@sjcrh/proteinpaint-client 2.207.1 → 2.208.0

package/dist/chunk-QP7EJXSU.js

@@ -0,0 +1,55 @@
+import {
+  colorinframe
+} from "./chunk-QJ3HYZH3.js";
+import {
+  IN_frame,
+  OUT_frame
+} from "./chunk-4EZLVENZ.js";
+
+// src/spliceevent.phrase.js
+function spliceevent_phrase_default(evt) {
+  const htmls = [];
+  if (evt.isaltexon || evt.isskipexon) {
+    const exonstart = Math.min(...evt.skippedexon);
+    const exonstop = Math.max(...evt.skippedexon);
+    htmls.push(
+      '<div style="display:inline-block">' + (exonstart == exonstop ? "exon " + (exonstart + 1) : "exons " + (exonstart + 1) + "-" + (exonstop + 1)) + " " + (evt.isaltexon ? "alternative usage" : "skipping") + "</div>"
+    );
+    if (evt.isaltexon) {
+      htmls.push(
+        "<div class=sja_tinylogo_body>" + evt.gmB.isoform + ", " + evt.gmA.isoform + "</div><div class=sja_tinylogo_head>ISOFORMS</div>"
+      );
+    } else {
+      htmls.push("<div class=sja_tinylogo_body>" + evt.gm.isoform + "</div><div class=sja_tinylogo_head>ISOFORM</div>");
+    }
+    if (evt.junctionB.data) {
+      htmls.push(
+        "<div class=sja_tinylogo_body>" + evt.junctionB.data.length + "</div><div class=sja_tinylogo_head>SAMPLE" + (evt.junctionB.data.length > 1 ? "S" : "") + "</div>"
+      );
+    }
+    htmls.push("<div class=sja_tinylogo_body>" + evt.percentage + " %</div><div class=sja_tinylogo_head>PERCENT</div>");
+    if (evt.framenocheck) {
+      if (evt.utr3) {
+        htmls.push(`<div class=sja_tinylogo_body style="background-color:#ededed">3' UTR</div>`);
+      } else if (evt.utr5) {
+        htmls.push(`<div class=sja_tinylogo_body style="background-color:#ededed">5' UTR</div>`);
+      }
+    } else if (evt.frame == IN_frame) {
+      htmls.push(
+        '<div class=sja_tinylogo_body style="background-color:' + colorinframe + ';color:white">IN</div><div class=sja_tinylogo_head>FRAME</div>'
+      );
+    } else if (evt.frame == OUT_frame) {
+      htmls.push("<div class=sja_tinylogo_body>OUT</div><div class=sja_tinylogo_head>FRAME</div>");
+    } else {
+      htmls.push("<div class=sja_tinylogo_body>?</div><div class=sja_tinylogo_head>FRAME</div>");
+    }
+  } else {
+    return "unknown event type!!";
+  }
+  return htmls.join(" ");
+}
+
+export {
+  spliceevent_phrase_default
+};
+//# sourceMappingURL=chunk-QP7EJXSU.js.map

package/dist/chunk-QUHXX7JE.js

@@ -0,0 +1,56 @@
+import {
+  sayerror
+} from "./chunk-QJ3HYZH3.js";
+import {
+  TermTypeGroups
+} from "./chunk-4EZLVENZ.js";
+
+// termdb/handlers/singleCellNumericValue.ts
+var SearchHandler = class {
+  async init(opts) {
+    this.validateOpts(opts);
+    this.callback = opts.callback;
+    this.app = opts.app;
+    const holder = opts.holder.append("div").style("padding", "10px 0px");
+    const scnvTerms = opts.app.vocabApi.termdbConfig?.termType2terms?.[TermTypeGroups.SINGLECELL_NUMERIC_VALUE];
+    if (!scnvTerms?.length) {
+      sayerror(
+        holder,
+        `termType2terms[${TermTypeGroups.SINGLECELL_NUMERIC_VALUE}]:[] is required in termdbConfig for singleCellNumericValue handler`
+      );
+      return;
+    }
+    const usecaseConfig = opts.usecase?.specialCase?.config;
+    const plots = usecaseConfig?.sample?.plots;
