@sjcrh/proteinpaint-client 2.204.0 → 2.206.0

package/dist/stattable-PR47XT4F.js

@@ -1,117 +0,0 @@
-import {
-  PlotBase
-} from "./chunk-7RX5UEF3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-L42F5J5C.js";
-import "./chunk-HKQDZKSF.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-FUSTNOQZ.js";
-import "./chunk-VSPUFGDX.js";
-import "./chunk-WVPFLPWB.js";
-import "./chunk-S5SOLLGM.js";
-import {
-  getCompInit
-} from "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-D6G64XPJ.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-YLJOZP4P.js";
-import "./chunk-HDTFYTEL.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// plots/stattable.js
-var TdbStatTable = class _TdbStatTable extends PlotBase {
-  static type = "stattable";
-  constructor(opts, api) {
-    super(opts, api);
-    this.type = _TdbStatTable.type;
-  }
-  async init() {
-    this.dom = {
-      div: this.opts.holder.append("div").style("margin", "10px")
-    };
-    setRenderers(this);
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    return {
-      activeCohort: appState.activeCohort,
-      termfilter: appState.termfilter,
-      config: {
-        term: config.term,
-        term0: config.term0,
-        term2: config.term2,
-        settings: {
-          common: config.settings.common,
-          barchart: config.settings.barchart
-        }
-      },
-      filter: appState.termfilter.filter
-    };
-  }
-  async main() {
-    try {
-      this.config = structuredClone(this.state.config);
-      if (this.state.isVisible) {
-        const reqOpts = this.getDataRequestOpts();
-        const data = await this.vocabApi.getNestedChartSeriesData(reqOpts);
-        this.app.vocabApi.syncTermData(this.state.config, data);
-      }
-      if (!this.state.isVisible || !this.data || !this.data.boxplot) {
-        this.dom.div.style("display", "none");
-        return;
-      }
-      this.render(this.data);
-    } catch (e) {
-      throw e;
-    }
-  }
-  // creates an opts object for the vocabApi.getNestedChartsData()
-  getDataRequestOpts() {
-    const c = this.config;
-    const opts = { term: c.term, filter: this.state.termfilter.filter };
-    if (c.term2) opts.term2 = c.term2;
-    if (c.term0) opts.term0 = c.term0;
-    if (this.state.ssid) opts.ssid = this.state.ssid;
-    return opts;
-  }
-};
-function setRenderers(self) {
-  self.render = function(data) {
-    self.dom.div.style("display", "block").selectAll("*").remove();
-    let exposed_data = "";
-    const sd = data.boxplot.sd ? " (" + data.boxplot.sd.toFixed(2) + ") " : "";
-    let rows = "";
-    if (Number.isFinite(data.boxplot.min)) {
-      rows += "<tr><td>Minimum</td><td>" + data.boxplot.min.toFixed(2) + "</td></tr>";
-    }
-    if (Number.isFinite(data.boxplot.max)) {
-      rows += "<tr><td>Maximum</td><td>" + data.boxplot.max.toFixed(2) + "</td></tr>";
-    }
-    rows += "<tr><td>Mean (SD)</td><td>" + data.boxplot.mean.toFixed(2) + sd + "</td></tr>";
-    if ("p50" in data.boxplot) {
-      rows += "<tr><td>Median (IQR)</td><td>" + data.boxplot.p50.toFixed(2) + " (" + data.boxplot.iqr.toFixed(2) + ") </td></tr><tr><td>5th Percentile</td><td>" + data.boxplot.p05.toFixed(2) + "</td></tr><tr><td>25th Percentile</td><td>" + data.boxplot.p25.toFixed(2) + "</td></tr><tr><td>75th Percentile</td><td>" + data.boxplot.p75.toFixed(2) + "</td></tr><tr><td>95th Percentile</td><td>" + data.boxplot.p95.toFixed(2) + "</td></tr>";
-    }
-    self.dom.div.html("<table><tr><th></th><th>Value</th></tr>" + exposed_data + rows + "</table>");
-    self.dom.div.selectAll("td, th, table").style("border", "1px solid black").style("padding", "0").style("border-collapse", "collapse");
-    self.dom.div.selectAll("th, td").style("padding", "2px 10px");
-  };
-}
-var statTableInit = getCompInit(TdbStatTable);
-export {
-  statTableInit
-};
-//# sourceMappingURL=stattable-PR47XT4F.js.map

package/dist/studyCatalog-GMUWIUL4.js

@@ -1,378 +0,0 @@
-import {
-  PlotBase,
-  addGeneSearchbox,
-  renderTable
-} from "./chunk-7RX5UEF3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-L42F5J5C.js";
-import "./chunk-HKQDZKSF.js";
-import {
-  Menu
-} from "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-FUSTNOQZ.js";
-import "./chunk-VSPUFGDX.js";
-import "./chunk-WVPFLPWB.js";
-import "./chunk-S5SOLLGM.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-D6G64XPJ.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-YLJOZP4P.js";
-import "./chunk-HDTFYTEL.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// plots/studyCatalog.ts
-var PTM_PROTEOMES = /* @__PURE__ */ new Set(["Phospho", "Ubiquitin"]);
-var FACET_CHART = {
-  disease: {
-    chartType: "animatedBubbleChart",
-    label: "Bubble Chart",
-    needsGene: false,
-    requires: (q) => !!q?.geneRanking
-  },
-  cellType: {
-    chartType: "cellTypeBubbleHeatmap",
-    label: "Cell-type Bubble Heatmap",
-    needsGene: true,
-    requires: (q) => !!q?.proteome?.cellTypeBubbleHeatmap
-  },
-  brainRegion: {
-    chartType: "brainRegions",
-    label: "Brain Regional Proteome",
-    needsGene: true,
-    requires: (q) => !!q?.proteome?.brainRegions
-  }
-};
-var defaultConfig = {
-  chartType: "studyCatalog"
-};
-var PANEL_GAP = 24;
-var FACET_WIDTH = 210;
-var StudyCatalog = class _StudyCatalog extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    /** active filter values per facet key; empty set (or absent) = no filter on that facet */
-    this.activeFilters = /* @__PURE__ */ new Map();
-    /** derived rows, one per cohort */
-    this.rows = [];
-    /** currently checked rows */
-    this.selected = [];
