@sjcrh/proteinpaint-client 2.206.0 → 2.207.0

package/dist/stattable-JCH2WPS6.js

@@ -0,0 +1,117 @@
+import {
+  PlotBase
+} from "./chunk-NQDF3U2C.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-CCYVGZGI.js";
+import "./chunk-ELJX3QIQ.js";
+import "./chunk-N7DVQTPC.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import "./chunk-GRVO7RW4.js";
+import "./chunk-7CJKL3LK.js";
+import "./chunk-HZ3TCGBK.js";
+import "./chunk-IZUYLFOX.js";
+import {
+  getCompInit
+} from "./chunk-WINIL2KN.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-7X6NF7NI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-Z2ZITHT4.js";
+import "./chunk-4OLM3KSB.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-JCH2WPS6.js.map

package/dist/studyCatalog-FDB7D26M.js

@@ -0,0 +1,414 @@
+import {
+  orderBy
+} from "./chunk-VRINIB6B.js";
+import "./chunk-ILEXRHF7.js";
+import {
+  PlotBase,
+  addGeneSearchbox,
+  renderTable
+} from "./chunk-NQDF3U2C.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-CCYVGZGI.js";
+import {
+  Menu
+} from "./chunk-ELJX3QIQ.js";
+import "./chunk-N7DVQTPC.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import "./chunk-GRVO7RW4.js";
+import "./chunk-7CJKL3LK.js";
+import "./chunk-HZ3TCGBK.js";
+import "./chunk-IZUYLFOX.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-WINIL2KN.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-7X6NF7NI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-Z2ZITHT4.js";
+import "./chunk-4OLM3KSB.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 DATA_TYPE_FACET = "dataType";
+var DATA_TYPE_CHILD = "proteome";
+var DATA_TYPE_LABEL = "Data type";
+var DATA_TYPE_ORDER = ["Protein", "PTM"];
+function proteomeOrder(organisms) {
+  const out = [];
+  for (const org of Object.values(organisms || {})) {
+    for (const assay in org?.assays || {}) {
+      const label = org.assays[assay].proteomeLabel || assay;
+      if (!out.includes(label)) out.push(label);
+    }
+  }
+  return out;
+}
+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) {
+          const dataType = assays[assay].PTMType ? "PTM" : "Protein";
+          rows.push({
+            species,
+            proteome,
+            dataType,
+            ...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) {
+    const excluded = new Set(Array.isArray(excludeFacet) ? excludeFacet : excludeFacet ? [excludeFacet] : []);
+    return this.rows.filter((row) => {
+      for (const [facet, values] of this.activeFilters) {
+        if (excluded.has(facet)) continue;
+        if (values.size === 0) continue;
+        if (!values.has(row[facet] || "")) return false;
+      }
+      return true;
+    });
+  }
+  facetLabel(ui, key) {
+    if (key === DATA_TYPE_FACET) return DATA_TYPE_LABEL;
+    return ui.columns.find((c) => c.key === key)?.label || key;
+  }
+  /** facet order to render: the proteome facet is replaced by its Data type parent,
+   *  which renders the proteome values nested under the active radio option */
+  effectiveFacets(ui) {
+    return ui.facets.map((f) => f === DATA_TYPE_CHILD ? DATA_TYPE_FACET : f);
+  }
+  sortValues(facet, values) {
+    const fixed = facet === DATA_TYPE_FACET ? DATA_TYPE_ORDER : facet === DATA_TYPE_CHILD ? proteomeOrder(this.app.vocabApi.termdbConfig?.queries?.proteome?.organisms) : null;
+    if (fixed)
+      return orderBy(
+        [...values].sort((a, b) => a.localeCompare(b)),
+        fixed
+      );
+    return [...values].sort((a, b) => a.localeCompare(b, void 0, { numeric: true }));
+  }
+  /** filters to ignore when computing a facet's own value counts: itself, plus — for the
+   *  Data type parent — its nested proteome filter, so that ticking e.g. "Insoluble" under
+   *  Protein never makes the PTM option disappear (it must stay clickable to switch class) */
+  facetScopeExclusions(facet) {