+    const isMeta = usecaseConfig?.sample?.isMetaResult;
+    const filtered = plots ? scnvTerms.filter((t) => plots.includes(t.plot)) : usecaseConfig?.name ? scnvTerms.filter((t) => t.plot === usecaseConfig.name) : scnvTerms;
+    const getLabel = (t) => isMeta || plots?.length == 1 ? t.name : `${t.name} (${t.plot})`;
+    const filteredTerms = new Set(
+      plots || !usecaseConfig?.name ? filtered.map((t) => ({ ...t, label: getLabel(t) })) : filtered
+    );
+    for (const t of Array.from(filteredTerms)) {
+      holder.append("div").classed("termdiv", true).style("padding", "0px 5px").append("div").classed("termlabel sja_filter_tag_btn sja_tree_click_term ts_pill", true).style("display", "inline-block").style("padding", "5px 8px").style("margin", "1px 0px").style("border-radius", "6px").text(t.label || t.name).on("click", () => {
+        const term = this.makeTerm(t, usecaseConfig);
+        this.callback(term);
+      });
+    }
+  }
+  makeTerm(_term, usecaseConfig) {
+    const term = { ..._term };
+    if (!term.sample && usecaseConfig?.sample) term.sample = usecaseConfig.sample;
+    return term;
+  }
+  validateOpts(opts) {
+    if (opts.callback == null) throw new Error("callback is required");
+    if (opts.app == null) throw new Error("app is required");
+    if (opts.holder == null) throw new Error("holder is required");
+    if (opts.usecase == null) throw new Error("usecase is required");
+    if (!opts.app.vocabApi.termdbConfig?.termType2terms)
+      throw new Error("termType2terms is required in termdbConfig for singleCellNumericValue handler");
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-QUHXX7JE.js.map

package/dist/chunk-QUHXX7JE.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../termdb/handlers/singleCellNumericValue.ts"],
+  "sourcesContent": ["import type { AppApi } from '#rx'\nimport { TermTypeGroups } from '#shared/terms.js'\nimport { sayerror } from '#dom'\n\nexport class SearchHandler {\n    callback?: (f?: any) => void\n    app?: AppApi\n\n    async init(opts) {\n        this.validateOpts(opts)\n        this.callback = opts.callback\n        this.app = opts.app\n\n        const holder = opts.holder.append('div').style('padding', '10px 0px')\n        const scnvTerms = opts.app.vocabApi.termdbConfig?.termType2terms?.[TermTypeGroups.SINGLECELL_NUMERIC_VALUE]\n        if (!scnvTerms?.length) {\n            sayerror(\n                holder,\n                `termType2terms[${TermTypeGroups.SINGLECELL_NUMERIC_VALUE}]:[] is required in termdbConfig for singleCellNumericValue handler`\n            )\n            return\n        }\n        const usecaseConfig = opts.usecase?.specialCase?.config\n        const plots = usecaseConfig?.sample?.plots\n        const isMeta = usecaseConfig?.sample?.isMetaResult\n\n        /** Use either the usecase.config.sample.plots:[] or usecase.config.name (i.e.