-    /** stable keys of the checked cohorts, so selection survives a table re-render */
-    this.selectedKeys = /* @__PURE__ */ new Set();
-    /** number of cohorts currently passing the filters (shown when nothing is selected) */
-    this.filteredCount = 0;
-    this.type = _StudyCatalog.type;
-  }
-  static {
-    this.type = "studyCatalog";
-  }
-  async init() {
-    const holder = this.opts.holder.append("div").style("padding", "10px");
-    const body = holder.append("div");
-    this.dom = {
-      holder,
-      body,
-      facetsDiv: void 0,
-      rightDiv: void 0,
-      actionBtn: void 0,
-      countSpan: void 0,
-      tableDiv: void 0,
-      tip: new Menu({ padding: "" }),
-      header: this.opts.header
-    };
-    if (this.dom.header) this.dom.header.html("Studies");
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) throw `No plot with id='${this.id}' found`;
-    return { config };
-  }
-  async main() {
-    const proteome = this.app.vocabApi.termdbConfig?.queries?.proteome;
-    const ui = proteome?.studyCatalog;
-    this.dom.body.selectAll("*").remove();
-    if (!ui || !proteome?.organisms) {
-      this.dom.body.append("div").style("padding", "20px").style("color", "#666").text("No study catalog is configured.");
-      return;
-    }
-    this.rows = this.deriveRows(proteome.organisms);
-    if (!this.rows.length) {
-      this.dom.body.append("div").style("padding", "20px").style("color", "#666").text("No cohorts found.");
-      return;
-    }
-    const topBar = this.dom.body.append("div").style("display", "flex").style("align-items", "center").style("gap", "12px").style("margin-bottom", "8px").style("padding-left", `${FACET_WIDTH + PANEL_GAP}px`);
-    this.dom.actionBtn = topBar.append("button").property("disabled", true).text("Analyze Cohort").on("click", () => this.onAction());
-    this.dom.countSpan = topBar.append("span").style("font-size", "0.85em").style("color", "#555");
-    const layout = this.dom.body.append("div").style("display", "flex").style("gap", `${PANEL_GAP}px`);
-    this.dom.facetsDiv = layout.append("div").style("flex", `0 0 ${FACET_WIDTH}px`).style("box-sizing", "border-box").style("max-height", "60vh").style("overflow-y", "auto").style("border-right", "1px solid #eee").style("padding-right", "12px");
-    this.dom.rightDiv = layout.append("div").style("flex", "1 1 auto").style("min-width", "0");
-    this.dom.tableDiv = this.dom.rightDiv.append("div");
-    this.renderFacets(ui);
-    this.renderTable(ui);
-  }
-  /** one row per organism→assay→cohort. `species` and `proteome` are derived from the query
-   *  structure (organism key + the assay's proteomeLabel); every other display field comes from
-   *  the cohort's `catalog` object in the dataset. A `catalog` key can still override either. */
-  deriveRows(organisms) {
-    const rows = [];
-    for (const organism in organisms) {
-      const species = organism.charAt(0).toUpperCase() + organism.slice(1);
-      const assays = organisms[organism].assays || {};
-      for (const assay in assays) {
-        const proteome = assays[assay].proteomeLabel || assay;
-        const cohorts = assays[assay].cohorts || {};
-        for (const cohort in cohorts) {
-          rows.push({ species, proteome, ...cohorts[cohort].catalog || {}, organism, assay, cohort });
-        }
-      }
-    }
-    return rows;
-  }
-  /** rows passing every active filter, optionally excluding one facet (for that facet's own counts) */
-  filteredRows(excludeFacet) {
-    return this.rows.filter((row) => {
-      for (const [facet, values] of this.activeFilters) {
-        if (facet === excludeFacet) continue;
-        if (values.size === 0) continue;
-        if (!values.has(row[facet] || "")) return false;
-      }
-      return true;
-    });
-  }
-  facetLabel(ui, key) {
-    return ui.columns.find((c) => c.key === key)?.label || key;
-  }
-  renderFacets(ui) {
-    const div = this.dom.facetsDiv;
-    div.selectAll("*").remove();
-    const queries = this.app.vocabApi.termdbConfig?.queries;
-    const singleSelect = new Set(ui.singleSelectFacets || []);
-    for (const facet of singleSelect) {
-      if (!ui.facets.includes(facet)) continue;
-      const scope = this.filteredRows(facet);
-      const values = [...new Set(scope.map((r) => r[facet]).filter(Boolean))].sort(
-        (a, b) => a.localeCompare(b, void 0, { numeric: true })
-      );
-      if (!values.length) {
-        this.activeFilters.delete(facet);
-        continue;
-      }
-      const active = this.activeFilters.get(facet);
-      const activeValue = active && active.size === 1 ? [...active][0] : null;
-      if (activeValue && values.includes(activeValue)) continue;
-      this.activeFilters.set(facet, /* @__PURE__ */ new Set([values[0]]));
-    }
-    const header = div.append("div").style("display", "flex").style("align-items", "center").style("margin-bottom", "8px");
-    header.append("span").style("font-weight", "bold").text("Filter by");
-    const anyActive = [...this.activeFilters.entries()].some(([f, s]) => !singleSelect.has(f) && s.size > 0);
-    header.append("span").style("margin-left", "auto").style("font-size", "0.8em").style("color", anyActive ? "#0a5" : "#aaa").style("cursor", anyActive ? "pointer" : "default").text("clear all").on("click", () => {
-      if (!anyActive) return;
-      this.activeFilters.clear();
-      this.renderFacets(ui);
-      this.renderTable(ui);
-    });
-    for (const facet of ui.facets) {
-      const scope = this.filteredRows(facet);
-      const counts = /* @__PURE__ */ new Map();