+    return facet === DATA_TYPE_FACET ? [DATA_TYPE_FACET, DATA_TYPE_CHILD] : [facet];
+  }
+  /** counts of one facet's values under all OTHER active filters (standard faceted behavior) */
+  facetCounts(facet) {
+    const counts = /* @__PURE__ */ new Map();
+    for (const row of this.filteredRows(this.facetScopeExclusions(facet))) {
+      const v = row[facet] || "";
+      if (!v) continue;
+      counts.set(v, (counts.get(v) || 0) + 1);
+    }
+    return counts;
+  }
+  /** one radio/checkbox line of a facet */
+  appendFacetOption(ui, group, facet, value, count, single, checked, indentPx = 0) {
+    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").style("margin-left", indentPx ? `${indentPx}px` : null);
+    line.append("input").attr("type", single ? "radio" : "checkbox").attr("name", single ? `sjpp-studyCatalog-facet-${this.id}-${facet}` : null).property("checked", checked).on("change", (event) => {
+      if (single) {
+        this.activeFilters.set(facet, /* @__PURE__ */ new Set([value]));
+        if (facet === DATA_TYPE_FACET) this.activeFilters.delete(DATA_TYPE_CHILD);
+      } 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(count);
+  }
+  renderFacets(ui) {
+    const div = this.dom.facetsDiv;
+    div.selectAll("*").remove();
+    const queries = this.app.vocabApi.termdbConfig?.queries;
+    const facets = this.effectiveFacets(ui);
+    const singleSelect = new Set(ui.singleSelectFacets || []);
+    if (facets.includes(DATA_TYPE_FACET)) singleSelect.add(DATA_TYPE_FACET);
+    for (const facet of singleSelect) {
+      if (!facets.includes(facet)) continue;
+      const scope = this.filteredRows(this.facetScopeExclusions(facet));
+      const values = this.sortValues(facet, [...new Set(scope.map((r) => r[facet]).filter(Boolean))]);
+      if (!values.length) {
+        this.activeFilters.delete(facet);
+        if (facet === DATA_TYPE_FACET) this.activeFilters.delete(DATA_TYPE_CHILD);
+        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]]));
+      if (facet === DATA_TYPE_FACET) this.activeFilters.delete(DATA_TYPE_CHILD);
+    }
+    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 facets) {
+      const counts = this.facetCounts(facet);
+      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();
+      for (const value of this.sortValues(facet, [...counts.keys()])) {
+        this.appendFacetOption(ui, group, facet, value, counts.get(value), single, active.has(value));
+        if (facet === DATA_TYPE_FACET && active.has(value)) {
+          const childCounts = this.facetCounts(DATA_TYPE_CHILD);
+          const childActive = this.activeFilters.get(DATA_TYPE_CHILD) || /* @__PURE__ */ new Set();
+          for (const cv of this.sortValues(DATA_TYPE_CHILD, [...childCounts.keys()])) {
+            this.appendFacetOption(ui, group, DATA_TYPE_CHILD, cv, childCounts.get(cv), false, childActive.has(cv), 22);
+          }
+        }
+      }
+    }
+  }
+  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 singleSelect = new Set(ui.singleSelectFacets || []);
+    const visibleColumns = rows.length ? ui.columns.filter((c) => !singleSelect.has(c.key) && rows.some((row) => row[c.key] != null && row[c.key] !== "")) : ui.columns;
+    const columns = visibleColumns.map((c) => ({ label: c.label, sortable: true }));
+    const tableRows = rows.map(
+      (row) => visibleColumns.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";
+            this.selected = idxs.map((i) => rows[i]);
+            this.selectedKeys = new Set(this.selected.map((r) => this.cohortKey(r)));
+            this.updateActionBtn();
+          }
+        }
+      ]
+    });
+  }
+  /** stable identity of a cohort row, used to keep the selection across re-renders */
+  cohortKey(row) {
+    return `${row.organism}|${row.assay}|${row.cohort}`;
+  }
+  /** 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-FDB7D26M.js.map