\n         * plot name) to filter the terms OR display all. If displaying all terms,\n         * append the plot name to the label. Only display a term once. */\n        const filtered = plots\n            ? scnvTerms.filter(t => plots.includes(t.plot))\n            : usecaseConfig?.name\n            ? scnvTerms.filter(t => t.plot === usecaseConfig.name)\n            : scnvTerms\n\n        const getLabel = t => ((isMeta || plots?.length == 1) ? t.name : `${t.name} (${t.plot})`)\n\n        const filteredTerms: Set<any> = new Set(\n            plots || !usecaseConfig?.name ? filtered.map(t => ({ ...t, label: getLabel(t)})) : filtered\n        )\n\n        for (const t of Array.from(filteredTerms)) {\n            holder\n                /** The divs and styling duplicates the appearance of the\n                 * tree terms. The tree is NOT called for this handler. */\n                .append('div')\n                .classed('termdiv', true)\n                .style('padding', '0px 5px')\n                .append('div')\n                .classed('termlabel sja_filter_tag_btn sja_tree_click_term ts_pill', true)\n                .style('display', 'inline-block')\n                .style('padding', '5px 8px')\n                .style('margin', '1px 0px')\n                .style('border-radius', '6px')\n                //End duplicated pill styling\n                .text(t.label || t.name)\n                .on('click', () => {\n                    const term = this.makeTerm(t, usecaseConfig)\n                    this.callback!(term)\n                })\n        }\n    }\n\n    makeTerm(_term, usecaseConfig) {\n        const term = { ..._term }\n        if (!term.sample && usecaseConfig?.sample) term.sample = usecaseConfig.sample\n        return term\n    }\n\n    validateOpts(opts) {\n        if (opts.callback == null) throw new Error('callback is required')\n        if (opts.app == null) throw new Error('app is required')\n        if (opts.holder == null) throw new Error('holder is required')\n        if (opts.usecase == null) throw new Error('usecase is required')\n        if (!opts.app.vocabApi.termdbConfig?.termType2terms)\n            throw new Error('termType2terms is required in termdbConfig for singleCellNumericValue handler')\n    }\n}\n"],
+  "mappings": ";;;;;;;;AAIO,IAAM,gBAAN,MAAoB;AAAA,EAIvB,MAAM,KAAK,MAAM;AACb,SAAK,aAAa,IAAI;AACtB,SAAK,WAAW,KAAK;AACrB,SAAK,MAAM,KAAK;AAEhB,UAAM,SAAS,KAAK,OAAO,OAAO,KAAK,EAAE,MAAM,WAAW,UAAU;AACpE,UAAM,YAAY,KAAK,IAAI,SAAS,cAAc,iBAAiB,eAAe,wBAAwB;AAC1G,QAAI,CAAC,WAAW,QAAQ;AACpB;AAAA,QACI;AAAA,QACA,kBAAkB,eAAe,wBAAwB;AAAA,MAC7D;AACA;AAAA,IACJ;AACA,UAAM,gBAAgB,KAAK,SAAS,aAAa;AACjD,UAAM,QAAQ,eAAe,QAAQ;AACrC,UAAM,SAAS,eAAe,QAAQ;AAKtC,UAAM,WAAW,QACX,UAAU,OAAO,OAAK,MAAM,SAAS,EAAE,IAAI,CAAC,IAC5C,eAAe,OACf,UAAU,OAAO,OAAK,EAAE,SAAS,cAAc,IAAI,IACnD;AAEN,UAAM,WAAW,OAAO,UAAU,OAAO,UAAU,IAAK,EAAE,OAAO,GAAG,EAAE,IAAI,KAAK,EAAE,IAAI;AAErF,UAAM,gBAA0B,IAAI;AAAA,MAChC,SAAS,CAAC,eAAe,OAAO,SAAS,IAAI,QAAM,EAAE,GAAG,GAAG,OAAO,SAAS,CAAC,EAAC,EAAE,IAAI;AAAA,IACvF;AAEA,eAAW,KAAK,MAAM,KAAK,aAAa,GAAG;AACvC,aAGK,OAAO,KAAK,EACZ,QAAQ,WAAW,IAAI,EACvB,MAAM,WAAW,SAAS,EAC1B,OAAO,KAAK,EACZ,QAAQ,4DAA4D,IAAI,EACxE,MAAM,WAAW,cAAc,EAC/B,MAAM,WAAW,SAAS,EAC1B,MAAM,UAAU,SAAS,EACzB,MAAM,iBAAiB,KAAK,EAE5B,KAAK,EAAE,SAAS,EAAE,IAAI,EACtB,GAAG,SAAS,MAAM;AACf,cAAM,OAAO,KAAK,SAAS,GAAG,aAAa;AAC3C,aAAK,SAAU,IAAI;AAAA,MACvB,CAAC;AAAA,IACT;AAAA,EACJ;AAAA,EAEA,SAAS,OAAO,eAAe;AAC3B,UAAM,OAAO,EAAE,GAAG,MAAM;AACxB,QAAI,CAAC,KAAK,UAAU,eAAe,OAAQ,MAAK,SAAS,cAAc;AACvE,WAAO;AAAA,EACX;AAAA,EAEA,aAAa,MAAM;AACf,QAAI,KAAK,YAAY,KAAM,OAAM,IAAI,MAAM,sBAAsB;AACjE,QAAI,KAAK,OAAO,KAAM,OAAM,IAAI,MAAM,iBAAiB;AACvD,QAAI,KAAK,UAAU,KAAM,OAAM,IAAI,MAAM,oBAAoB;AAC7D,QAAI,KAAK,WAAW,KAAM,OAAM,IAAI,MAAM,qBAAqB;AAC/D,QAAI,CAAC,KAAK,IAAI,SAAS,cAAc;AACjC,YAAM,IAAI,MAAM,+EAA+E;AAAA,EACvG;AACJ;",
