@sjcrh/proteinpaint-client 2.210.1 → 2.211.1-0

package/dist/stattable-R7O6OIMB.js

@@ -1,117 +0,0 @@
-import {
-  PlotBase
-} from "./chunk-CSAS3PVJ.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-T4RYLTR3.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-Y3SDMRDX.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VTHZGUSZ.js";
-import "./chunk-3TV5WWUN.js";
-import "./chunk-4Y5W26UF.js";
-import "./chunk-UYKJOBRO.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-R7O6OIMB.js.map

package/dist/studyCatalog-OMDE4JRD.js

@@ -1,414 +0,0 @@
-import {
-  orderBy
-} from "./chunk-HPCKKXRK.js";
-import "./chunk-ILEXRHF7.js";
-import {
-  PlotBase,
-  addGeneSearchbox,
-  renderTable
-} from "./chunk-CSAS3PVJ.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-T4RYLTR3.js";
-import {
-  Menu
-} from "./chunk-ELJX3QIQ.js";
-import "./chunk-Y3SDMRDX.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VTHZGUSZ.js";
-import "./chunk-3TV5WWUN.js";
-import "./chunk-4Y5W26UF.js";
-import "./chunk-UYKJOBRO.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-OMDE4JRD.js.map

package/dist/summarizeCnvGeneexp-A7HW6FJI.js

@@ -1,158 +0,0 @@
-import {
-  launchPlot
-} from "./chunk-WMQDFVJK.js";
-import {
-  addGeneSearchbox,
-  fillTermWrapper,
-  make_one_checkbox,
-  table2col
-} from "./chunk-CSAS3PVJ.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-T4RYLTR3.js";
-import {
-  Menu
-} from "./chunk-ELJX3QIQ.js";
-import "./chunk-Y3SDMRDX.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VTHZGUSZ.js";
-import "./chunk-3TV5WWUN.js";
-import "./chunk-4Y5W26UF.js";
-import {
-  dtcnv
-} from "./chunk-UYKJOBRO.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-A7HW6FJI.js.map