@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/geneRanking-SFK4UBKQ.js

@@ -1,553 +0,0 @@
-import {
-  PlotBase,
-  renderTable,
-  sayerror
-} from "./chunk-5VOPABBA.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-Z5U6HOE4.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5ABGFJSP.js";
-import {
-  icons
-} from "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-XPY6AWXO.js";
-import "./chunk-NELOT3NJ.js";
-import {
-  dofetch3
-} from "./chunk-M6EF3WVV.js";
-import "./chunk-7IYJZZQI.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-LFCYMSVA.js";
-import "./chunk-I6WR4CG7.js";
-import "./chunk-2X6W4E3W.js";
-import "./chunk-NYRZNRG5.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-3XVVN66M.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import {
-  linear
-} from "./chunk-NSTL4MY2.js";
-import {
-  roundValueAuto
-} from "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/geneRanking.ts
-var Integrative_rank_COLUMN = "Integrative rank";
-var MISSING_COLOR = "#d9d9d9";
-var SEQ_COLOR_LOW = "#08306b";
-var SEQ_COLOR_HIGH = "#f7fbff";
-var GeneRanking = class _GeneRanking extends PlotBase {
-  constructor(opts) {
-    super(opts);
-    this.sortIdx = -1;
-    this.sortAsc = true;
-    this.pageSize = 10;
-    this.currentPage = 1;
-    this.searchQuery = "";
-    this.heatmapOrder = "clustered";
-    this.minAssays = 3;
-    /** identity-tag of the data the current heatmap was rendered for; used to abort stale responses */
-    this.heatmapRenderKey = "";
-    this.type = _GeneRanking.type;
-    const main = opts.holder.append("div").style("padding", "12px").style("max-width", "95vw");
-    this.errDiv = main.append("div").style("color", "red").style("display", "none").style("padding", "8px");
-    this.loadingDiv = main.append("div").style("padding", "8px").text("Loading...");
-    this.toolbarDiv = main.append("div").style("display", "none").style("align-items", "center").style("justify-content", "space-between").style("flex-wrap", "wrap").style("gap", "8px").style("margin-bottom", "6px").style("font-size", "12px");
-    const leftBar = this.toolbarDiv.append("div").style("display", "flex").style("align-items", "center").style("gap", "6px");
-    const dlBtn = leftBar.append("button").style("display", "inline-flex").style("align-items", "center").style("gap", "6px").style("padding", "4px 10px").style("cursor", "pointer").on("click", () => this.downloadAll());
-    icons["download"](dlBtn.append("span").style("display", "inline-flex").style("align-items", "center"), {
-      width: 14,
-      height: 14,
-      title: "Download data as TSV"
-    });
-    dlBtn.append("span").text("Download data");
-    const rightBar = this.toolbarDiv.append("div");
-    rightBar.append("span").text("Search: ").style("margin-right", "4px");
-    this.searchInput = rightBar.append("input").attr("type", "search").attr("placeholder", "gene name").style("padding", "3px 6px").on("input", (event) => {
-      this.searchQuery = (event.target.value || "").trim().toLowerCase();
-      this.currentPage = 1;
-      this.renderTable();
-    });
-    this.noteDiv = main.append("div").style("display", "none").style("font-size", "0.85em").style("color", "#555").style("margin-bottom", "10px").style("line-height", "1.4").style("white-space", "normal").style("word-break", "normal").style("overflow-wrap", "break-word");
-    this.tableDiv = main.append("div").attr("data-testid", "sjpp-geneRanking-table").style("font-size", "12px");
-    this.heatmapSection = main.append("div").style("display", "none").style("margin-top", "24px").attr("data-testid", "sjpp-geneRanking-heatmap");
-    const hmHeader = this.heatmapSection.append("div").style("display", "flex").style("align-items", "center").style("gap", "12px").style("margin-bottom", "8px");
-    hmHeader.append("div").style("font-weight", "bold").text("Heatmap of the current page");