+  "names": []
+}

package/dist/chunk-REPQKF5L.js

@@ -0,0 +1,182 @@
+import {
+  Tabs,
+  addGeneSearchbox,
+  make_one_checkbox,
+  make_radios
+} from "./chunk-QJ3HYZH3.js";
+import {
+  Menu
+} from "./chunk-ELJX3QIQ.js";
+import {
+  termType2label
+} from "./chunk-GMRIEUBW.js";
+import {
+  TermTypeGroups
+} from "./chunk-4EZLVENZ.js";
+
+// termdb/handlers/pseudobulk.ts
+var SearchHandler = class {
+  async init(opts) {
+    const pseudobulkTerms = this.validateOpts(opts);
+    this.callback = opts.callback;
+    this.app = opts.app;
+    this.genome = opts.genomeObj;
+    const holder = opts.holder.append("div").style("padding", "10px 0px");
+    this.multiSelect = opts?.usecase?.target == "aggregateMatrix";
+    this.selectedTerm = void 0;
+    this.map = this.buildRenderingDataMap(pseudobulkTerms);
+    this.renderPseudobulkSearch(holder);
+  }
+  validateOpts(opts) {
+    if (!opts) throw new Error("opts is required");
+    if (!opts.app) throw new Error("opts.app is required");
+    if (!opts.holder) throw new Error("opts.holder is required");
+    if (opts.genomeObj == null || typeof opts.genomeObj !== "object") throw new Error("genomeObj is required");
+    if (!opts.callback) throw new Error("opts.callback is required");
+    const pseudobulkTerms = opts.app.vocabApi.termdbConfig?.termType2terms?.[TermTypeGroups.PSEUDOBULK];
+    if (!pseudobulkTerms?.length) {
+      throw new Error(
+        `termType2terms[${TermTypeGroups.PSEUDOBULK}]:[] is required in termdbConfig for pseudobulk handler`
+      );
+    }
+    return pseudobulkTerms;
+  }
+  /** Builds a map from assay to memberId to terms */
+  buildRenderingDataMap(pseudobulkTerms) {
+    const map = /* @__PURE__ */ new Map();
+    for (const term of pseudobulkTerms) {
+      const { assay, memberId } = term;
+      if (!map.has(assay)) map.set(assay, /* @__PURE__ */ new Map());
+      const assayMap = map.get(assay);
+      if (!assayMap.has(memberId)) assayMap.set(memberId, []);
+      assayMap.get(memberId).push(term);
+    }
+    return map;
+  }
+  /** If more than one assay, render tabs for each assay. Member IDs within
+   * an assay are rendered as tabs when there is more than one. */
+  renderPseudobulkSearch(holder) {
+    if (!this.map || this.map.size < 1) throw new Error("map is not initialized");
+    if (this.map.size === 1) {
+      const label = termType2label(this.map.keys().next().value);
+      holder.append("div").style("padding-bottom", "10px").text("Single-cell pseudobulk " + label);
+      this.renderMemberIdsByAssay(holder.append("div"), this.map);
+      return;
+    }
+    const tabs = this.buildTabsOpts(this.map);
+    new Tabs({ holder, tabs, tabsPosition: "vertical" }).main();
+  }
+  buildTabsOpts(map) {
+    const tabs = [];
+    for (const [key, valuesMap] of map.entries()) {
+      const label = termType2label(key);
+      tabs.push({
+        label,
+        active: false,
+        callback: (_, tab) => {