-      for (const row of scope) {
-        const v = row[facet] || "";
-        if (!v) continue;
-        counts.set(v, (counts.get(v) || 0) + 1);
-      }
-      if (counts.size === 0) continue;
-      const group = div.append("div").style("margin-bottom", "12px");
-      const titleRow = group.append("div").style("display", "flex").style("align-items", "center").style("gap", "6px").style("margin-bottom", "4px");
-      titleRow.append("span").style("font-weight", "600").style("font-size", "0.9em").text(this.facetLabel(ui, facet));
-      const chart = FACET_CHART[facet];
-      if (chart && chart.requires(queries)) {
-        titleRow.append("button").attr("class", "sja_menuoption sja_sharp_border").style("font-size", "0.72em").style("padding", "1px 5px").style("cursor", "pointer").attr("title", `Open ${chart.label}`).text("\u{1F4CA}").on("click", (event) => this.openChartMenu(chart, event));
-      }
-      const single = singleSelect.has(facet);
-      const active = this.activeFilters.get(facet) || /* @__PURE__ */ new Set();
-      const values = [...counts.keys()].sort((a, b) => a.localeCompare(b, void 0, { numeric: true }));
-      for (const value of values) {
-        const line = group.append("label").style("display", "flex").style("align-items", "center").style("gap", "6px").style("font-size", "0.85em").style("cursor", "pointer").style("padding", "1px 0");
-        line.append("input").attr("type", single ? "radio" : "checkbox").attr("name", single ? `sjpp-studyCatalog-facet-${this.id}-${facet}` : null).property("checked", active.has(value)).on("change", (event) => {
-          if (single) {
-            this.activeFilters.set(facet, /* @__PURE__ */ new Set([value]));
-          } else {
-            const set = this.activeFilters.get(facet) || /* @__PURE__ */ new Set();
-            if (event.target.checked) set.add(value);
-            else set.delete(value);
-            if (set.size) this.activeFilters.set(facet, set);
-            else this.activeFilters.delete(facet);
-          }
-          this.renderFacets(ui);
-          this.renderTable(ui);
-        });
-        line.append("span").style("flex", "1 1 auto").text(value);
-        line.append("span").style("color", "#999").text(counts.get(value));
-      }
-    }
-  }
-  renderTable(ui) {
-    const rows = this.filteredRows();
-    this.filteredCount = rows.length;
-    this.dom.tableDiv.selectAll("*").remove();
-    this.dom.tableDiv.style("font-size", "13px");
-    const selectedRows = [];
-    rows.forEach((r, i) => {
-      if (this.selectedKeys.has(this.cohortKey(r))) selectedRows.push(i);
-    });
-    this.selected = selectedRows.map((i) => rows[i]);
-    this.selectedKeys = new Set(this.selected.map((r) => this.cohortKey(r)));
-    this.updateActionBtn();
-    const columns = ui.columns.map((c) => ({ label: c.label, sortable: true }));
-    const tableRows = rows.map(
-      (row) => ui.columns.map((c) => {
-        const value = row[c.key] ?? "";
-        return c.urlBase && value ? { value, url: c.urlBase + value } : { value };
-      })
-    );
-    renderTable({
-      columns,
-      rows: tableRows,
-      div: this.dom.tableDiv,
-      showLines: true,
-      striped: true,
-      maxHeight: "60vh",
-      maxWidth: "72vw",
-      resize: true,
-      selectedRows,
-      header: { allowSort: true, style: { "font-weight": "bold", color: "#000" } },
-      buttons: [
-        {
-          text: "select",
-          callback: () => {
-          },
-          onChange: (idxs, button) => {
-            button.style.display = "none";
-            let sel = idxs.map((i) => rows[i]);
-            if (sel.length > 1) {
-              const cls = this.proteomeClass(sel[0]);
-              const offIdx = new Set(idxs.filter((i) => this.proteomeClass(rows[i]) !== cls));
-              if (offIdx.size) {
-                sel = idxs.filter((i) => !offIdx.has(i)).map((i) => rows[i]);
-                const nodes = this.dom.tableDiv.selectAll('tbody input[type="checkbox"]').nodes();
-                for (const node of nodes) if (offIdx.has(Number(node.getAttribute("value")))) node.checked = false;
-              }
-            }
-            this.selected = sel;
-            this.selectedKeys = new Set(sel.map((r) => this.cohortKey(r)));
-            this.updateActionBtn();
-            this.applyClassLock(rows);
-          }
-        }
-      ]
-    });
-  }
-  /** stable identity of a cohort row, used to keep the selection across re-renders */
-  cohortKey(row) {
-    return `${row.organism}|${row.assay}|${row.cohort}`;
-  }
-  /** PTM (site-level) vs non-PTM (protein-level) class of a cohort row */
-  proteomeClass(row) {
-    return PTM_PROTEOMES.has(row.proteome) ? "ptm" : "nonptm";
-  }
-  /** PTM/non-PTM lock: once a cohort is selected, disable + dim checkboxes
-   *  for cohorts of the OTHER class. */
-  applyClassLock(rows) {
-    const locked = this.selected.length ? this.proteomeClass(this.selected[0]) : null;
-    const nodes = this.dom.tableDiv.selectAll('tbody input[type="checkbox"]').nodes();
-    for (const input of nodes) {
-      const vAttr = input.getAttribute("value");
-      if (vAttr === null) continue;
-      const idx = Number(vAttr);
-      if (!Number.isInteger(idx) || idx < 0 || idx >= rows.length) continue;
-      const disable = locked !== null && !input.checked && this.proteomeClass(rows[idx]) !== locked;
-      input.disabled = disable;
-      const tr = input.closest("tr");
-      if (tr) tr.style.opacity = disable ? "0.4" : "";
-    }
-  }
-  /** update the action button + count text from the current selection.