-    this.heatmapControls = hmHeader.append("div").style("display", "flex").style("align-items", "center").style("gap", "6px");
-    this.heatmapControls.append("span").style("font-size", "0.85em").style("color", "#555").text("Row order:");
-    const orderSelect = this.heatmapControls.append("select").style("padding", "2px 4px").on("change", (event) => {
-      this.heatmapOrder = event.target.value;
-      this.renderHeatmap();
-    });
-    orderSelect.append("option").attr("value", "clustered").text("Clustered").property("selected", true);
-    orderSelect.append("option").attr("value", "rank").text("Ranking score");
-    const minAssaysWrap = this.heatmapControls.append("span").attr("class", "sjpp-mr-min-assays-wrap").style("display", "inline-flex").style("align-items", "center").style("gap", "6px");
-    minAssaysWrap.append("span").style("font-size", "0.85em").style("color", "#555").text("Min assays:");
-    this.minAssaysSelect = minAssaysWrap.append("select").style("padding", "2px 4px").on("change", (event) => {
-      this.minAssays = Number(event.target.value);
-      this.renderHeatmap();
-    });
-    this.heatmapStatus = this.heatmapSection.append("div").style("font-size", "0.85em").style("color", "#777").style("margin-bottom", "6px");
-    this.heatmapDiv = this.heatmapSection.append("div").style("overflow-x", "auto");
-    this.dom = {
-      holder: main,
-      header: opts.header,
-      errDiv: this.errDiv,
-      loadingDiv: this.loadingDiv,
-      toolbarDiv: this.toolbarDiv,
-      noteDiv: this.noteDiv,
-      tableDiv: this.tableDiv
-    };
-  }
-  static {
-    this.type = "geneRanking";
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) throw `No plot with id='${this.id}' found`;
-    return { config, vocab: appState.vocab, termdbConfig: appState.termdbConfig };
-  }
-  reactsTo(action) {
-    if (action.type.startsWith("plot_")) return action.id === this.id;
-    return false;
-  }
-  async main() {
-    this.config = structuredClone(this.state.config);
-    const key = this.config.rankingKey;
-    if (!key) {
-      this.loadingDiv.style("display", "none");
-      this.errDiv.style("display", "block").text("No ranking key selected");
-      return;
-    }
-    if (this.dom.header)
-      this.dom.header.html(`${key} <span style="font-size:.8em;opacity:.7">MULTIOMIC RANKINGS</span>`);
-    if (this.dataKey !== key) {
-      this.loadingDiv.style("display", "block");
-      this.tableDiv.selectAll("*").remove();
-      try {
-        const resp = await dofetch3("termdb/geneRanking", {
-          body: {
-            genome: this.state.vocab.genome,
-            dslabel: this.state.vocab.dslabel,
-            key
-          }
-        });
-        if (resp.error) throw resp.error;
-        this.cachedData = { columns: resp.columns, rows: resp.rows };
-        this.dataKey = key;
-        const integrativeRankIdx = resp.columns.indexOf(Integrative_rank_COLUMN);
-        this.sortIdx = integrativeRankIdx >= 0 ? integrativeRankIdx : -1;
-        this.sortAsc = true;
-        this.currentPage = 1;
-        this.searchQuery = "";
-        if (this.searchInput) this.searchInput.node().value = "";
-      } catch (e) {
-        this.loadingDiv.style("display", "none");
-        sayerror(this.errDiv.style("display", "block"), e.message || e);
-        return;
-      }
-      this.loadingDiv.style("display", "none");
-    }
-    this.toolbarDiv.style("display", "flex");
-    const desc = this.state.termdbConfig?.queries?.geneRanking?.description;
-    this.noteDiv.style("display", desc ? "block" : "none").text(desc || "");
-    this.renderTable();
-  }
-  downloadAll() {
-    if (!this.cachedData) return;
-    const { columns, rows } = this.cachedData;
-    const filtered = this.searchQuery ? rows.filter((r) => {
-      const gene = r[0];