+          this.renderMemberIdsByAssay(tab.contentHolder, /* @__PURE__ */ new Map([[key, valuesMap]]));
+        }
+      });
+    }
+    return tabs;
+  }
+  renderMemberIdsByAssay(holder, map) {
+    const memberIdMap = map.values().next().value;
+    holder.selectAll("*").remove();
+    this.renderTermdByMemberId(holder, memberIdMap);
+  }
+  renderTermdByMemberId(holder, memberIdMap) {
+    const layout = holder.append("div").style("display", "flex").style("align-items", "flex-start").style("gap", "30px");
+    const pseudoTermsWrapper = layout.append("div").attr("data-testid", "sjpp-pseudobulk-terms-wrapper");
+    const geneSearchWrapper = layout.append("div").attr("data-testid", "sjpp-pseudobulk-gene-search-wrapper");
+    this.renderPseudobulkTerms(pseudoTermsWrapper, memberIdMap, geneSearchWrapper);
+  }
+  renderPseudobulkTerms(holder, memberIdMap, geneSearchHolder) {
+    if (memberIdMap.size === 1) {
+      const [memberId, terms] = memberIdMap.entries().next().value;
+      if (this.multiSelect) {
+        this.renderCategoriesAsTerms(holder, terms);
+      } else this.renderCategoryRadios(holder, memberId, terms, geneSearchHolder);
+      return;
+    }
+    const memberEntries = Array.from(memberIdMap.entries());
+    const tabs = memberEntries.map(([memberId, terms]) => ({
+      label: memberId,
+      active: false,
+      testid: `sjpp-pseudobulk-member-${memberId}`,
+      callback: (_, tab) => {
+        geneSearchHolder.selectAll("*").remove();
+        tab.contentHolder.selectAll("*").remove();
+        if (this.multiSelect) this.renderCategoriesAsTerms(tab.contentHolder, terms);
+        else this.renderCategoryRadios(tab.contentHolder, memberId, terms, geneSearchHolder);
+      }
+    }));
+    new Tabs({ holder, tabs, tabsPosition: "vertical" }).main();
+  }
+  renderCategoryRadios(holder, memberId, terms, geneSearchHolder) {
+    if (!terms || terms.length < 1) throw new Error("No terms found for memberId");
+    const options = terms.map((term) => ({
+      label: term.name,
+      value: term.id,
+      checked: false,
+      testid: `sjpp-pseudobulk-category-${term.id}`
+    }));
+    make_radios({
+      holder,
+      inputName: `sjpp-pseudobulk-category-radios-${memberId}`,
+      options,
+      styles: { display: "block", padding: "3px 5px" },
+      callback: (value) => {
+        const term = terms.find((term2) => term2.id == value);
+        if (!term) throw new Error(`No pseudobulk term found for category ${value}`);
+        this.selectedTerm = term;
+        this.renderGeneSelection(geneSearchHolder);
+      }
+    });
+  }
+  renderGeneSelection(holder) {
+    holder.selectAll("*").remove();
+    const geneSearch = addGeneSearchbox({
+      tip: new Menu({ padding: "0px" }),
+      genome: this.genome,
+      row: holder,
+      searchOnly: "gene",
+      callback: () => {
+        if (!geneSearch.geneSymbol) throw new Error("No gene selected");
+        if (!this.selectedTerm) throw new Error("No pseudobulk cell type selected");
+        this.callback(createPseudobulkTerm(this.selectedTerm, geneSearch.geneSymbol));
+      }
+    });
+  }
+  /** Mimics the style and functionality of pills created in tree.js.