-   *  count: nothing selected → total filtered cohorts; 1 selected → hidden; ≥2 → selected count */
-  updateActionBtn() {
-    const btn = this.dom.actionBtn;
-    if (!btn) return;
-    const n = this.selected.length;
-    btn.property("disabled", n === 0).text(n >= 2 ? "Compare cohorts" : "Analyze Cohort");
-    const cs = this.dom.countSpan;
-    if (n === 1) cs.style("display", "none");
-    else if (n >= 2) cs.style("display", "").text(`${n} cohorts`);
-    else cs.style("display", "").text(`${this.filteredCount} cohort${this.filteredCount === 1 ? "" : "s"}`);
-  }
-  /** run the action for the current selection: 1 cohort → Analyze; ≥2 → Compare */
-  onAction() {
-    const sel = this.selected;
-    if (sel.length === 1) this.openAnalyticsTools(sel[0]);
-    else if (sel.length >= 2) this.openCompare(sel);
-  }
-  /** launch a facet's chart. Charts that don't need a gene open directly; gene-centric ones
-   *  prompt for a gene first. Dispatches exactly chart.chartType (no importPlot indirection). */
-  openChartMenu(chart, event) {
-    if (!chart.needsGene) {
-      this.app.dispatch({ type: "plot_create", config: { chartType: chart.chartType } });
-      return;
-    }
-    this.dom.tip.clear().show(event.clientX, event.clientY);
-    const row = this.dom.tip.d.append("div").style("padding", "5px");
-    row.append("span").style("font-weight", "bold").text("Enter a gene name:");
-    const geneSearch = addGeneSearchbox({
-      row,
-      genome: this.app.opts.genome,
-      tip: new Menu({ padding: "0px" }),
-      searchOnly: "gene",
-      callback: () => {
-        if (!geneSearch.geneSymbol) throw new Error("A valid gene selection is required");
-        this.dom.tip.hide();
-        this.app.dispatch({ type: "plot_create", config: { chartType: chart.chartType, gene: geneSearch.geneSymbol } });
-      }
-    });
-  }
-  /** open the ProteomeInput "Analytics Tools" panel for a cohort, mirroring the
-   *  Sample Selection (proteomeAbundance) chart's "Analytics Tools" button */
-  openAnalyticsTools(row) {
-    this.app.dispatch({
-      type: "plot_create",
-      config: {
-        chartType: "ProteomeInput",
-        proteomeDetails: { organism: row.organism, assay: row.assay, cohort: row.cohort },
-        hidePlotFilter: true
-      }
-    });
-  }
-  /** open the cross-cohort log2FC-z comparison for the selected cohorts */
-  openCompare(selected) {
-    this.app.dispatch({
-      type: "plot_create",
-      config: {
-        chartType: "proteomeCohortCompare",
-        cohorts: selected.map((r) => ({ organism: r.organism, assay: r.assay, cohort: r.cohort, label: r.cohort }))
-      }
-    });
-  }
-};
-var componentInit = getCompInit(StudyCatalog);
-async function getPlotConfig(opts) {
-  const config = structuredClone(defaultConfig);
-  return copyMerge(config, opts);
-}
-export {
-  componentInit,
-  getPlotConfig
-};
-//# sourceMappingURL=studyCatalog-GMUWIUL4.js.map

package/dist/studyCatalog-GMUWIUL4.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/studyCatalog.ts"],
-  "sourcesContent": ["import type { MassState, BasePlotConfig } from '#mass/types/mass'\nimport { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport { PlotBase } from './PlotBase'\nimport { Menu, renderTable, addGeneSearchbox } from '#dom'\nimport type { TableColumn, TableRow } from '#dom'\n\n/** PTM proteome layers \u2014 kept separate from protein-level (Whole/Insoluble) layers because\n *  PTM z is site-level collapsed to gene, so the two aren't directly comparable in a scatter/heatmap */\nconst PTM_PROTEOMES = new Set(['Phospho', 'Ubiquitin'])\n\n/** facets that get a \"launch chart\" button. needsGene=false charts launch directly (no gene\n *  picker); gene-centric charts prompt for a gene first. `requires(queries)` gates the button on\n *  the dataset config that chart needs, so it only shows where the chart can actually run. */\nconst FACET_CHART: Record<\n\tstring,\n\t{ chartType: string; label: string; needsGene: boolean; requires: (q: any) => boolean }\n> = {\n\tdisease: {\n\t\tchartType: 'animatedBubbleChart',\n\t\tlabel: 'Bubble Chart',\n\t\tneedsGene: false,\n\t\trequires: q => !!q?.geneRanking\n\t},\n\tcellType: {\n\t\tchartType: 'cellTypeBubbleHeatmap',\n\t\tlabel: 'Cell-type Bubble Heatmap',\n\t\tneedsGene: true,\n\t\trequires: q => !!q?.proteome?.cellTypeBubbleHeatmap\n\t},\n\tbrainRegion: {\n\t\tchartType: 'brainRegions',\n\t\tlabel: 'Brain Regional Proteome',\n\t\tneedsGene: true,\n\t\trequires: q => !!q?.proteome?.brainRegions\n\t}\n}\n\nconst defaultConfig = {\n\tchartType: 'studyCatalog'\n}\n\n/** urlBase renders the cell as a link to urlBase+value (e.g. a PubMed ID column) */\ntype CatalogColumn = { key: string; label: string; urlBase?: string }\ntype CatalogUiConfig = {\n\tcolumns: CatalogColumn[]\n\tfacets: string[]\n\t/** facets rendered as radio buttons instead of checkboxes: exactly one value is active at\n\t *  all times (defaults to the first value), so rows of different values never mix in the table */\n\tsingleSelectFacets?: string[]\n}\ntype CatalogRow = { [key: string]: string } & { organism: string; assay: string; cohort: string }\n\nconst PANEL_GAP = 24\nconst FACET_WIDTH = 210\n\nclass StudyCatalog extends PlotBase implements RxComponent {\n\tstatic type = 'studyCatalog'\n\ttype: string\n\tdom!: {\n\t\tholder: any\n\t\tbody: any\n\t\tfacetsDiv: any\n\t\trightDiv: any\n\t\tactionBtn: any\n\t\tcountSpan: any\n\t\ttableDiv: any\n\t\ttip: Menu\n\t\theader?: any\n\t}\n\t/** active filter values per facet key; empty set (or absent) = no filter on that facet */\n\tactiveFilters: Map<string, Set<string>> = new Map()\n\t/** derived rows, one per cohort */\n\trows: CatalogRow[] = []\n\t/** currently checked rows */\n\tselected: CatalogRow[] = []\n\t/** stable keys of the checked cohorts, so selection survives a table re-render */\n\tselectedKeys: Set<string> = new Set()\n\t/** number of cohorts currently passing the filters (shown when nothing is selected) */\n\tfilteredCount = 0\n\n\tconstructor(opts: any, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = StudyCatalog.type\n\t}\n\n\tasync init() {\n\t\tconst holder = this.opts.holder.append('div').style('padding', '10px')\n\t\tconst body = holder.append('div')\n\t\tthis.dom = {\n\t\t\tholder,\n\t\t\tbody,\n\t\t\tfacetsDiv: undefined,\n\t\t\trightDiv: undefined,\n\t\t\tactionBtn: undefined,\n\t\t\tcountSpan: undefined,\n\t\t\ttableDiv: undefined,\n\t\t\ttip: new Menu({ padding: '' }),\n\t\t\theader: this.opts.header\n\t\t}\n\t\tif (this.dom.header) this.dom.header.html('Studies')\n\t}\n\n\tgetState(appState: MassState) {\n\t\tconst config: any = appState.plots.find((p: BasePlotConfig) => p.id === this.id)\n\t\tif (!config) throw `No plot with id='${this.id}' found`\n\t\treturn { config }\n\t}\n\n\tasync main() {\n\t\tconst proteome = this.app.vocabApi.termdbConfig?.queries?.proteome\n\t\tconst ui: CatalogUiConfig | undefined = proteome?.studyCatalog\n\t\tthis.dom.body.selectAll('*').remove()\n\t\tif (!ui || !proteome?.organisms) {\n\t\t\tthis.dom.body\n\t\t\t\t.append('div')\n\t\t\t\t.style('padding', '20px')\n\t\t\t\t.style('color', '#666')\n\t\t\t\t.text('No study catalog is configured.')\n\t\t\treturn\n\t\t}\n\n\t\tthis.rows = this.deriveRows(proteome.organisms)\n\t\tif (!this.rows.length) {\n\t\t\tthis.dom.body.append('div').style('padding', '20px').style('color', '#666').text('No cohorts found.')\n\t\t\treturn\n\t\t}\n\n\t\t// top bar (above facets + table): action button + count, indented so they line up with\n\t\t// the table's left edge (its line-number column), not with the filter rail\n\t\tconst topBar = this.dom.body\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('gap', '12px')\n\t\t\t.style('margin-bottom', '8px')\n\t\t\t.style('padding-left', `${FACET_WIDTH + PANEL_GAP}px`)\n\t\tthis.dom.actionBtn = topBar\n\t\t\t.append('button')\n\t\t\t.property('disabled', true)\n\t\t\t.text('Analyze Cohort')\n\t\t\t.on('click', () => this.onAction())\n\t\tthis.dom.countSpan = topBar.append('span').style('font-size', '0.85em').style('color', '#555')\n\n\t\tconst layout = this.dom.body.append('div').style('display', 'flex').style('gap', `${PANEL_GAP}px`)\n\n\t\t// left rail \u2014 filters; border-box so its total width is exactly FACET_WIDTH (keeps the\n\t\t// button/table alignment above), capped to the table's height so the two line up\n\t\tthis.dom.facetsDiv = layout\n\t\t\t.append('div')\n\t\t\t.style('flex', `0 0 ${FACET_WIDTH}px`)\n\t\t\t.style('box-sizing', 'border-box')\n\t\t\t.style('max-height', '60vh')\n\t\t\t.style('overflow-y', 'auto')\n\t\t\t.style('border-right', '1px solid #eee')\n\t\t\t.style('padding-right', '12px')\n\n\t\t// right \u2014 table\n\t\tthis.dom.rightDiv = layout.append('div').style('flex', '1 1 auto').style('min-width', '0')\n\t\tthis.dom.tableDiv = this.dom.rightDiv.append('div')\n\n\t\tthis.renderFacets(ui)\n\t\tthis.renderTable(ui)\n\t}\n\n\t/** one row per