-      return typeof gene === "string" && gene.toLowerCase().includes(this.searchQuery);
-    }) : rows;
-    const sorted = this.sortIdx >= 0 ? sortRows(filtered, this.sortIdx, this.sortAsc) : filtered;
-    const lines = [columns.join("	")];
-    for (const row of sorted) {
-      lines.push(row.map((v) => v == null ? "NA" : String(v)).join("	"));
-    }
-    const blob = new Blob([lines.join("\n")], { type: "text/tab-separated-values" });
-    const url = URL.createObjectURL(blob);
-    const a = document.createElement("a");
-    const slug = (this.dataKey || "geneRanking").replace(/[^A-Za-z0-9_-]+/g, "_");
-    a.href = url;
-    a.download = `${slug}.tsv`;
-    document.body.appendChild(a);
-    a.click();
-    document.body.removeChild(a);
-    URL.revokeObjectURL(url);
-  }
-  renderTable() {
-    if (!this.cachedData) return;
-    const { columns, rows } = this.cachedData;
-    const filtered = this.searchQuery ? rows.filter((r) => {
-      const gene = r[0];
-      return typeof gene === "string" && gene.toLowerCase().includes(this.searchQuery);
-    }) : rows;
-    const sortedRows = this.sortIdx >= 0 ? sortRows(filtered, this.sortIdx, this.sortAsc) : filtered;
-    const cols = columns.map((label, i) => ({
-      label,
-      sortable: true,
-      align: i === 0 ? "left" : "right",
-      nowrap: i === 0
-    }));
-    const tableRows = sortedRows.map(
-      (row) => row.map((v) => {
-        if (v === null || v === void 0) return { value: "" };
-        if (typeof v === "number") return { value: roundValueAuto(v) };
-        return { value: v };
-      })
-    );
-    this.tableDiv.selectAll("*").remove();
-    renderTable({
-      columns: cols,
-      rows: tableRows,
-      div: this.tableDiv,
-      showLines: true,
-      striped: true,
-      showHeader: true,
-      header: { allowSort: false },
-      maxWidth: "95vw",
-      maxHeight: "70vh",
-      pagination: {
-        pageSize: this.pageSize,
-        pageSizeOptions: [10, 25, 50, 100],
-        currentPage: this.currentPage,
-        onChange: ({ currentPage, pageSize }) => {
-          this.currentPage = currentPage;
-          this.pageSize = pageSize;
-          this.renderHeatmap();
-        }
-      }
-    });
-    const ths = this.tableDiv.selectAll("thead th");
-    ths.each((_d, i, nodes) => {
-      const th = nodes[i];
-      th.style.cursor = "pointer";
-      th.style.userSelect = "none";
-      th.style.whiteSpace = "nowrap";
-      th.style.color = "#000";
-      th.style.fontWeight = "bold";
-      th.style.opacity = "1";
-      const colIdx = i;
-      const label = columns[colIdx];
-      if (!label) return;
-      const active = this.sortIdx === colIdx;
-      const upColor = active && this.sortAsc ? "#000" : "#ccc";
-      const downColor = active && !this.sortAsc ? "#000" : "#ccc";
-      th.innerHTML = `<span>${escapeHtml(label)}</span><span style="display:inline-flex;flex-direction:column;line-height:0.6em;margin-left:4px;vertical-align:middle;font-size:0.7em;"><span style="color:${upColor}">\u25B2</span><span style="color:${downColor}">\u25BC</span></span>`;
-      th.onclick = () => {
-        if (this.sortIdx === colIdx) this.sortAsc = !this.sortAsc;
-        else {
-          this.sortIdx = colIdx;
-          this.sortAsc = true;
-        }
-        this.currentPage = 1;
-        this.renderTable();
-      };
-    });
-    requestAnimationFrame(() => {
-      const wrapper = this.tableDiv.select(":scope > div").node();
-      const measured = wrapper || this.tableDiv.select("table").node();
-      if (!measured) return;
-      const w = measured.getBoundingClientRect().width;
-      if (w > 0) {
-        const px = `${Math.ceil(w)}px`;
-        this.toolbarDiv.style("width", px).style("box-sizing", "border-box");
-        this.noteDiv.style("width", px).style("box-sizing", "border-box");
-      }
-    });
-    this.renderHeatmap();