+   * Returns the term object(s) from termdbConfig.termType2terms.[TermTypeGroups.PSEUDOBULK]
+   * without the gene. */
+  renderCategoriesAsTerms(holder, terms) {
+    holder.style("padding", "0px 10px");
+    make_one_checkbox({
+      holder,
+      labeltext: "Select all",
+      divstyle: { opacity: "0.7" },
+      callback: () => this.callback(terms)
+    });
+    const wrapper = holder.append("div").style("display", "block").style("padding", "10px 15px 0px");
+    wrapper.selectAll(".pseudobulk-term").data(terms, (term) => term.id).join((enter) => {
+      const row = enter.append("div").attr("class", "pseudobulk-term");
+      row.append("div").attr("class", "termlabel sja_filter_tag_btn sja_tree_click_term ts_pill").style("padding", "5px 8px").style("margin", "1px 0px").style("border-radius", "6px").text((term) => term.name).on("click", async (_, term) => {
+        await this.callback(term);
+      });
+      return row;
+    });
+  }
+};
+function createPseudobulkTerm(selectedTerm, gene) {
+  const category = selectedTerm.category || selectedTerm.id;
+  const name = `${selectedTerm.assay} ${category} ${gene}`;
+  return { ...selectedTerm, id: name, category, gene, name };
+}
+
+export {
+  SearchHandler,
+  createPseudobulkTerm
+};
+//# sourceMappingURL=chunk-REPQKF5L.js.map

package/dist/chunk-REPQKF5L.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../termdb/handlers/pseudobulk.ts"],
+  "sourcesContent": ["import type { AppApi } from '#rx'\nimport { TermTypeGroups, termType2label } from '#shared/terms.js'\nimport { Tabs, type TabsInputEntry, make_radios, type OptionEntry, Menu, addGeneSearchbox, make_one_checkbox } from '#dom'\nimport type { ClientGenome } from 'types/clientGenome'\nimport type { PseudobulkTerm } from '#types'\n\n/** Human readable labels */\n\ntype PseudobulkSelection = Omit<PseudobulkTerm, 'category' | 'gene'> & {\n\tid: string\n\tcategory?: string\n}\n\nexport class SearchHandler {\n\tcallback!: (term: PseudobulkSelection | PseudobulkSelection[]) => void | Promise<void>\n\tapp!: AppApi\n\tgenome!: ClientGenome\n\tmap?: Map<string, Map<string, any[]>>\n\tselectedTerm?: PseudobulkSelection\n\tmultiSelect!: boolean\n\n\tasync init(opts) {\n\t\tconst pseudobulkTerms = this.validateOpts(opts)\n\t\tthis.callback = opts.callback\n\t\tthis.app = opts.app\n\t\tthis.genome = opts.genomeObj\n\t\tconst holder = opts.holder.append('div').style('padding', '10px 0px')\n\t\tthis.multiSelect = opts?.usecase?.target == \"aggregateMatrix\"\n\t\tthis.selectedTerm = undefined\n\n\t\tthis.map = this.buildRenderingDataMap(pseudobulkTerms)\n\t\tthis.renderPseudobulkSearch(holder)\n\t}\n\n\tvalidateOpts(opts): any[] {\n\t\tif (!opts) throw new Error('opts is required')\n\t\tif (!opts.app) throw new Error('opts.app is required')\n\t\tif (!opts.holder) throw new Error('opts.holder is required')\n\t\tif (opts.genomeObj == null || typeof opts.genomeObj !== 'object') throw new Error('genomeObj is required')\n\t\tif (!opts.callback) throw new Error('opts.callback is required')\n\t\tconst pseudobulkTerms = opts.app.vocabApi.termdbConfig?.termType2terms?.