@sjcrh/proteinpaint-client 2.185.0 → 2.186.0

package/dist/grin2-LGI535FF.js

@@ -1,1554 +0,0 @@
-import {
-  make_one_checkbox,
-  renderTable,
-  sayerror,
-  table2col,
-  to_svg
-} from "./chunk-YWUVCXFS.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-3QBZ2Y77.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-LSEFWW72.js";
-import {
-  icons
-} from "./chunk-KWM6B3NL.js";
-import "./chunk-UCLS2SVB.js";
-import {
-  dofetch3
-} from "./chunk-6ZCHECOT.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-X4NI4JLQ.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-UWYCEYML.js";
-import "./chunk-7UHUOC6F.js";
-import "./chunk-ZYY54HBU.js";
-import "./chunk-EGWVYY7K.js";
-import {
-  bplen,
-  class2SOterm,
-  dtsnvindel,
-  mclass
-} from "./chunk-AMYSEKPF.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-KSGA62R2.js";
-import {
-  axisLeft
-} from "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import {
-  linear
-} from "./chunk-OAWQ6LOO.js";
-import "./chunk-KYBIQBXE.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-
-// gdc/grin2/ui-components.ts
-var STYLES = {
-  // Layout styles
-  flexRow: {
-    display: "flex",
-    "align-items": "center",
-    gap: "8px"
-  },
-  gridTwoColumn: {
-    display: "grid",
-    "grid-template-columns": "auto auto",
-    gap: "15px",
-    "max-width": "fit-content"
-  },
-  // Form element styles
-  label: {
-    "font-size": "14px",
-    "font-weight": "500"
-  },
-  numberInput: {
-    padding: "4px 8px",
-    border: "1px solid #ccc",
-    "border-radius": "4px",
-    "font-size": "14px"
-  },
-  checkbox: {
-    margin: "0",
-    cursor: "pointer"
-  },
-  checkboxLabel: {
-    cursor: "pointer",
-    "font-weight": "500"
-  },
-  // Table styles
-  tableHeader: {
-    padding: "12px",
-    "background-color": "#f8f9fa",
-    border: "1px solid #ddd",
-    "font-weight": "bold",
-    "text-align": "left"
-  },
-  tableCell: {
-    padding: "12px",
-    border: "1px solid #ddd",
-    "vertical-align": "top"
-  },
-  optionsTable: {
-    width: "auto",
-    "border-collapse": "collapse",
-    "margin-top": "10px",
-    border: "1px solid #ddd"
-  },
-  // Panel styles
-  infoPanel: {
-    padding: "8px",
-    "background-color": "#f8f9fa",
-    "border-radius": "4px",
-    "border-left": "3px solid #6c757d",
-    "font-size": "12px",
-    color: "#495057",
-    "line-height": "1.4"
-  },
-  // Expandable section styles
-  expandableHeader: {
-    display: "flex",
-    "align-items": "center",
-    gap: "8px",
-    cursor: "pointer",
-    padding: "8px",
-    "border-radius": "4px",
-    transition: "background-color 0.2s"
-  },
-  expandIcon: {
-    "font-size": "12px",
-    transition: "transform 0.2s"
-  },
-  expandableContent: {
-    display: "none",
-    "margin-top": "12px",
-    padding: "12px",
-    "background-color": "#fff",
-    "border-radius": "4px",
-    "box-shadow": "inset 0 1px 3px rgba(0, 0, 0, 0.1)"
-  },
-  expandHeaderText: {
-    "text-decoration": "underline",
-    "font-size": "13px",
-    "font-weight": "500"
-  }
-};
-function applyStyles(selection, styles) {
-  Object.entries(styles).forEach(([property, value]) => {
-    selection.style(property, value);
-  });
-  return selection;
-}
-function createNumberInput(container, config) {
-  const inputContainer = container.append("div");
-  applyStyles(inputContainer, STYLES.flexRow);
-  const label = inputContainer.append("label");
-  applyStyles(label, STYLES.label);
-  if (config.labelWidth) {
-    label.style("min-width", config.labelWidth);
-  }
-  label.text(config.label);
-  const input = inputContainer.append("input").attr("type", "number").attr("value", config.value);
-  applyStyles(input, STYLES.numberInput);
-  if (config.min !== void 0) input.attr("min", config.min);
-  if (config.max !== void 0) input.attr("max", config.max);
-  if (config.step !== void 0) input.attr("step", config.step);
-  if (config.width) input.style("width", config.width);
-  input.on("input", function() {
-    const value = parseFloat(this.value);
-    if (!isNaN(value)) {
-      config.onChange(value);
-    }
-  });
-  return { container: inputContainer, input, label };
-}
-function createCheckbox(container, config) {
-  const checkboxContainer = container.append("div");
-  applyStyles(checkboxContainer, STYLES.flexRow);
-  const checkbox = checkboxContainer.append("input").attr("type", "checkbox").attr("id", config.id).property("checked", config.checked);
-  applyStyles(checkbox, STYLES.checkbox);
-  const label = checkboxContainer.append("label").attr("for", config.id).text(config.label);
-  applyStyles(label, STYLES.checkboxLabel);
-  checkbox.on("change", function() {
-    config.onChange(this.checked);
-  });
-  return { container: checkboxContainer, checkbox, label };
-}
-function createOptionsTable(container) {
-  const table = container.append("table");
-  applyStyles(table, STYLES.optionsTable);
-  return table;
-}
-function createTableHeader(table, columns) {
-  const headerRow = table.append("tr");
-  columns.forEach((columnText, index) => {
-    const th = headerRow.append("th");
-    applyStyles(th, STYLES.tableHeader);
-    if (index === 0) {
-      th.style("width", "200px");
-    }
-    th.text(columnText);
-  });
-  return headerRow;
-}
-function createDataTypeRow(table, config) {
-  const row = table.append("tr");
-  const checkboxCell = row.append("td");
-  applyStyles(checkboxCell, STYLES.tableCell);
-  const { checkbox } = createCheckbox(checkboxCell, {
-    id: config.id,
-    label: config.label,
-    checked: config.checked,
-    onChange: config.onChange
-  });
-  const optionsCell = row.append("td");
-  applyStyles(optionsCell, STYLES.tableCell);
-  const optionsContainer = optionsCell.append("div").style("display", config.checked ? "block" : "none");
-  config.createOptionsContent(optionsContainer);
-  return { row, optionsContainer, checkbox };
-}
-function createInfoPanel(container, config) {
-  const panel = container.append("div");
-  applyStyles(panel, STYLES.infoPanel);
-  if (config.color) {
-    panel.style("border-left-color", config.color);