-  }
-  /** rows displayed on the current page after filter + sort + pagination */
-  getVisibleRows() {
-    if (!this.cachedData) return [];
-    const { rows } = this.cachedData;
-    const filtered = this.searchQuery ? rows.filter((r) => {
-      const gene = r[0];
-      return typeof gene === "string" && gene.toLowerCase().includes(this.searchQuery);
-    }) : rows;
-    const sorted = this.sortIdx >= 0 ? sortRows(filtered, this.sortIdx, this.sortAsc) : filtered;
-    const start = (this.currentPage - 1) * this.pageSize;
-    return sorted.slice(start, start + this.pageSize);
-  }
-  async renderHeatmap() {
-    if (!this.cachedData) {
-      this.heatmapSection.style("display", "none");
-      return;
-    }
-    const { columns } = this.cachedData;
-    const colNameToIdx = new Map(columns.map((c, i) => [c, i]));
-    const modalities = this.state.termdbConfig?.queries?.geneRanking?.modalities || [];
-    const usedCols = modalities.filter((m) => colNameToIdx.has(m));
-    if (usedCols.length < 2) {
-      this.heatmapSection.style("display", "none");
-      return;
-    }
-    this.heatmapSection.style("display", "block");
-    if (this.minAssays > usedCols.length) this.minAssays = usedCols.length;
-    if (this.minAssays < 2) this.minAssays = 2;
-    const optionVals = this.minAssaysSelect.selectAll("option").nodes().map((o) => Number(o.value));
-    const want = Array.from({ length: usedCols.length - 1 }, (_, i) => i + 2);
-    if (optionVals.length !== want.length || optionVals.some((v, i) => v !== want[i])) {
-      this.minAssaysSelect.selectAll("option").remove();
-      for (const n of want) {
-        this.minAssaysSelect.append("option").attr("value", n).text(String(n)).property("selected", n === this.minAssays);
-      }
-    }
-    const visible = this.getVisibleRows();
-    const geneNames = visible.map((r) => String(r[0]));
-    const matrix = visible.map(
-      (r) => usedCols.map((c) => {
-        const v = r[colNameToIdx.get(c)];
-        return typeof v === "number" && Number.isFinite(v) ? v : null;
-      })
-    );
-    const fullStats = computeColStats(
-      this.cachedData.rows,
-      usedCols.map((c) => colNameToIdx.get(c))
-    );
-    const toPct = (val, c) => {
-      if (val === null || !Number.isFinite(val)) return null;
-      const lo = fullStats.min[c];
-      const hi = fullStats.max[c];
-      if (!Number.isFinite(lo) || !Number.isFinite(hi) || hi === lo) return 0;
-      return (val - lo) / (hi - lo);
-    };
-    const buildPct = (raw) => raw.map((row) => row.map((v, c) => toPct(v, c)));
-    const renderKey = `${this.dataKey}|${this.heatmapOrder}|${this.minAssays}|${this.currentPage}|${this.pageSize}|${this.searchQuery}|${this.sortIdx}|${this.sortAsc}|${geneNames.join(",")}`;
-    this.heatmapRenderKey = renderKey;
-    this.heatmapDiv.selectAll("*").remove();
-    this.heatmapStatus.text("Computing heatmap\u2026");
-    this.heatmapControls.select(".sjpp-mr-min-assays-wrap").style("display", this.heatmapOrder === "clustered" ? "inline-flex" : "none");
-    if (this.heatmapOrder === "rank") {
-      if (geneNames.length < 1) {
-        this.heatmapStatus.text("No rows to display.");
-        return;
-      }
-      this.heatmapStatus.text(
-        `${geneNames.length} rows in current page order. Missing values shown in gray; cells colored by rank within the full dataset per column (lower = better).`
-      );
-      this.drawHeatmap({
-        rowNames: geneNames,
-        colNames: usedCols,
-        matrix: buildPct(matrix),
-        rankMatrix: matrix,
-        totals: fullStats.n,
-        dendrogram: null
-      });
-      return;
-    }
-    try {
-      const resp = await dofetch3("termdb/geneRanking", {
-        body: {
-          for: "cluster",
-          matrix,
-          row_names: geneNames,
-          col_names: usedCols,
-          minAssays: this.minAssays