[TermTypeGroups.PSEUDOBULK]\n\t\tif (!pseudobulkTerms?.length) {\n\t\t\tthrow new Error(\n\t\t\t\t`termType2terms[${TermTypeGroups.PSEUDOBULK}]:[] is required in termdbConfig for pseudobulk handler`\n\t\t\t)\n\t\t}\n\t\treturn pseudobulkTerms\n\t}\n\n\t/** Builds a map from assay to memberId to terms */\n\tbuildRenderingDataMap(pseudobulkTerms): Map<string, Map<string, any[]>> {\n\t\tconst map = new Map()\n\t\tfor (const term of pseudobulkTerms) {\n\t\t\tconst { assay, memberId } = term\n\t\t\tif (!map.has(assay)) map.set(assay, new Map())\n\t\t\tconst assayMap = map.get(assay)\n\t\t\tif (!assayMap.has(memberId)) assayMap.set(memberId, [])\n\t\t\tassayMap.get(memberId).push(term)\n\t\t}\n\t\treturn map\n\t}\n\n\t/** If more than one assay, render tabs for each assay. Member IDs within\n\t * an assay are rendered as tabs when there is more than one. */\n\trenderPseudobulkSearch(holder) {\n\t\tif (!this.map || this.map.size < 1) throw new Error('map is not initialized')\n\t\tif (this.map.size === 1) {\n\t\t\t// only one assay\n\t\t\tconst label = termType2label(this.map.keys().next().value!)\n\t\t\tholder.append('div').style('padding-bottom', '10px').text('Single-cell pseudobulk ' + label)\n\t\t\tthis.renderMemberIdsByAssay(holder.append('div'), this.map)\n\t\t\treturn\n\t\t}\n\t\tconst tabs = this.buildTabsOpts(this.map)\n\t\tnew Tabs({ holder, tabs, tabsPosition: 'vertical' }).main()\n\t}\n\n\tbuildTabsOpts(map) {\n\t\tconst tabs: TabsInputEntry[] = []\n\t\tfor (const [key, valuesMap] of map.entries()) {\n\t\t\tconst label = termType2label(key)\n\t\t\ttabs.push({\n\t\t\t\tlabel,\n\t\t\t\tactive: false,\n\t\t\t\tcallback: (_, tab) => {\n\t\t\t\t\tthis.renderMemberIdsByAssay(tab.contentHolder, new Map([[key, valuesMap]]))\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t\treturn tabs\n\t}\n\n\trenderMemberIdsByAssay(holder, map) {\n\t\tconst memberIdMap = map.values().next().value\n\t\tholder.selectAll('*').remove()\n\t\tthis.renderTermdByMemberId(holder, memberIdMap)\n\t}\n\n\trenderTermdByMemberId(holder, memberIdMap) {\n\t\tconst layout = holder.append('div').style('display', 'flex').style('align-items', 'flex-start').style('gap', '30px')\n\t\tconst pseudoTermsWrapper = layout.append('div').attr('data-testid', 'sjpp-pseudobulk-terms-wrapper')\n\t\tconst geneSearchWrapper = layout.append('div').attr('data-testid', 'sjpp-pseudobulk-gene-search-wrapper')\n\t\tthis.renderPseudobulkTerms(pseudoTermsWrapper, memberIdMap, geneSearchWrapper)\n\t}\n\n\trenderPseudobulkTerms(holder, memberIdMap, geneSearchHolder) {\n\t\tif (memberIdMap.size === 1) {\n\t\t\tconst [memberId, terms] = memberIdMap.entries().next().value\n\t\t\tif (this.multiSelect) {\n\t\t\t\tthis.renderCategoriesAsTerms(holder, terms)\n\t\t\t}\n\t\t\telse this.renderCategoryRadios(holder, memberId, terms, geneSearchHolder)\n\t\t\treturn\n\t\t}\n\n\t\tconst memberEntries = Array.from(memberIdMap.entries()) as [string, any[]][]\n\t\tconst tabs: TabsInputEntry[] = memberEntries.map(([memberId, terms]) => ({\n\t\t\tlabel: memberId,\n\t\t\tactive: false,\n\t\t\ttestid: `sjpp-pseudobulk-member-${memberId}`,\n\t\t\tcallback: (_, tab) => {\n\t\t\t\tgeneSearchHolder.selectAll('*').remove()\n\t\t\t\ttab.contentHolder.selectAll('*').remove()\n\t\t\t\tif (this.multiSelect) this.renderCategoriesAsTerms(tab.contentHolder, terms)\n\t\t\t\telse this.renderCategoryRadios(tab.contentHolder, memberId, terms, geneSearchHolder)\n\t\t\t}\n\t\t}))\n\t\tnew Tabs({ holder, tabs, tabsPosition: 'vertical' }).main()\n\t}\n\n\trenderCategoryRadios(holder, memberId, terms, geneSearchHolder) {\n\t\tif (!terms || terms.length < 1) throw new Error('No terms found for memberId')\n\n\t\tconst options: OptionEntry[] = terms.map(term => ({\n\t\t\tlabel: term.name,\n\t\t\tvalue: term.id,\n\t\t\tchecked: false,\n\t\t\ttestid: `sjpp-pseudobulk-category-${term.id}`\n\t\t}))\n\t\tmake_radios({\n\t\t\tholder,\n\t\t\tinputName: `sjpp-pseudobulk-category-radios-${memberId}`,\n\t\t\toptions,\n\t\t\tstyles: { display: 'block', padding: '3px 5px' },\n\t\t\tcallback: value => {\n\t\t\t\tconst term = terms.find(term => term.id == value)\n\t\t\t\tif (!term) throw new Error(`No pseudobulk term found for category ${value}`)\n\t\t\t\tthis.selectedTerm = term\n\t\t\t\tthis.renderGeneSelection(geneSearchHolder)\n\t\t\t}\n\t\t})\n\t}\n\n\trenderGeneSelection(holder) {\n\t\tholder.selectAll('*').remove()\n\t\tconst geneSearch = addGeneSearchbox({\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tgenome: this.genome,\n\t\t\trow: holder,\n\t\t\tsearchOnly: 'gene',\n\t\t\tcallback: () => {\n\t\t\t\tif (!geneSearch.geneSymbol) throw new Error('No gene selected')\n\t\t\t\tif (!this.selectedTerm) throw new Error('No pseudobulk cell type selected')\n\t\t\t\tthis.callback(createPseudobulkTerm(this.selectedTerm, geneSearch.geneSymbol))\n\t\t\t}\n\t\t})\n\t}\n\n\t/** Mimics the style and functionality of pills created in tree.js.\n\t * Returns the term object(s) from termdbConfig.termType2terms.[TermTypeGroups.PSEUDOBULK]\n\t * without the gene. */\n\trenderCategoriesAsTerms(holder: any, terms: PseudobulkTerm[]) {\n\t\tholder.style('padding', '0px 10px')\n\n\t\tmake_one_checkbox({\n\t\t\tholder,\n\t\t\tlabeltext: 'Select all',\n\t\t\tdivstyle: { opacity: '0.7' },\n\t\t\tcallback: () => this.callback(terms)\n\t\t})\n\n\t\tconst wrapper = holder.append('div').style('display', 'block').style('padding', '10px 15px 0px')\n\n\t\twrapper\n\t\t\t.selectAll('.pseudobulk-term')\n\t\t\t.data(terms, term => term.id)\n\t\t\t.join(enter => {\n\t\t\t\tconst row = enter.append('div').attr('class', 'pseudobulk-term')\n\n\t\t\t\trow\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'termlabel sja_filter_tag_btn sja_tree_click_term ts_pill')\n\t\t\t\t\t.style('padding', '5px 8px')\n\t\t\t\t\t.style('margin', '1px 0px')\n\t\t\t\t\t.style('border-radius', '6px')\n\t\t\t\t\t.text(term => term.name)\n\t\t\t\t\t.on('click', async (_, term) => { await this.callback(term) })\n\n\t\t\t\treturn row\n\t\t\t})\n\t}\n}\n\n/** Create a pseudobulk term for the selected cell type and gene. */\nexport function createPseudobulkTerm(selectedTerm: PseudobulkSelection, gene: string): PseudobulkTerm {\n\tconst category = selectedTerm.category || selectedTerm.id\n\tconst name = `${selectedTerm.assay} ${category} ${gene}`\n\treturn { ...selectedTerm, id: name, category, gene, name }\n}\n"],
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+}