-  }
-  if (config.title) {
-    panel.append("strong").text(config.title);
-    panel.append("br");
-  }
-  panel.append("span").html(config.content);
-  return panel;
-}
-
-// plots/manhattan/manhattanGDC.ts
-function plotManhattanGDC(div, data, settings, app) {
-  settings = {
-    pngDotRadius: 2,
-    plotWidth: 1e3,
-    plotHeight: 400,
-    yAxisX: 70,
-    yAxisY: 40,
-    yAxisSpace: 40,
-    fontSize: 12,
-    showLegend: true,
-    legendItemWidth: 80,
-    legendDotRadius: 3,
-    legendRightOffset: 15,
-    legendTextOffset: 12,
-    legendVerticalOffset: 4,
-    legendFontSize: 12,
-    showInteractiveDots: true,
-    showDownload: true,
-    interactiveDotRadius: 3,
-    interactiveDotStrokeWidth: 1,
-    ...settings
-  };
-  div.style("position", "relative");
-  const geneTip = new Menu({ padding: "" });
-  const svg = div.append("svg").attr("width", data.plotData.png_width + settings.yAxisX + settings.yAxisSpace).attr("height", data.plotData.png_height + settings.yAxisY * 4);
-  const yAxisG = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`);
-  const yScale = linear().domain([0, data.plotData.y_max]).range([data.plotData.png_height, 0]);
-  yAxisG.call(axisLeft(yScale));
-  svg.append("text").attr("x", -(data.plotData.png_height / 2) - settings.yAxisY).attr("y", settings.yAxisX / 2).attr("transform", "rotate(-90)").attr("text-anchor", "middle").attr("font-size", `${settings.fontSize}px`).attr("fill", "black").text("-log\u2081\u2080(q-value)");
-  svg.append("image").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).attr("width", data.plotData.png_width).attr("height", data.plotData.png_height).attr("href", `data:image/png;base64,${data.pngImg || data.png}`);
-  const xScale = linear().domain([-data.plotData.x_buffer, data.plotData.total_genome_length + data.plotData.x_buffer]).range([0, data.plotData.png_width]);
-  if (settings.showInteractiveDots && data.plotData.points && data.plotData.points.length > 0) {
-    const pointsLayer = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`);
-    pointsLayer.selectAll("circle").data(data.plotData.points).enter().append("circle").attr("cx", (d) => xScale(d.x)).attr("cy", (d) => yScale(d.y)).attr("r", settings.interactiveDotRadius).attr("fill-opacity", 0).attr("stroke", "black").attr("stroke-width", settings.interactiveDotStrokeWidth).attr("stroke-opacity", 0).on("mouseover", (event, d) => {
-      event.target.setAttribute("stroke-opacity", 1);
-      geneTip.clear().show(event.clientX, event.clientY);
-      const table = table2col({
-        holder: geneTip.d.append("div"),
-        margin: "10px"
-      });
-      table.addRow("Gene", d.gene);
-      const [t1, t2] = table.addRow();
-      t1.text("Type");
-      t2.html(`<span style="color:${d.color}">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`);
-      table.addRow("-log\u2081\u2080(q-value)", d.y.toFixed(3));
-      if (d.nsubj) table.addRow("Subject count", d.nsubj);
-      table.addRow("Chromosome", d.chrom);
-    }).on("mouseout", (event) => {
-      event.target.setAttribute("stroke-opacity", 0);
-      geneTip.hide();
-    }).on("click", (event, d) => {
-      if (app) {
-        app.dispatch({
-          type: "plot_create",
-          config: {
-            chartType: "genomeBrowser",
-            geneSearchResult: { geneSymbol: d.gene }
-          }
-        });
-      }
-    });
-  }
-  if (data.plotData.chrom_data) {
-    const chromLabelY = data.plotData.png_height + settings.yAxisY + 20;
-    Object.entries(data.plotData.chrom_data).forEach(([chrom, chromData]) => {
-      const chromLabel = chrom.replace("chr", "");
-      if (chromLabel === "M") return;
-      const centerPos = settings.yAxisX + settings.yAxisSpace + xScale(chromData.center);
-      svg.append("text").attr("x", centerPos).attr("y", chromLabelY).attr("text-anchor", "middle").attr("font-size", `${settings.fontSize - 2}px`).attr("fill", "black").text(chromLabel);
-    });
-  }
-  svg.append("text").attr("x", settings.yAxisX + settings.yAxisSpace + data.plotData.png_width / 2).attr("y", data.plotData.png_height + settings.yAxisY + 45).attr("text-anchor", "middle").attr("font-size", `${settings.fontSize}px`).attr("fill", "black").text("Chromosomes");
-  svg.append("text").attr("x", settings.yAxisX + settings.yAxisSpace).attr("y", settings.yAxisY / 2).attr("text-anchor", "left").attr("font-weight", "bold").attr("font-size", `${settings.fontSize + 2}px`).attr("fill", "black").text("Manhattan Plot");
-  if (settings.showDownload) {
-    const downloadDiv = div.append("div").style("position", "absolute").style("top", "5px").style("left", `${settings.yAxisX + settings.yAxisSpace + 108}px`).style("z-index", "10").style("background", `${settings.background}`).style("padding", `${settings.padding + 2}px`).style("border-radius", `${settings.borderRadius + 10}px`);
-    icons["download"](downloadDiv, {
-      width: 16,
-      height: 16,
-      title: "Download Manhattan plot",
-      handler: () => {
-        to_svg(
-          svg.node(),
-          `manhattan_plot_${(/* @__PURE__ */ new Date()).toISOString().replace(/[:.]/g, "-").slice(0, -5)}`,
-          { apply_dom_styles: true }
-        );
-      }
-    });
-  }
-  const mutationTypes = [...new Set(data.plotData.points.map((p) => p.type))];
-  const legendData = mutationTypes.map((type) => {
-    const point = data.plotData.points.find((p) => p.type === type);
-    return {
-      type: String(type).charAt(0).toUpperCase() + String(type).slice(1),
-      color: point?.color
-    };
-  });
-  if (settings.showLegend && legendData.length > 0) {
-    const legendY = settings.yAxisY / 2;
-    const totalWidth = legendData.length * settings.legendItemWidth;
-    const legendX = settings.yAxisX + settings.yAxisSpace + data.plotData.png_width - totalWidth - settings.legendRightOffset;
-    legendData.forEach((item, i) => {
-      const x = legendX + i * settings.legendItemWidth;
-      svg.append("circle").attr("cx", x + 8).attr("cy", legendY).attr("r", settings.legendDotRadius).attr("fill", item.color).attr("stroke", "black").attr("stroke-width", 1);