organism\u2192assay\u2192cohort. `species` and `proteome` are derived from the query\n\t *  structure (organism key + the assay's proteomeLabel); every other display field comes from\n\t *  the cohort's `catalog` object in the dataset. A `catalog` key can still override either. */\n\tderiveRows(organisms: any): CatalogRow[] {\n\t\tconst rows: CatalogRow[] = []\n\t\tfor (const organism in organisms) {\n\t\t\tconst species = organism.charAt(0).toUpperCase() + organism.slice(1)\n\t\t\tconst assays = organisms[organism].assays || {}\n\t\t\tfor (const assay in assays) {\n\t\t\t\tconst proteome = assays[assay].proteomeLabel || assay\n\t\t\t\tconst cohorts = assays[assay].cohorts || {}\n\t\t\t\tfor (const cohort in cohorts) {\n\t\t\t\t\t// species/proteome first so catalog may override them; identity keys last so it can't\n\t\t\t\t\trows.push({ species, proteome, ...(cohorts[cohort].catalog || {}), organism, assay, cohort } as CatalogRow)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\treturn rows\n\t}\n\n\t/** rows passing every active filter, optionally excluding one facet (for that facet's own counts) */\n\tfilteredRows(excludeFacet?: string): CatalogRow[] {\n\t\treturn this.rows.filter(row => {\n\t\t\tfor (const [facet, values] of this.activeFilters) {\n\t\t\t\tif (facet === excludeFacet) continue\n\t\t\t\tif (values.size === 0) continue\n\t\t\t\tif (!values.has(row[facet] || '')) return false\n\t\t\t}\n\t\t\treturn true\n\t\t})\n\t}\n\n\tfacetLabel(ui: CatalogUiConfig, key: string): string {\n\t\treturn ui.columns.find(c => c.key === key)?.label || key\n\t}\n\n\trenderFacets(ui: CatalogUiConfig) {\n\t\tconst div = this.dom.facetsDiv\n\t\tdiv.selectAll('*').remove()\n\n\t\t// dataset query config, used to gate each facet's chart button on what the chart needs\n\t\tconst queries = this.app.vocabApi.termdbConfig?.queries\n\n\t\t// single-select facets always have exactly one active value; default to the first available value\n\t\t// under the other active filters (also reapplied after \"clear all\"), so the table never mixes e.g. species\n\t\tconst singleSelect = new Set(ui.singleSelectFacets || [])\n\t\tfor (const facet of singleSelect) {\n\t\t\tif (!ui.facets.includes(facet)) continue\n\t\t\t// available values given the other active filters (exclude this facet itself)\n\t\t\tconst scope = this.filteredRows(facet)\n\t\t\tconst values = [...new Set(scope.map(r => r[facet]).filter(Boolean))].sort((a, b) =>\n\t\t\t\ta.localeCompare(b, undefined, { numeric: true })\n\t\t\t)\n\t\t\tif (!values.length) {\n\t\t\t\tthis.activeFilters.delete(facet)\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tconst active = this.activeFilters.get(facet)\n\t\t\tconst activeValue = active && active.size === 1 ? [...active][0] : null\n\t\t\tif (activeValue && values.includes(activeValue)) continue\n\t\t\tthis.activeFilters.set(facet, new Set([values[0]]))\n\t\t}\n\n\t\tconst header = div\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('margin-bottom', '8px')\n\t\theader.append('span').style('font-weight', 'bold').text('Filter by')\n\t\t// single-select facets are always active by design, so they don't count towards \"clear all\"\n\t\tconst anyActive = [...this.activeFilters.entries()].some(([f, s]) => !singleSelect.has(f) && s.size > 0)\n\t\theader\n\t\t\t.append('span')\n\t\t\t.style('margin-left', 'auto')\n\t\t\t.style('font-size', '0.8em')\n\t\t\t.style('color', anyActive ? '#0a5' : '#aaa')\n\t\t\t.style('cursor', anyActive ? 'pointer' : 'default')\n\t\t\t.text('clear all')\n\t\t\t.on('click', () => {\n\t\t\t\tif (!anyActive) return\n\t\t\t\tthis.activeFilters.clear()\n\t\t\t\tthis.renderFacets(ui)\n\t\t\t\tthis.renderTable(ui)\n\t\t\t})\n\n\t\tfor (const facet of ui.facets) {\n\t\t\t// counts reflect all OTHER active filters (standard faceted behavior)\n\t\t\tconst scope = this.filteredRows(facet)\n\t\t\tconst counts = new Map<string, number>()\n\t\t\tfor (const row of scope) {\n\t\t\t\tconst v = row[facet] || ''\n\t\t\t\tif (!v) continue\n\t\t\t\tcounts.set(v, (counts.get(v) || 0) + 1)\n\t\t\t}\n\t\t\tif (counts.size === 0) continue\n\n\t\t\tconst group = div.append('div').style('margin-bottom', '12px')\n\t\t\tconst titleRow = group\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'flex')\n\t\t\t\t.style('align-items', 'center')\n\t\t\t\t.style('gap', '6px')\n\t\t\t\t.style('margin-bottom', '4px')\n\t\t\ttitleRow.append('span').style('font-weight', '600').style('font-size', '0.9em').text(this.facetLabel(ui, facet))\n\t\t\t// some