-        }
-      });
-      if (renderKey !== this.heatmapRenderKey) return;
-      if (resp.error) throw resp.error;
-      const keptCount = resp.usedRowNames?.length ?? 0;
-      this.heatmapStatus.text(
-        `${keptCount} of ${visible.length} rows shown (proteins with \u2265${this.minAssays} assays). Missing values shown in gray; cells colored by rank within the full dataset per column (lower = better).`
-      );
-      const nameToIdx = new Map(geneNames.map((n, i) => [n, i]));
-      const keptRawMatrix = resp.usedRowNames.map((n) => matrix[nameToIdx.get(n)]);
-      const keptNameToIdx = new Map(resp.usedRowNames.map((n, i) => [n, i]));
-      const orderedRowNames = resp.row.order.map((o) => o.name);
-      const orderedRank = orderedRowNames.map((name) => keptRawMatrix[keptNameToIdx.get(name)]);
-      const orderedPct = buildPct(orderedRank);
-      this.drawHeatmap({
-        rowNames: orderedRowNames,
-        colNames: resp.usedColNames,
-        matrix: orderedPct,
-        rankMatrix: orderedRank,
-        totals: fullStats.n,
-        dendrogram: resp.row
-      });
-    } catch (e) {
-      if (renderKey !== this.heatmapRenderKey) return;
-      this.heatmapStatus.text(`Heatmap error: ${e?.message || e}`);
-    }
-  }
-  drawHeatmap(opts) {
-    const { rowNames, colNames, matrix, rankMatrix, totals, dendrogram } = opts;
-    const cellW = 44;
-    const cellH = 22;
-    const dendroW = dendrogram ? 110 : 0;
-    const dendroPad = dendrogram ? 8 : 0;
-    const colLabelH = 110;
-    const rowLabelW = 130;
-    const legendBlockW = 110;
-    const gridW = colNames.length * cellW;
-    const gridH = rowNames.length * cellH;
-    const legendGradH = Math.max(120, Math.min(gridH, 240));
-    const missingSwatchExtra = 18 + 12;
-    const totalW = dendroW + dendroPad + gridW + 8 + rowLabelW + legendBlockW;
-    const totalH = colLabelH + Math.max(gridH, legendGradH + missingSwatchExtra) + 16;
-    this.heatmapDiv.selectAll("*").remove();
-    const svg = this.heatmapDiv.append("svg").attr("width", totalW).attr("height", totalH).attr("font-family", "sans-serif");
-    const seq = linear().domain([0, 1]).range([SEQ_COLOR_LOW, SEQ_COLOR_HIGH]).clamp(true);
-    const color = (v) => seq(v);
-    if (dendrogram) {
-      const g = svg.append("g").attr("transform", `translate(0,${colLabelH})`);
-      drawRowDendrogram(g, dendrogram, dendroW, gridH, cellH);
-    }
-    const gridX = dendroW + dendroPad;
-    const labelsG = svg.append("g").attr("transform", `translate(${gridX},${colLabelH - 4})`);
-    labelsG.selectAll("text").data(colNames).enter().append("text").attr("x", (_d, i) => i * cellW + cellW / 2).attr("y", 0).attr("transform", (_d, i) => `rotate(-45,${i * cellW + cellW / 2},0)`).attr("text-anchor", "start").attr("font-size", "13px").attr("fill", "#000").text((d) => d);
-    const cellsG = svg.append("g").attr("transform", `translate(${gridX},${colLabelH})`);
-    const cellData = [];
-    for (let r = 0; r < matrix.length; r++) {
-      for (let c = 0; c < matrix[r].length; c++) {
-        cellData.push({ x: c * cellW, y: r * cellH, v: matrix[r][c], row: r, col: c });
-      }
-    }
-    cellsG.selectAll("rect").data(cellData).enter().append("rect").attr("x", (d) => d.x).attr("y", (d) => d.y).attr("width", cellW).attr("height", cellH).attr("fill", (d) => d.v === null || !Number.isFinite(d.v) ? MISSING_COLOR : color(d.v)).attr("stroke", "#fff").attr("stroke-width", 0.5).append("title").text((d) => {
-      if (d.v === null || !Number.isFinite(d.v)) return `${rowNames[d.row]} \u2014 ${colNames[d.col]}
-missing`;
-      const r = rankMatrix[d.row][d.col];
-      const n = totals[d.col];
-      const rStr = Number.isInteger(r) ? String(r) : r.toFixed(1);
-      return `${rowNames[d.row]} \u2014 ${colNames[d.col]}
-rank: ${rStr} of ${n}
-scaled rank: ${d.v.toFixed(
-        3