-      svg.append("text").attr("x", x + 8 + settings.legendTextOffset).attr("y", legendY + settings.legendVerticalOffset).attr("font-size", `${settings.legendFontSize}px`).attr("fill", "black").text(item.type);
-    });
-  }
-}
-
-// gdc/grin2.ts
-var defaultCheckedClasses = ["M", "F", "N", "StopLost", "StartLost", "L", "I", "D", "ProteinAltering"];
-var skipMAFclasses = ["WT", "Blank", "X"];
-function transformRows(rows, columns) {
-  return rows.map((row) => {
-    const transformedRow = [];
-    for (let i = 0; i < columns.length; i++) {
-      const cellData = row[i];
-      let value = null;
-      if (cellData && cellData.value && Array.isArray(cellData.value)) {
-        value = cellData.value[0];
-      } else if (cellData && "value" in cellData) {
-        value = cellData.value;
-      } else {
-        value = cellData;
-      }
-      transformedRow.push({ value });
-    }
-    return transformedRow;
-  });
-}
-function parseRecordsByCaseData(recordsByCase, excludedByMaxRecord = {}) {
-  const columns = [
-    { label: "Case ID", sortable: true },
-    { label: "MAF Total Processed", sortable: true },
-    { label: "MAF Included", sortable: true },
-    { label: "MAF Excluded by Depth", sortable: true },
-    { label: "MAF Excluded by Alt Count", sortable: true },
-    { label: "MAF Excluded by Consequence", sortable: true },
-    { label: "MAF Skipped Chromosomes", sortable: true },
-    { label: "MAF Excluded by Records Cap", sortable: true },
-    { label: "CNV Total Processed", sortable: true },
-    { label: "CNV Included", sortable: true },
-    { label: "CNV Excluded by Thresholds", sortable: true },
-    { label: "CNV Excluded by Length", sortable: true },
-    { label: "CNV Skipped Chromosomes", sortable: true },
-    { label: "CNV Excluded by Records Cap", sortable: true },
-    { label: "Invalid Rows", sortable: true }
-  ];
-  const rows = [];
-  Object.entries(recordsByCase).forEach(([caseId, caseData]) => {
-    const row = [];
-    row.push({ value: caseId });
-    let parsedData;
-    try {
-      parsedData = typeof caseData === "string" ? JSON.parse(caseData) : caseData;
-    } catch (_e) {
-      parsedData = caseData;
-    }
-    let mafTotalProcessed = 0;
-    let mafIncluded = 0;
-    let mafExcludedByDepth = 0;
-    let mafExcludedByAltCount = 0;
-    let mafExcludedByConsequence = 0;
-    let mafSkippedChromosomes = 0;
-    if (parsedData.maf) {
-      mafTotalProcessed = parsedData.maf.total_processed || 0;
-      mafIncluded = parsedData.maf.total_included || 0;
-      mafExcludedByDepth = parsedData.maf.excluded_by_min_depth || 0;
-      mafExcludedByAltCount = parsedData.maf.excluded_by_min_alt_count || 0;
-      mafExcludedByConsequence = parsedData.maf.excluded_by_consequence_type || 0;
-      if (parsedData.maf.skipped_chromosomes && typeof parsedData.maf.skipped_chromosomes === "object") {
-        mafSkippedChromosomes = Object.values(parsedData.maf.skipped_chromosomes).reduce(
-          (sum, count) => sum + (Number(count) || 0),
-          0
-        );
-      }
-    }
-    row.push({ value: mafTotalProcessed });
-    row.push({ value: mafIncluded });
-    row.push({ value: mafExcludedByDepth });
-    row.push({ value: mafExcludedByAltCount });
-    row.push({ value: mafExcludedByConsequence });
-    if (parsedData.maf?.skipped_chromosomes && Object.keys(parsedData.maf.skipped_chromosomes).length > 0) {
-      const chromosomeEntries = Object.entries(parsedData.maf.skipped_chromosomes);
-      const tableHtml = `
-				<div style="text-align: center;">
-				<table style="border-collapse: collapse; margin: 0 auto; font-size: 11px; border: 1px solid #ddd;">
-					<thead>
-					<tr style="background-color: #f8f9fa;">
-						<th style="border: 1px solid #ddd; padding: 2px 6px;">Chr</th>
-						<th style="border: 1px solid #ddd; padding: 2px 6px;">Count</th>
-					</tr>
-					</thead>
-					<tbody>
-					${chromosomeEntries.map(
-        ([chr, count]) => `<tr>
-						<td style="border: 1px solid #ddd; padding: 2px 6px;">${chr}</td>
-						<td style="border: 1px solid #ddd; padding: 2px 6px; text-align: right;">${count}</td>
-						</tr>`
-      ).join("")}
-					</tbody>
-				</table>
-				</div>
-			`;
-      row.push({
-        html: tableHtml,
-        value: mafSkippedChromosomes,
-        rawData: parsedData.maf.skipped_chromosomes,
-        dataType: "chromosome-details"
-      });
-    } else {
-      row.push({
-        value: mafSkippedChromosomes,
-        rawData: null,
-        dataType: "chromosome-details"
-      });
-    }
-    const mafExcludedByMax = excludedByMaxRecord.maf?.includes(caseId) ? "Yes" : "No";
-    row.push({
-      value: mafExcludedByMax,
-      html: mafExcludedByMax === "Yes" ? `<span style="color: #dc3545; font-weight: bold;">${mafExcludedByMax}</span>` : mafExcludedByMax
-    });
-    let cnvTotalProcessed = 0;
-    let cnvIncluded = 0;
-    let cnvExcludedByThresholds = 0;
-    let cnvExcludedByLength = 0;
-    let cnvSkippedChromosomes = 0;
-    if (parsedData.cnv) {
-      cnvTotalProcessed = parsedData.cnv.total_processed || 0;
-      cnvIncluded = parsedData.cnv.total_included || 0;
-      cnvExcludedByThresholds = (parsedData.cnv.excluded_by_loss_threshold || 0) + (parsedData.cnv.excluded_by_gain_threshold || 0);
-      cnvExcludedByLength = parsedData.cnv.excluded_by_segment_length || 0;
-      if (parsedData.cnv.skipped_chromosomes && typeof parsedData.cnv.skipped_chromosomes === "object") {
-        cnvSkippedChromosomes = Object.values(parsedData.cnv.skipped_chromosomes).reduce(
-          (sum, count) => sum + (Number(count) || 0),
-          0
-        );
-      }
-    }
-    row.push({ value: cnvTotalProcessed });
-    row.push({ value: cnvIncluded });
-    row.push({ value: cnvExcludedByThresholds });
-    row.push({ value: cnvExcludedByLength });
-    if (parsedData.cnv?.skipped_chromosomes && Object.keys(parsedData.cnv.skipped_chromosomes).length > 0) {
-      const chromosomeEntries = Object.entries(parsedData.cnv.skipped_chromosomes);
-      const tableHtml = `
-    <div style="text-align: center;">