facets get a button that launches a related chart \u2014 only if the dataset supports it\n\t\t\tconst chart = FACET_CHART[facet]\n\t\t\tif (chart && chart.requires(queries)) {\n\t\t\t\ttitleRow\n\t\t\t\t\t.append('button')\n\t\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t\t.style('font-size', '0.72em')\n\t\t\t\t\t.style('padding', '1px 5px')\n\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t\t.attr('title', `Open ${chart.label}`)\n\t\t\t\t\t.text('\uD83D\uDCCA')\n\t\t\t\t\t.on('click', (event: any) => this.openChartMenu(chart, event))\n\t\t\t}\n\n\t\t\tconst single = singleSelect.has(facet)\n\t\t\tconst active = this.activeFilters.get(facet) || new Set<string>()\n\t\t\tconst values = [...counts.keys()].sort((a, b) => a.localeCompare(b, undefined, { numeric: true }))\n\t\t\tfor (const value of values) {\n\t\t\t\tconst line = group\n\t\t\t\t\t.append('label')\n\t\t\t\t\t.style('display', 'flex')\n\t\t\t\t\t.style('align-items', 'center')\n\t\t\t\t\t.style('gap', '6px')\n\t\t\t\t\t.style('font-size', '0.85em')\n\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t\t.style('padding', '1px 0')\n\t\t\t\tline\n\t\t\t\t\t.append('input')\n\t\t\t\t\t.attr('type', single ? 'radio' : 'checkbox')\n\t\t\t\t\t.attr('name', single ? `sjpp-studyCatalog-facet-${this.id}-${facet}` : null)\n\t\t\t\t\t.property('checked', active.has(value))\n\t\t\t\t\t.on('change', (event: any) => {\n\t\t\t\t\t\tif (single) {\n\t\t\t\t\t\t\t// radio: picking a value replaces the facet's single active value\n\t\t\t\t\t\t\tthis.activeFilters.set(facet, new Set([value]))\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tconst set = this.activeFilters.get(facet) || new Set<string>()\n\t\t\t\t\t\t\tif (event.target.checked) set.add(value)\n\t\t\t\t\t\t\telse set.delete(value)\n\t\t\t\t\t\t\tif (set.size) this.activeFilters.set(facet, set)\n\t\t\t\t\t\t\telse this.activeFilters.delete(facet)\n\t\t\t\t\t\t}\n\t\t\t\t\t\tthis.renderFacets(ui)\n\t\t\t\t\t\tthis.renderTable(ui)\n\t\t\t\t\t})\n\t\t\t\tline.append('span').style('flex', '1 1 auto').text(value)\n\t\t\t\tline.append('span').style('color', '#999').text(counts.get(value)!)\n\t\t\t}\n\t\t}\n\t}\n\n\trenderTable(ui: CatalogUiConfig) {\n\t\tconst rows = this.filteredRows()\n\t\tthis.filteredCount = rows.length\n\t\tthis.dom.tableDiv.selectAll('*').remove()\n\t\tthis.dom.tableDiv.style('font-size', '13px')\n\n\t\t// preserve selection across re-renders (rx main() rebuilds the table): preselect the\n\t\t// still-visible rows whose cohort is selected, and prune keys that got filtered out\n\t\tconst selectedRows: number[] = []\n\t\trows.forEach((r, i) => {\n\t\t\tif (this.selectedKeys.has(this.cohortKey(r))) selectedRows.push(i)\n\t\t})\n\t\tthis.selected = selectedRows.map(i => rows[i])\n\t\tthis.selectedKeys = new Set(this.selected.map(r => this.cohortKey(r)))\n\t\tthis.updateActionBtn()\n\n\t\tconst columns: TableColumn[] = ui.columns.map(c => ({ label: c.label, sortable: true }))\n\t\tconst tableRows: TableRow[] = rows.map(\n\t\t\trow =>\n\t\t\t\tui.columns.map(c => {\n\t\t\t\t\tconst value = row[c.key] ?? ''\n\t\t\t\t\treturn c.urlBase && value ? { value, url: c.urlBase + value } : { value }\n\t\t\t\t}) as TableRow\n\t\t)\n\n\t\trenderTable({\n\t\t\tcolumns,\n\t\t\trows: tableRows,\n\t\t\tdiv: this.dom.tableDiv,\n\t\t\tshowLines: true,\n\t\t\tstriped: true,\n\t\t\tmaxHeight: '60vh',\n\t\t\tmaxWidth: '72vw',\n\t\t\tresize: true,\n\t\t\tselectedRows,\n\t\t\theader: { allowSort: true, style: { 'font-weight': 'bold', color: '#000' } },\n\t\t\tbuttons: [\n\t\t\t\t{\n\t\t\t\t\ttext: 'select',\n\t\t\t\t\tcallback: () => {},\n\t\t\t\t\tonChange: (idxs: number[], button: any) => {\n\t\t\t\t\t\tbutton.style.display = 'none'\n\t\t\t\t\t\tlet sel = idxs.map(i => rows[i])\n\t\t\t\t\t\tif (sel.length > 1) {\n\t\t\t\t\t\t\tconst cls = this.proteomeClass(sel[0])\n\t\t\t\t\t\t\tconst offIdx = new Set(idxs.filter(i => this.proteomeClass(rows[i]) !== cls))\n\t\t\t\t\t\t\tif (offIdx.size) {\n\t\t\t\t\t\t\t\tsel = idxs.filter(i => !offIdx.has(i)).map(i => rows[i])\n\t\t\t\t\t\t\t\tconst nodes = this.dom.tableDiv.selectAll('tbody input[type=\"checkbox\"]').nodes() as HTMLInputElement[]\n\t\t\t\t\t\t\t\tfor (const node of nodes) if (offIdx.has(Number(node.getAttribute('value')))) node.checked = false\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tthis.selected = sel\n\t\t\t\t\t\tthis.selectedKeys = new Set(sel.map(r => this.cohortKey(r)))\n\t\t\t\t\t\tthis.updateActionBtn()\n\t\t\t\t\t\tthis.applyClassLock(rows)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t})\n\t}\n\n\t/** stable identity of a cohort row, used to keep the selection across re-renders */\n\tcohortKey(row: CatalogRow): string {\n\t\treturn `${row.organism}|${row.assay}|${row.cohort}`\n\t}\n\n\t/** PTM (site-level) vs non-PTM (protein-level) class of a cohort row */\n\tproteomeClass(row: CatalogRow): 'ptm' | 'nonptm' {\n\t\treturn PTM_PROTEOMES.has(row.proteome) ? 