounded)break;const t=F.stop+l.bin_size;const s=F.stop;F={startinclusive:l.startinclusive,stopinclusive:l.stopinclusive,start:s,stop:w&&(s==m||t>h)?h:g&&t>m&&s!=m?m:t};if(F.stop>=d){F.stop=d;if(l.last_bin&&l.last_bin.stopunbounded)F.stopunbounded=1;if(l.last_bin&&l.last_bin.stopinclusive)F.stopinclusive=1}if(g&&F.start==m){if(l.last_bin&&l.last_bin.stopunbounded)F.stopunbounded=1}if(F.start>F.stop){if(g&&F.stop==m&&l.last_bin&&l.last_bin.stopunbounded)F.stopunbounded=true;else break}if(y.length+1>=U){l.error="max_num_bins_reached";break}}delete l.binLabelFormatter;if(y.length>1){delete y[y.length-1].stop}const L=s(y.length);for(const t of y)t.color=L(t.label);return y}function r(t){return"rounding"in t?n(t.rounding):t=>t}function a(s,e,n){const i=e;if(!i.binLabelFormatter)i.binLabelFormatter=r(i);if(!s.startunbounded&&!s.stopunbounded&&!("startinclusive"in s)&&!("stopinclusive"in s)){if(i.startinclusive)s.startinclusive=true;else if(i.stopinclusive)s.stopinclusive=true}const o=i.use_as=="bins"||s.start;const a=i.use_as=="bins"||s.stop;let l=0;if("label_offset"in i){i.label_offset_ignored="bin_size"in i&&i.bin_size<i.label_offset;if(!i.label_offset_ignored)l=i.label_offset}else if(i.bin_size===1&&i.termtype=="integer"){l=1}if(s.startunbounded){const e=s.stopinclusive?"≤":"<";const o=n?t(a,n.fromUnit,n.toUnit,n.scaleFactor,true):i.binLabelFormatter(a);return e+o}if(s.stopunbounded||o===a){const e=s.startinclusive?"≥":">";const r=n?t(o,n.fromUnit,n.toUnit,n.scaleFactor,true):i.binLabelFormatter(o);return e+r}if(l&&s.startinclusive&&!s.stopinclusive){if(Number.isInteger(i.bin_size)&&Math.abs(o-a)===l){return""+(n?t(o,n.fromUnit,n.toUnit,n.scaleFactor,true):i.binLabelFormatter(o))}else{const s=n?t(o,n.fromUnit,n.toUnit,n.scaleFactor,true):i.binLabelFormatter(o);const e=n?t(a-l,n.fromUnit,n.toUnit,n.scaleFactor,true):i.binLabelFormatter(a-l);return+s>=+e?s.toString():s+" to "+e}}else{const e=s.startinclusive?"":">";const r=s.stopinclusive?"":"<";const l=n?t(o,n.fromUnit,n.toUnit,n.scaleFactor,true):Number.isInteger(o)?o:i.binLabelFormatter(o);const u=n?t(a,n.fromUnit,n.toUnit,n.scaleFactor,true):Number.isInteger(a)?a:i.binLabelFormatter(a);if(+l>=+u){const t=s.startinclusive?"≥":">";return t+l}else{return e+l+" to "+r+u}}}function l(t,s){const e='<span style="font-family:Times;font-style:italic;">x</span>';let n;const i=a(t,s);if(t.startunbounded||t.stopunbounded){n=e+"&nbsp;"+i}else if(t.startinclusive){n=i.replace("to <","≤ "+e+" <")}else if(t.stopinclusive){n=i.replace(">","").replace("to","< "+e+" ≤")}return n}function u(t){const s=[];const n=t.first_bin;if(n&&e(n.start_percentile))s.push(n.start_percentile);if(n&&e(n.stop_percentile))s.push(n.stop_percentile);const i=t.last_bin;if(i&&e(i.start_percentile))s.push(i.start_percentile);if(i&&e(i.stop_percentile))s.push(i.stop_percentile);return s}export{l as a,o as c,a as g};