-      <table style="border-collapse: collapse; margin: 0 auto; font-size: 11px; border: 1px solid #ddd;">
-        <thead>
-          <tr style="background-color: #f8f9fa;">
-            <th style="border: 1px solid #ddd; padding: 2px 6px;">Chr</th>
-            <th style="border: 1px solid #ddd; padding: 2px 6px;">Count</th>
-          </tr>
-        </thead>
-        <tbody>
-          ${chromosomeEntries.map(
-        ([chr, count]) => `<tr>
-              <td style="border: 1px solid #ddd; padding: 2px 6px;">${chr}</td>
-              <td style="border: 1px solid #ddd; padding: 2px 6px; text-align: right;">${count}</td>
-            </tr>`
-      ).join("")}
-        </tbody>
-      </table>
-    </div>
-  `;
-      row.push({
-        html: tableHtml,
-        value: cnvSkippedChromosomes,
-        rawData: parsedData.cnv.skipped_chromosomes,
-        dataType: "chromosome-details"
-      });
-    } else {
-      row.push({
-        value: cnvSkippedChromosomes,
-        rawData: null,
-        dataType: "chromosome-details"
-      });
-    }
-    const cnvExcludedByMax = excludedByMaxRecord.cnv?.includes(caseId) ? "Yes" : "No";
-    row.push({
-      value: cnvExcludedByMax,
-      html: cnvExcludedByMax === "Yes" ? `<span style="color: #dc3545; font-weight: bold;">${cnvExcludedByMax}</span>` : cnvExcludedByMax
-    });
-    let totalInvalidRows = 0;
-    if (parsedData.maf && parsedData.maf.invalid_rows !== void 0) {
-      totalInvalidRows += Number(parsedData.maf.invalid_rows) || 0;
-    }
-    if (parsedData.cnv && parsedData.cnv.invalid_rows !== void 0) {
-      totalInvalidRows += Number(parsedData.cnv.invalid_rows) || 0;
-    }
-    row.push({ value: totalInvalidRows });
-    rows.push(row);
-  });
-  return { columns, rows };
-}
-function addExpandableFailedFilesToStats(statsContainer, failedFilesInfo) {
-  const expandableContainer = statsContainer.append("div").style("margin-top", "12px");
-  const expandableHeader = expandableContainer.append("div").style("display", "flex").style("align-items", "center").style("gap", "8px").style("cursor", "pointer").style("padding", "8px").style("border-radius", "4px").style("transition", "background-color 0.2s").style("background-color", "rgba(220, 53, 69, 0.1)").style("border", "1px solid rgba(220, 53, 69, 0.2)").on("mouseenter", function() {
-    select_default(this).style("background-color", "rgba(220, 53, 69, 0.15)");
-  }).on("mouseleave", function() {
-    select_default(this).style("background-color", "rgba(220, 53, 69, 0.1)");
-  });
-  const expandIcon = expandableHeader.append("span").style("font-size", "12px").style("color", "#dc3545").style("transition", "transform 0.2s").text("\u25B6");
-  expandableHeader.append("span").style("color", "#dc3545").style("text-decoration", "underline").style("font-size", "13px").style("font-weight", "500").text(`View ${failedFilesInfo.count} failed files details`);
-  if (failedFilesInfo.errorSummary) {
-    const { errorSummary } = failedFilesInfo;
-    const summaryItems = [];
-    if (errorSummary.connectionErrors > 0) {
-      summaryItems.push(`${errorSummary.connectionErrors} connection`);
-    }
-    if (errorSummary.timeoutErrors > 0) {
-      summaryItems.push(`${errorSummary.timeoutErrors} timeout`);
-    }
-    if (errorSummary.serverErrors > 0) {
-      summaryItems.push(`${errorSummary.serverErrors} server`);
-    }
-    if (errorSummary.otherErrors > 0) {
-      summaryItems.push(`${errorSummary.otherErrors} other`);
-    }
-    if (summaryItems.length > 0) {
-      expandableHeader.append("span").style("margin-left", "8px").style("font-size", "12px").style("color", "#666").style("font-weight", "normal").text(`(${summaryItems.join(", ")})`);
-    }
-  }
-  const expandableContent = expandableContainer.append("div").style("display", "none").style("margin-top", "12px").style("padding", "12px").style("background-color", "#fff").style("border", "1px solid #f5c6cb").style("border-radius", "4px").style("box-shadow", "inset 0 1px 3px rgba(0, 0, 0, 0.1)");
-  const tableSection = expandableContent.append("div");
-  tableSection.append("h6").style("margin", "0 0 12px 0").style("color", "#721c24").style("font-size", "14px").style("font-weight", "bold").text("Failed Files Details");
-  const tableContainer = tableSection.append("div").style("max-height", "300px").style("overflow-y", "auto").style("border", "1px solid #dee2e6").style("border-radius", "4px");
-  renderTable({
-    div: tableContainer,
-    columns: failedFilesInfo.tableData.headers.map((header) => ({
-      label: header,
-      sortable: true
-    })),
-    rows: failedFilesInfo.tableData.rows.map((row) => row.map((cell) => ({ value: cell }))),
-    showLines: true,
-    striped: true,
-    showHeader: true,
-    maxHeight: "280px",
-    resize: false,
-    header: {
-      allowSort: true,
-      style: {
-        "background-color": "#f8f9fa",
-        "font-weight": "bold",
-        "border-bottom": "2px solid #dee2e6"
-      }
-    }
-  });
-  expandableContent.append("div").style("margin-top", "12px").style("padding", "8px").style("background-color", "#f8f9fa").style("border-radius", "4px").style("font-size", "12px").style("color", "#495057").style("line-height", "1.4").text("These files could not be downloaded due to network or server issues and were excluded from the analysis.");
-  let isExpanded = false;
-  expandableHeader.on("click", function() {
-    isExpanded = !isExpanded;
-    if (isExpanded) {
-      expandableContent.style("display", "block");
-      expandIcon.style("transform", "rotate(90deg)").text("\u25BC");
-    } else {
-      expandableContent.style("display", "none");
-      expandIcon.style("transform", "rotate(0deg)").text("\u25B6");
-    }
-  });
-}
-function createExpandableDeduplicationSection(container, deduplicationStats) {
-  const duplicatesRemoved = deduplicationStats.duplicatesRemoved || 0;
-  const sizeFilteredCount = deduplicationStats.filteredFiles ? deduplicationStats.filteredFiles.length : 0;
-  const totalExcluded = duplicatesRemoved + sizeFilteredCount;
-  if (totalExcluded === 0) {