package/dist/summarizeCnvGeneexp-KNW23YAI.js

@@ -0,0 +1,158 @@
+import {
+  launchPlot
+} from "./chunk-VZKDGKCP.js";
+import {
+  addGeneSearchbox,
+  fillTermWrapper,
+  make_one_checkbox,
+  table2col
+} from "./chunk-NQDF3U2C.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-CCYVGZGI.js";
+import {
+  Menu
+} from "./chunk-ELJX3QIQ.js";
+import "./chunk-N7DVQTPC.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import "./chunk-GRVO7RW4.js";
+import "./chunk-7CJKL3LK.js";
+import "./chunk-HZ3TCGBK.js";
+import {
+  dtcnv
+} from "./chunk-IZUYLFOX.js";
+import "./chunk-WINIL2KN.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-7X6NF7NI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-Z2ZITHT4.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// plots/summarizeCnvGeneexp.ts
+var tip = new Menu({ padding: "0px" });
+async function makeChartBtnMenu(holder, chartsInstance) {
+  let expTw, cnvTw, cnvGeneSameAsExp = true, expSearchPrompt, cnvTableRow;
+  make_one_checkbox({
+    holder: holder.append("div").style("margin", "20px 10px 5px 15px"),
+    labeltext: "Use Same Gene For CNV",
+    checked: true,
+    testid: "sjpp-summarizeCnvGeneexp-useSameGeneCheckbox",
+    callback: async (checked) => {
+      cnvGeneSameAsExp = checked;
+      await updateUi();
+    }
+  });
+  const table = table2col({
+    holder: holder.append("div"),
+    margin: "10px",
+    cellPadding: "10px"
+  });
+  {
+    const [td1, td2] = table.addRow();
+    td1.text("Search Gene For Expression");
+    const searchDiv = td2.append("div");
+    expSearchPrompt = td2.append("div").style("font-size", ".7em");
+    const result = addGeneSearchbox({
+      row: searchDiv,
+      tip,
+      searchOnly: "gene",
+      testid: "sjpp-summarizeCnvGeneexp-genesearch-exp",
+      genome: chartsInstance.app.opts.genome,
+      callback: async () => {
+        expSearchPrompt.text("LOADING ...");
+        try {
+          expTw = { term: { gene: result.geneSymbol, type: "geneExpression" }, q: {} };
+          await updateUi();
+          if (cnvGeneSameAsExp) launch();
+          expSearchPrompt.text("");
+        } catch (e) {
+          expSearchPrompt.text("Error: " + (e.message || e));
+          console.log(e.stack);
+        }
+      }
+    });
+  }
+  {
+    const [td1, td2] = table.addRow();
+    cnvTableRow = select_default(td1.node().parentNode);
+    td1.text("Search Gene for CNV");
+    const searchDiv = td2.append("div");
+    const cnvSearchPrompt = td2.append("div").style("font-size", ".7em");
+    const result = addGeneSearchbox({
+      row: searchDiv,
+      tip,
+      searchOnly: "gene",
+      testid: "sjpp-summarizeCnvGeneexp-genesearch-cnv",
+      genome: chartsInstance.app.opts.genome,
+      callback: async () => {
+        cnvSearchPrompt.text("LOADING ...");
+        try {
+          cnvTw = await fillGvTw(result.geneSymbol, dtcnv);
+          await updateUi();
+          cnvSearchPrompt.text("");
+        } catch (e) {
+          cnvSearchPrompt.text("Error: " + (e.message || e));
+          if (e.stack) console.log(e.stack);
+        }
+      }
+    });
+  }
+  const submitBtn = holder.append("button").attr("data-testid", "sjpp-summarizeCnvGeneexp-submitBtn").text("Launch Plot").style("margin", "0px 15px 15px 15px").property("disabled", true).on("click", launch);
+  async function updateUi() {
+    if (cnvGeneSameAsExp) {
+      if (expTw) {
+        cnvTw = await fillGvTw(expTw.term.gene, dtcnv);
+      }
+    }
+    cnvTableRow.style("display", cnvGeneSameAsExp ? "none" : "");
+    expSearchPrompt.text(cnvGeneSameAsExp ? "Hit ENTER to launch plot." : "");
+    submitBtn.style("display", cnvGeneSameAsExp ? "none" : "").property("disabled", !expTw || !cnvTw);
+  }
+  updateUi();
+  async function fillGvTw(geneSymbol, dt) {
+    const name = geneSymbol;
+    const tw = {
+      term: {
+        id: name,
+        name,
+        genes: [
+          {
+            kind: "gene",
+            id: name,
+            gene: name,
+            name,
+            type: "geneVariant"
+          }
+        ],
+        type: "geneVariant"
+      },
+      q: { type: "predefined-groupset", dtLst: [dt] }
+    };
+    await fillTermWrapper(tw, chartsInstance.app.vocabApi);
+    return tw;
+  }
+  function launch() {
+    if (!expTw || !cnvTw) throw "either tw is missing";
+    launchPlot({
+      tw1: expTw,
+      tw2: cnvTw,
+      chartsInstance,
+      holder
+    });
+  }
+}
+export {
+  makeChartBtnMenu
+};
+//# sourceMappingURL=summarizeCnvGeneexp-KNW23YAI.js.map