'ptm' : 'nonptm'\n\t}\n\n\t/** PTM/non-PTM lock: once a cohort is selected, disable + dim checkboxes\n\t *  for cohorts of the OTHER class. */\n\tapplyClassLock(rows: CatalogRow[]) {\n\t\tconst locked = this.selected.length ? this.proteomeClass(this.selected[0]) : null\n\t\tconst nodes = this.dom.tableDiv.selectAll('tbody input[type=\"checkbox\"]').nodes() as HTMLInputElement[]\n\t\tfor (const input of nodes) {\n\t\t\tconst vAttr = input.getAttribute('value')\n\t\t\tif (vAttr === null) continue\n\t\t\tconst idx = Number(vAttr)\n\t\t\tif (!Number.isInteger(idx) || idx < 0 || idx >= rows.length) continue\n\t\t\tconst disable = locked !== null && !input.checked && this.proteomeClass(rows[idx]) !== locked\n\t\t\tinput.disabled = disable\n\t\t\tconst tr = input.closest('tr') as HTMLElement | null\n\t\t\tif (tr) tr.style.opacity = disable ? '0.4' : ''\n\t\t}\n\t}\n\n\t/** update the action button + count text from the current selection.\n\t *  count: nothing selected \u2192 total filtered cohorts; 1 selected \u2192 hidden; \u22652 \u2192 selected count */\n\tupdateActionBtn() {\n\t\tconst btn = this.dom.actionBtn\n\t\tif (!btn) return\n\t\tconst n = this.selected.length\n\t\tbtn.property('disabled', n === 0).text(n >= 2 ? 'Compare cohorts' : 'Analyze Cohort')\n\t\tconst cs = this.dom.countSpan\n\t\tif (n === 1) cs.style('display', 'none')\n\t\telse if (n >= 2) cs.style('display', '').text(`${n} cohorts`)\n\t\telse cs.style('display', '').text(`${this.filteredCount} cohort${this.filteredCount === 1 ? '' : 's'}`)\n\t}\n\n\t/** run the action for the current selection: 1 cohort \u2192 Analyze; \u22652 \u2192 Compare */\n\tonAction() {\n\t\tconst sel = this.selected\n\t\tif (sel.length === 1) this.openAnalyticsTools(sel[0])\n\t\telse if (sel.length >= 2) this.openCompare(sel)\n\t}\n\n\t/** launch a facet's chart. Charts that don't need a gene open directly; gene-centric ones\n\t *  prompt for a gene first. Dispatches exactly chart.chartType (no importPlot indirection). */\n\topenChartMenu(chart: { chartType: string; needsGene: boolean }, event: any) {\n\t\tif (!chart.needsGene) {\n\t\t\tthis.app.dispatch({ type: 'plot_create', config: { chartType: chart.chartType } })\n\t\t\treturn\n\t\t}\n\t\tthis.dom.tip.clear().show(event.clientX, event.clientY)\n\t\tconst row = this.dom.tip.d.append('div').style('padding', '5px')\n\t\trow.append('span').style('font-weight', 'bold').text('Enter a gene name:')\n\t\tconst geneSearch = addGeneSearchbox({\n\t\t\trow,\n\t\t\tgenome: this.app.opts.genome,\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tsearchOnly: 'gene',\n\t\t\tcallback: () => {\n\t\t\t\tif (!geneSearch.geneSymbol) throw new Error('A valid gene selection is required')\n\t\t\t\tthis.dom.tip.hide()\n\t\t\t\tthis.app.dispatch({ type: 'plot_create', config: { chartType: chart.chartType, gene: geneSearch.geneSymbol } })\n\t\t\t}\n\t\t})\n\t}\n\n\t/** open the ProteomeInput \"Analytics Tools\" panel for a cohort, mirroring the\n\t *  Sample Selection (proteomeAbundance) chart's \"Analytics Tools\" button */\n\topenAnalyticsTools(row: CatalogRow) {\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_create',\n\t\t\tconfig: {\n\t\t\t\tchartType: 'ProteomeInput',\n\t\t\t\tproteomeDetails: { organism: row.organism, assay: row.assay, cohort: row.cohort },\n\t\t\t\thidePlotFilter: true\n\t\t\t}\n\t\t})\n\t}\n\n\t/** open the cross-cohort log2FC-z comparison for the selected cohorts */\n\topenCompare(selected: CatalogRow[]) {\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_create',\n\t\t\tconfig: {\n\t\t\t\tchartType: 'proteomeCohortCompare',\n\t\t\t\tcohorts: selected.map(r => ({ organism: r.organism, assay: r.assay, cohort: r.cohort, label: r.cohort }))\n\t\t\t}\n\t\t})\n\t}\n}\n\nexport const componentInit = getCompInit(StudyCatalog)\n\nexport async function getPlotConfig(opts: any) {\n\tconst config = structuredClone(defaultConfig)\n\treturn copyMerge(config, opts)\n}\n"],
-  "mappings": 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