-    return;
-  }
-  const expandableContainer = container.append("div").style("margin-top", "8px");
-  const expandableHeader = expandableContainer.append("div").style("display", "flex").style("align-items", "center").style("gap", "8px").style("cursor", "pointer").style("padding", "6px 8px").style("border-radius", "4px").style("transition", "background-color 0.2s").style("background-color", "rgba(216, 67, 21, 0.1)").style("border", "1px solid rgba(216, 67, 21, 0.2)").on("mouseenter", function() {
-    select_default(this).style("background-color", "rgba(216, 67, 21, 0.15)");
-  }).on("mouseleave", function() {
-    select_default(this).style("background-color", "rgba(216, 67, 21, 0.1)");
-  });
-  const expandIcon = expandableHeader.append("span").style("font-size", "12px").style("color", "#d84315").style("transition", "transform 0.2s").text("\u25B6");
-  expandableHeader.append("span").style("color", "#d84315").style("text-decoration", "underline").style("font-size", "12px").style("font-weight", "500").text("View excluded files details");
-  const exclusionDetails = [];
-  if (duplicatesRemoved > 0) {
-    exclusionDetails.push(`${duplicatesRemoved} duplicates`);
-  }
-  if (sizeFilteredCount > 0) {
-    exclusionDetails.push(`${sizeFilteredCount} oversized`);
-  }
-  if (exclusionDetails.length > 0) {
-    expandableHeader.append("span").style("margin-left", "8px").style("font-size", "11px").style("color", "#666").style("font-weight", "normal").text(`(${exclusionDetails.join(", ")})`);
-  }
-  const expandableContent = expandableContainer.append("div").style("display", "none").style("margin-top", "8px").style("padding", "12px").style("background-color", "#fff").style("border", "1px solid rgba(216, 67, 21, 0.3)").style("border-radius", "4px").style("box-shadow", "inset 0 1px 3px rgba(0, 0, 0, 0.1)").style("max-height", "400px").style("overflow-y", "auto");
-  if (deduplicationStats.caseDetails && deduplicationStats.caseDetails.length > 0) {
-    const duplicatesSection = expandableContent.append("div").style("margin-bottom", "16px");
-    duplicatesSection.append("h6").style("margin", "0 0 8px 0").style("color", "#d84315").style("font-size", "13px").style("font-weight", "bold").text("Duplicate Files Removed");
-    duplicatesSection.append("p").style("margin", "0 0 12px 0").style("font-size", "12px").style("color", "#666").text(`${deduplicationStats.duplicatesRemoved} duplicate files were removed (largest file kept for each case)`);
-    const duplicatesCasesContainer = duplicatesSection.append("div").style("display", "grid").style("grid-template-columns", "repeat(auto-fill, minmax(300px, 1fr))").style("gap", "8px");
-    deduplicationStats.caseDetails.forEach((caseInfo) => {
-      const caseDiv = duplicatesCasesContainer.append("div").style("padding", "6px 8px").style("background-color", "#fff3e0").style("border-radius", "3px").style("border-left", "3px solid #ff9800");
-      caseDiv.append("div").style("font-size", "12px").style("color", "#333").style("line-height", "1.3").html(
-        `<strong>Case ${caseInfo.caseName}:</strong> Found ${caseInfo.fileCount} MAF files, keeping largest (${bplen(
-          caseInfo.keptFileSize
-        )})`
-      );
-    });
-  }
-  if (deduplicationStats.filteredFiles && deduplicationStats.filteredFiles.length > 0) {
-    if (deduplicationStats.caseDetails && deduplicationStats.caseDetails.length > 0) {
-      expandableContent.append("hr").style("margin", "12px 0").style("border", "none").style("border-top", "1px solid #e0e0e0");
-    }
-    const sizeFilterSection = expandableContent.append("div");
-    sizeFilterSection.append("h6").style("margin", "0 0 8px 0").style("color", "#c62828").style("font-size", "13px").style("font-weight", "bold").text("Files Excluded by Size");
-    sizeFilterSection.append("p").style("margin", "0 0 12px 0").style("font-size", "12px").style("color", "#666").text(`${deduplicationStats.filteredFiles.length} files were excluded for being too large (>${bplen(1e6)})`);
-    const oversizedFilesContainer = sizeFilterSection.append("div").style("display", "grid").style("grid-template-columns", "repeat(auto-fill, minmax(280px, 1fr))").style("gap", "8px");
-    deduplicationStats.filteredFiles.forEach((fileInfo) => {
-      const fileDiv = oversizedFilesContainer.append("div").style("padding", "6px 8px").style("background-color", "#ffebee").style("border-radius", "3px").style("border-left", "3px solid #f44336");
-      fileDiv.append("div").style("font-size", "11px").style("color", "#333").style("margin-bottom", "2px").style("line-height", "1.2").html(`<strong>File ID:</strong> ${fileInfo.fileId}`);
-      fileDiv.append("div").style("font-size", "10px").style("color", "#666").style("line-height", "1.2").text(`Size: ${bplen(fileInfo.fileSize)} - ${fileInfo.reason}`);
-    });
-  }
-  expandableContent.append("div").style("margin-top", "12px").style("padding", "6px 8px").style("background-color", "#f8f9fa").style("border-radius", "4px").style("font-size", "11px").style("color", "#495057").style("line-height", "1.3").text("Files are filtered to ensure optimal performance and avoid duplicates.");
-  let isExpanded = false;
-  expandableHeader.on("click", function() {
-    isExpanded = !isExpanded;
-    if (isExpanded) {
-      expandableContent.style("display", "block");
-      expandIcon.style("transform", "rotate(90deg)").text("\u25BC");
-    } else {
-      expandableContent.style("display", "none");
-      expandIcon.style("transform", "rotate(0deg)").text("\u25B6");
-    }
-  });
-}
-function updateDedupStatus(obj, deduplicationStats) {
-  if (!obj.dedupStatusElement) return;
-  const dedupElement = obj.dedupStatusElement;
-  dedupElement.selectAll("*").remove();
-  if (!deduplicationStats) {
-    dedupElement.style("color", "#666").text("No deduplication data available");
-    return;
-  }
-  const dedupContainer = dedupElement.append("div").style("display", "flex").style("flex-direction", "column").style("gap", "6px");
-  const duplicatesRemoved = deduplicationStats.duplicatesRemoved || 0;