-      )}`;
-    });
-    cellsG.selectAll("text.sjpp-mr-rank").data(cellData.filter((d) => d.v !== null && Number.isFinite(d.v))).enter().append("text").attr("class", "sjpp-mr-rank").attr("x", (d) => d.x + cellW / 2).attr("y", (d) => d.y + cellH / 2 + 3).attr("text-anchor", "middle").attr("font-size", "9px").attr("font-weight", 300).attr("pointer-events", "none").attr("fill", (d) => d.v < 0.5 ? "rgba(255,255,255,0.85)" : "rgba(40,40,40,0.7)").text((d) => {
-      const r = rankMatrix[d.row][d.col];
-      return Number.isInteger(r) ? String(r) : r.toFixed(1);
-    });
-    const rowLabelsG = svg.append("g").attr("transform", `translate(${gridX + gridW + 6},${colLabelH})`);
-    rowLabelsG.selectAll("text").data(rowNames).enter().append("text").attr("x", 0).attr("y", (_d, i) => i * cellH + cellH / 2 + 4).attr("font-size", "13px").attr("fill", "#000").text((d) => d);
-    const legendGradW = 16;
-    const legendX = gridX + gridW + 8 + rowLabelW + 8;
-    const legendY = colLabelH;
-    const legendG = svg.append("g").attr("transform", `translate(${legendX},${legendY})`);
-    legendG.append("text").attr("transform", `translate(-6,${legendGradH / 2}) rotate(-90)`).attr("text-anchor", "middle").attr("font-size", "11px").attr("fill", "#555").text("scaled rank (per column)");
-    const stops = 32;
-    for (let i = 0; i < stops; i++) {
-      const v = i / (stops - 1);
-      legendG.append("rect").attr("x", 0).attr("y", i * legendGradH / stops).attr("width", legendGradW).attr("height", legendGradH / stops + 0.5).attr("fill", color(v));
-    }
-    legendG.append("rect").attr("x", 0).attr("y", 0).attr("width", legendGradW).attr("height", legendGradH).attr("fill", "none").attr("stroke", "#999").attr("stroke-width", 0.5);
-    const maxRank = totals.reduce((m, t) => Number.isFinite(t) && t > m ? t : m, 0);
-    const midRank = Math.round((1 + maxRank) / 2);
-    legendG.append("text").attr("x", legendGradW + 6).attr("y", 4).attr("font-size", "11px").text("1 (top)");
-    legendG.append("text").attr("x", legendGradW + 6).attr("y", legendGradH / 2 + 4).attr("font-size", "11px").text(String(midRank));
-    legendG.append("text").attr("x", legendGradW + 6).attr("y", legendGradH).attr("font-size", "11px").text(`${maxRank} (bottom)`);
-    const missingG = svg.append("g").attr("transform", `translate(${legendX},${legendY + legendGradH + 18})`);
-    missingG.append("rect").attr("width", legendGradW).attr("height", 12).attr("fill", MISSING_COLOR).attr("stroke", "#999").attr("stroke-width", 0.5);
-    missingG.append("text").attr("x", legendGradW + 6).attr("y", 10).attr("font-size", "11px").attr("fill", "#555").text("missing");
-  }
-};
-function escapeHtml(s) {
-  return s.replace(/[&<>"']/g, (c) => ({ "&": "&amp;", "<": "&lt;", ">": "&gt;", '"': "&quot;", "'": "&#39;" })[c]);
-}
-function sortRows(rows, idx, asc) {
-  const sign = asc ? 1 : -1;
-  return rows.map((r, i) => ({ r, i })).sort((a, b) => {
-    const va = a.r[idx];
-    const vb = b.r[idx];
-    if (va == null && vb == null) return a.i - b.i;
-    if (va == null) return 1;
-    if (vb == null) return -1;
-    if (typeof va === "number" && typeof vb === "number") return (va - vb) * sign;
-    return String(va).localeCompare(String(vb)) * sign;
-  }).map((x) => x.r);
-}
-function computeColStats(allRows, colIdxs) {
-  const min = colIdxs.map(() => Infinity);
-  const max = colIdxs.map(() => -Infinity);
-  const n = colIdxs.map(() => 0);
-  for (const row of allRows) {
-    for (let i = 0; i < colIdxs.length; i++) {
-      const v = row[colIdxs[i]];
-      if (typeof v === "number" && Number.isFinite(v)) {
-        if (v < min[i]) min[i] = v;
-        if (v > max[i]) max[i] = v;
-        n[i]++;
-      }
-    }
-  }
-  return { min, max, n };
-}
-function drawRowDendrogram(g, dend, width, gridH, cellH) {
-  const heights = dend.height.map((h) => h.height);