-  const sizeFilteredCount = deduplicationStats.filteredFiles ? deduplicationStats.filteredFiles.length : 0;
-  const totalExcluded = duplicatesRemoved + sizeFilteredCount;
-  const originalTotal = deduplicationStats.originalFileCount + sizeFilteredCount;
-  if (totalExcluded > 0) {
-    const summaryDiv = dedupContainer.append("div").style("font-size", "14px").style("color", "#d84315").style("font-weight", "500");
-    summaryDiv.html(
-      `Found <strong>${originalTotal}</strong> total MAF files, excluded <strong>${totalExcluded}</strong>`
-    );
-    const resultDiv = dedupContainer.append("div").style("font-size", "13px").style("color", "#28a745").style("font-weight", "500");
-    resultDiv.html(`Showing <strong>${deduplicationStats.deduplicatedFileCount}</strong> unique cases`);
-    if (duplicatesRemoved > 0) {
-      resultDiv.append("span").style("color", "#666").style("font-weight", "normal").text(" (largest file per case)");
-    }
-    createExpandableDeduplicationSection(dedupContainer, deduplicationStats);
-  } else {
-    dedupContainer.append("div").style("color", "#28a745").style("font-weight", "500").style("font-size", "14px").html(`All <strong>${deduplicationStats.deduplicatedFileCount}</strong> files included`);
-    dedupContainer.append("div").style("color", "#666").style("font-size", "13px").text("No duplicates or oversized files found");
-  }
-}
-function createMAFOptionsContent(container, obj) {
-  container.selectAll("*").remove();
-  const optionsGrid = container.append("div");
-  applyStyles(optionsGrid, STYLES.gridTwoColumn);
-  optionsGrid.style("margin-top", "10px");
-  createNumberInput(optionsGrid, {
-    label: "Min Total Depth:",
-    value: obj.mafOptions.minTotalDepth || 10,
-    min: 0,
-    step: 1,
-    width: "80px",
-    labelWidth: "140px",
-    onChange: (value) => {
-      if (value >= 0) obj.mafOptions.minTotalDepth = value;
-    }
-  });
-  createNumberInput(optionsGrid, {
-    label: "Min Mutant Allele Count:",
-    value: obj.mafOptions.minAltAlleleCount || 2,
-    min: 0,
-    step: 1,
-    width: "80px",
-    labelWidth: "160px",
-    onChange: (value) => {
-      if (value >= 0) obj.mafOptions.minAltAlleleCount = value;
-    }
-  });
-  createConsequencesSection(optionsGrid, obj);
-  createNumberInput(optionsGrid, {
-    label: "Hypermutator Max Cut Off:",
-    value: obj.mafOptions.hyperMutator || 8e3,
-    min: 0,
-    step: 100,
-    width: "70px",
-    labelWidth: "160px",
-    onChange: (value) => {
-      if (value >= 0) obj.mafOptions.hyperMutator = value;
-    }
-  });
-  createWorkflowSection(optionsGrid);
-  createDeduplicationSection(optionsGrid, obj);
-}
-function createConsequencesSection(optionsGrid, obj) {
-  const consequencesContainer = optionsGrid.append("div").style("display", "flex").style("align-items", "flex-start").style("gap", "8px").style("grid-column", "1 / -1");
-  consequencesContainer.append("label").style("font-size", "14px").style("font-weight", "500").style("min-width", "100px").style("margin-top", "4px").text("Consequences:");
-  const selectionDiv = consequencesContainer.append("div").style("flex", "1");
-  const checkboxContainer = selectionDiv.append("div").style("display", "grid").style("grid-template-columns", "repeat(auto-fit, minmax(200px, 1fr))").style("gap", "8px").style("margin-bottom", "12px");
-  createMutationClassCheckboxes(checkboxContainer, obj);
-  createInfoPanel(selectionDiv, {
-    title: "Mutation Types:",
-    content: `Select the types of mutations to include in your analysis.
-              High-impact mutations (missense, nonsense, frameshift) are selected by default.
-              Silent/synonymous mutations are excluded by default as they don't change protein sequence.`
-  });
-}
-function createMutationClassCheckboxes(container, obj) {
-  const seenLabels = /* @__PURE__ */ new Set();
-  for (const cls in mclass) {
-    if (mclass[cls].dt !== dtsnvindel) continue;
-    if (skipMAFclasses.includes(cls)) continue;
-    const labelText = mclass[cls].label;
-    if (seenLabels.has(labelText)) continue;
-    seenLabels.add(labelText);
-    const isDefaultChecked = defaultCheckedClasses.includes(cls);
-    const checkboxDiv = container.append("div");
-    make_one_checkbox({
-      holder: checkboxDiv,
-      labeltext: labelText,
-      checked: isDefaultChecked,
-      id: `consequence-${cls}`,
-      divstyle: {
-        "font-size": "13px",
-        margin: "0"
-      },
-      callback: async (isChecked) => {
-        if (isChecked) {
-          if (!obj.mafOptions.consequences.includes(cls)) {
-            obj.mafOptions.consequences.push(cls);
-          }
-        } else {
-          obj.mafOptions.consequences = obj.mafOptions.consequences.filter((c) => c !== cls);
-        }
-      }
-    });
-    checkboxDiv.select("label").attr("title", mclass[cls].desc);
-    if (isDefaultChecked && !obj.mafOptions.consequences.includes(cls)) {
-      obj.mafOptions.consequences.push(cls);
-    }
-  }
-}
-function createWorkflowSection(optionsGrid) {
-  const workflowContainer = optionsGrid.append("div");
-  applyStyles(workflowContainer, STYLES.flexRow);
-  workflowContainer.style("grid-column", "1 / -1");
-  const label = workflowContainer.append("label");
-  applyStyles(label, STYLES.label);
-  label.style("min-width", "100px").text("Workflow Type:");
-  workflowContainer.append("span").style("font-size", "14px").style("color", "#666").text("Aliquot Ensemble Somatic Variant Merging and Masking");
-}
-function createDeduplicationSection(optionsGrid, obj) {
-  const dedupContainer = optionsGrid.append("div");
-  applyStyles(dedupContainer, STYLES.flexRow);
-  dedupContainer.style("grid-column", "1 / -1");
-  const label = dedupContainer.append("label");
-  applyStyles(label, STYLES.label);
-  label.style("min-width", "100px").text("Deduplication:");
-  const dedupStatus = dedupContainer.append("span").attr("id", "dedup-status").style("font-size", "14px").style("color", "#666");
-  obj.dedupStatusElement = dedupStatus;
-}
-function createCNVOptionsContent(container, obj) {
-  container.selectAll("*").remove();
-  if (!obj.cnvOptions.dataType) {
-    obj.cnvOptions.dataType = "segment_mean";
-  }
-  const optionsGrid = container.append("div");
-  applyStyles(optionsGrid, STYLES.gridTwoColumn);
-  optionsGrid.style("margin-top", "10px");
-  createDataTypeRadioSection(optionsGrid, obj);
-  createNumberInput(optionsGrid, {
-    label: "Loss Threshold:",
-    value: obj.cnvOptions.lossThreshold || -0.4,
-    min: -10,
-    max: 0,
-    step: 0.1,
-    width: "70px",
-    labelWidth: "120px",
-    onChange: (value) => {
-      if (value <= 0) obj.cnvOptions.lossThreshold = value;
-    }
-  });
-  createNumberInput(optionsGrid, {
-    label: "Gain Threshold:",
-    value: obj.cnvOptions.gainThreshold || 0.3,
-    min: 0,
-    max: 10,
-    step: 0.1,
-    width: "70px",
-    labelWidth: "120px",
-    onChange: (value) => {
-      if (value >= 0) obj.cnvOptions.gainThreshold = value;
-    }
-  });
-  createNumberInput(optionsGrid, {
-    label: "Hypermutator Max Cut Off:",
-    value: obj.cnvOptions.hyperMutator || 500,
-    min: 0,
-    step: 100,
-    width: "70px",
-    labelWidth: "160px",
-    onChange: (value) => {
-      if (value >= 0) obj.cnvOptions.hyperMutator = value;
-    }
-  });
-  createSegmentLengthSection(optionsGrid, obj);
-  createCNVHelpSection(optionsGrid);
-}
-function createDataTypeRadioSection(optionsGrid, obj) {
-  const dataTypeContainer = optionsGrid.append("div");
-  applyStyles(dataTypeContainer, STYLES.flexRow);
-  dataTypeContainer.style("grid-column", "1 / -1");
-  const label = dataTypeContainer.append("label");
-  applyStyles(label, STYLES.label);
-  label.style("min-width", "80px").text("Data Type:");
-  const radioContainer = dataTypeContainer.append("div");
-  applyStyles(radioContainer, STYLES.flexRow);
-  radioContainer.style("gap", "6px");
-  const radio = radioContainer.append("input").attr("type", "radio").attr("id", "cnv-segment-mean").attr("name", "cnv-data-type").attr("value", "segment_mean").property("checked", obj.cnvOptions.dataType === "segment_mean").style("margin", "0").style("cursor", "pointer");
-  radioContainer.append("label").attr("for", "cnv-segment-mean").style("cursor", "pointer").style("font-size", "14px").style("color", "#333").text("Segment mean");
-  radio.on("change", function() {
-    if (this.checked) {
-      obj.cnvOptions.dataType = this.value;
-    }
-  });
-}
-function createSegmentLengthSection(optionsGrid, obj) {
-  const segmentContainer = optionsGrid.append("div");
-  applyStyles(segmentContainer, STYLES.flexRow);
-  segmentContainer.style("grid-column", "1 / -1");
-  const label = segmentContainer.append("label");
-  applyStyles(label, STYLES.label);
-  label.style("min-width", "140px").text("Segment Length Cutoff:");
-  const input = segmentContainer.append("input").attr("type", "number").attr("min", "0").attr("max", "2000000").attr("step", "1000").attr("value", obj.cnvOptions.segLength || 0);
-  applyStyles(input, STYLES.numberInput);
-  input.style("width", "100px");
-  segmentContainer.append("span").style("font-size", "13px").style("color", "#666").text("bp");
-  input.on("input", function() {
-    const value = parseInt(this.value, 10);
-    if (!isNaN(value) && value >= 0) {
-      obj.cnvOptions.segLength = value;
-    }
-  });
-}
-function createCNVHelpSection(optionsGrid) {
-  const helpContainer = optionsGrid.append("div").style("grid-column", "1 / -1").style("margin-top", "8px");
-  createInfoPanel(helpContainer, {
-    title: "CNV Options:",
-    content: `\u2022 Loss Threshold: Log2 ratio for copy number loss (negative values)<br>
-              \u2022 Gain Threshold: Log2 ratio for copy number gain (positive values)<br>
-              \u2022 Hypermutator Max Cut Off: Maximum number of CNVs per case<br>
-              \u2022 Segment Length: Maximum CNV segment size to include (no filter if 0)`
-  });
-}
-function makeControls(obj) {
-  if (!obj.mafOptions) {
-    obj.mafOptions = {
-      minTotalDepth: 10,
-      minAltAlleleCount: 2,
-      consequences: [],
-      hyperMutator: 8e3
-    };
-  }
-  if (!obj.cnvOptions) {
-    obj.cnvOptions = {
-      lossThreshold: -0.4,
-      gainThreshold: 0.3,
-      segLength: 0,
-      hyperMutator: 500
-    };
-  }
-  obj.dataTypeStates = {
-    maf: true,
-    cnv: true,
-    fusion: false
-  };
-  const optionsTable = createOptionsTable(obj.controlDiv);
-  createTableHeader(optionsTable, ["Data Type", "Options"]);
-  const mafRow = createDataTypeRow(optionsTable, {
-    id: "maf-checkbox",
-    label: "MAF (Mutation)",
-    checked: true,
-    onChange: (isChecked) => {
-      obj.dataTypeStates.maf = isChecked;
-      mafRow.optionsContainer.style("display", isChecked ? "block" : "none");
-      obj.updateSubmitButtonState?.();
-    },
-    createOptionsContent: (container) => createMAFOptionsContent(container, obj)
-  });
-  const cnvRow = createDataTypeRow(optionsTable, {
-    id: "cnv-checkbox",
-    label: "CNV (Copy Number)",
-    checked: true,
-    onChange: (isChecked) => {
-      obj.dataTypeStates.cnv = isChecked;
-      cnvRow.optionsContainer.style("display", isChecked ? "block" : "none");
-      if (isChecked) {
-        createCNVOptionsContent(cnvRow.optionsContainer, obj);
-      }
-      obj.updateSubmitButtonState?.();
-    },
-    createOptionsContent: (container) => createCNVOptionsContent(container, obj)
-  });
-  const fusionRow = createDataTypeRow(optionsTable, {
-    id: "fusion-checkbox",
-    label: "Fusion",
-    checked: false,
-    onChange: (isChecked) => {
-      obj.dataTypeStates.fusion = isChecked;
-      fusionRow.optionsContainer.style("display", isChecked ? "block" : "none");
-      obj.updateSubmitButtonState?.();
-    },
-    createOptionsContent: (container) => {
-      container.append("div").style("color", "#666").style("font-style", "italic").text("Please login to access RNA fusion data.");
-    }
-  });
-  createGRIN2InfoRow(optionsTable);
-  createSubmitButton(obj);
-  obj.mafOptionsContainer = mafRow.optionsContainer;
-  obj.cnvOptionsContainer = cnvRow.optionsContainer;
-  obj.fusionOptionsContainer = fusionRow.optionsContainer;
-}