-  const maxH = Math.max(...heights, 1e-9);
-  const hToX = linear().domain([0, maxH]).range([width, 0]);
-  const leafYByName = /* @__PURE__ */ new Map();
-  dend.order.forEach((leaf, i) => {
-    leafYByName.set(leaf.name, i * cellH + cellH / 2);
-  });
-  const merged = /* @__PURE__ */ new Map();
-  for (let i = 0; i < dend.merge.length; i++) {
-    const { n1, n2 } = dend.merge[i];
-    const pos = (n) => {
-      if (n < 0) {
-        const name = dend.inputOrder[-n - 1];
-        return { x: width, y: leafYByName.get(name) ?? 0 };
-      }
-      return merged.get(n) || { x: width, y: 0 };
-    };
-    const a = pos(n1);
-    const b = pos(n2);
-    const x = hToX(heights[i]);
-    const y = (a.y + b.y) / 2;
-    g.append("line").attr("x1", a.x).attr("x2", x).attr("y1", a.y).attr("y2", a.y).attr("stroke", "#000").attr("stroke-width", 1);
-    g.append("line").attr("x1", b.x).attr("x2", x).attr("y1", b.y).attr("y2", b.y).attr("stroke", "#000").attr("stroke-width", 1);
-    g.append("line").attr("x1", x).attr("x2", x).attr("y1", a.y).attr("y2", b.y).attr("stroke", "#000").attr("stroke-width", 1);
-    merged.set(i + 1, { x, y });
-  }
-}
-async function getPlotConfig(opts) {
-  const config = {
-    chartType: GeneRanking.type,
-    rankingKey: opts.rankingKey || ""
-  };
-  return copyMerge(config, opts);
-}
-var componentInit = getCompInit(GeneRanking);
-function makeChartBtnMenu(holder, chartsInstance) {
-  chartsInstance.dom.tip.clear();
-  const cfg = chartsInstance.state.termdbConfig?.queries?.geneRanking;
-  const rankings = cfg?.rankings;
-  if (!rankings || !Object.keys(rankings).length) {
-    holder.append("div").style("padding", "8px").style("color", "#888").text("No multiomic rankings available for this dataset.");
-    return;
-  }
-  for (const key of Object.keys(rankings)) {
-    holder.append("div").attr("class", "sja_menuoption sja_sharp_border").text(key).on("click", () => {
-      chartsInstance.dom.tip.hide();
-      chartsInstance.prepPlot({
-        config: {
-          chartType: "geneRanking",
-          rankingKey: key
-        }
-      });
-    });
-  }
-}
-export {
-  componentInit,
-  getPlotConfig,
-  makeChartBtnMenu
-};
-//# sourceMappingURL=geneRanking-SFK4UBKQ.js.map

package/dist/geneVariant-IYEHB4H7.js

@@ -1,41 +0,0 @@
-import {
-  SearchHandler,
-  addParentTerm,
-  getChildTerms
-} from "./chunk-5VOPABBA.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-Z5U6HOE4.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5ABGFJSP.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-XPY6AWXO.js";
-import "./chunk-NELOT3NJ.js";
-import "./chunk-M6EF3WVV.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-LFCYMSVA.js";
-import "./chunk-I6WR4CG7.js";
-import "./chunk-2X6W4E3W.js";
-import "./chunk-NYRZNRG5.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-3XVVN66M.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-NSTL4MY2.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  SearchHandler,
-  addParentTerm,
-  getChildTerms
-};
-//# sourceMappingURL=geneVariant-IYEHB4H7.js.map

package/dist/geneVariant-LIRRLUFR.js

@@ -1,39 +0,0 @@
-import {
-  getDtsFromGroups,
-  getHandler
-} from "./chunk-5VOPABBA.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-Z5U6HOE4.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5ABGFJSP.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-XPY6AWXO.js";
-import "./chunk-NELOT3NJ.js";
-import "./chunk-M6EF3WVV.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-LFCYMSVA.js";
-import "./chunk-I6WR4CG7.js";
-import "./chunk-2X6W4E3W.js";
-import "./chunk-NYRZNRG5.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-3XVVN66M.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-NSTL4MY2.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  getDtsFromGroups,
-  getHandler
-};
-//# sourceMappingURL=geneVariant-LIRRLUFR.js.map