-function createGRIN2InfoRow(optionsTable) {
-  const grin2Row = optionsTable.append("tr");
-  const labelCell = grin2Row.append("td");
-  applyStyles(labelCell, STYLES.tableCell);
-  labelCell.append("div").style("font-weight", "500").style("color", "#333").text("GRIN2 Analysis");
-  const optionsCell = grin2Row.append("td");
-  applyStyles(optionsCell, STYLES.tableCell);
-  optionsCell.append("div").style("color", "#666").text("GRIN2 analysis options will be configured here");
-}
-function createSubmitButton(obj) {
-  const submitButtonContainer = obj.controlDiv.append("div").style("margin-top", "2px").style("margin-bottom", "2px").style("text-align", "left");
-  const submitButton = submitButtonContainer.append("button").attr("id", "submit-options-button").style("margin", "10px 10px 0 0").text("Apply Options & Refresh Files");
-  obj.submitButton = submitButton;
-  submitButton.on("click", function() {
-    if (!this.disabled) {
-      getFilesAndShowTable(obj);
-    }
-  });
-  obj.updateSubmitButtonState = function() {
-    const hasAnyDataTypeSelected = obj.dataTypeStates.maf || obj.dataTypeStates.cnv || obj.dataTypeStates.fusion;
-    if (hasAnyDataTypeSelected) {
-      submitButton.attr("disabled", null).text("Apply Options & Refresh Files");
-    } else {
-      submitButton.attr("disabled", true).text("Select at least one data type");
-    }
-  };
-  obj.updateSubmitButtonState();
-}
-async function getFilesAndShowTable(obj) {
-  obj.tableDiv.selectAll("*").remove();
-  obj.resultDiv.selectAll("*").remove();
-  const wait = obj.tableDiv.append("div").style("margin", "30px 10px 10px 10px").text("Loading...");
-  let result;
-  try {
-    const body = {};
-    if (obj.opts.filter0) body.filter0 = obj.opts.filter0;
-    if (obj.dataTypeStates.maf) {
-      body.mafOptions = {
-        experimentalStrategy: obj.opts.experimentalStrategy || "WXS"
-      };
-    }
-    if (obj.dataTypeStates.cnv) {
-      body.cnvOptions = {
-        dataType: obj.cnvOptions.dataType
-      };
-    }
-    console.log("Request body for GRIN2list:", body);
-    result = await dofetch3("gdc/GRIN2list", { body });
-    console.log("GRIN2list result:", result);
-    if (result.error) throw result.error;
-    if (obj.dataTypeStates.maf && (!result.mafFiles || !Array.isArray(result.mafFiles.files))) {
-      throw "Invalid response: missing mafFiles.files array";
-    }
-    if (obj.dataTypeStates.cnv && (!result.cnvFiles || !Array.isArray(result.cnvFiles.files))) {
-      throw "Invalid response: missing cnvFiles.files array";
-    }
-    const hasMafFiles = result.mafFiles?.files?.length > 0;
-    const hasCnvFiles = result.cnvFiles?.files?.length > 0;
-    if (obj.dataTypeStates.maf && !hasMafFiles) {
-      throw "No MAF files available for the selected criteria.";
-    }
-    if (obj.dataTypeStates.cnv && !hasCnvFiles) {
-      throw "No CNV files available for the selected criteria.";
-    }
-    if (!hasMafFiles && !hasCnvFiles) {
-      throw "No files available for the selected data types.";
-    }
-    if (result.mafFiles && result.mafFiles.deduplicationStats) {
-      updateDedupStatus(obj, result.mafFiles.deduplicationStats);
-    }
-    const cnvFilesByCase = /* @__PURE__ */ new Map();
-    if (obj.dataTypeStates.cnv && result.cnvFiles && result.cnvFiles.files) {
-      for (const cnvFile of result.cnvFiles.files) {
-        const caseId = cnvFile.case_submitter_id;
-        if (!cnvFilesByCase.has(caseId)) {
-          cnvFilesByCase.set(caseId, cnvFile);
-        }
-      }
-    }
-    let filteredFiles = result.mafFiles ? result.mafFiles.files : [];
-    let filteringMessage = "";
-    const mafSelected = obj.dataTypeStates.maf;
-    const cnvSelected = obj.dataTypeStates.cnv;
-    if (mafSelected && cnvSelected) {
-      const originalCount = filteredFiles.length;
-      filteredFiles = filteredFiles.filter((mafFile) => {
-        const caseId = mafFile.case_submitter_id;
-        const hasCnv = cnvFilesByCase.has(caseId);
-        return hasCnv;
-      });
-      const filteredCount = filteredFiles.length;
-      const excludedCount = originalCount - filteredCount;
-      if (excludedCount > 0) {
-        filteringMessage = `Filtered to ${filteredCount} cases with both MAF and CNV files (excluded ${excludedCount} cases with only MAF files)`;
-      } else {
-        filteringMessage = `All ${filteredCount} cases have both MAF and CNV files`;
-      }
-    } else if (cnvSelected && !mafSelected) {
-      const originalCount = filteredFiles.length;
-      filteredFiles = result.cnvFiles ? result.cnvFiles.files : [];
-      const filteredCount = filteredFiles.length;
-      const excludedCount = originalCount - filteredCount;
-      if (excludedCount > 0) {
-        filteringMessage = `Filtered to ${filteredCount} cases with CNV files (excluded ${excludedCount} cases without CNV files)`;
-      }
-    } else if (mafSelected && !cnvSelected) {
-      filteringMessage = `Showing ${filteredFiles.length} cases with MAF files`;
-    }
-    if (filteredFiles.length === 0) {
-      throw "No files match the selected data type criteria. Try adjusting your data type selections.";
-    }
-    const mafFiles = result.mafFiles ? result.mafFiles.files : [];
-    const cnvFiles = result.cnvFiles ? result.cnvFiles.files : [];
-    const mafTotal = result.mafFiles ? result.mafFiles.filesTotal : 0;
-    let statusMessage = "";
-    if (mafSelected && cnvSelected) {
-      if (mafTotal > mafFiles.length) {
-        statusMessage = `Showing first ${mafFiles.length.toLocaleString()} files out of ${mafTotal.toLocaleString()} total.`;
-      } else {
-        statusMessage = `Showing ${filteredFiles.length.toLocaleString()} files.`;
-      }
-    } else if (mafSelected && !cnvSelected) {
-      if (mafTotal > mafFiles.length) {
-        statusMessage = `Showing first ${mafFiles.length.toLocaleString()} MAF files out of ${mafTotal.toLocaleString()} total.`;
-      } else {
-        statusMessage = `Showing ${filteredFiles.length.toLocaleString()} MAF files.`;
-      }
-    } else if (!mafSelected && cnvSelected) {
-      statusMessage = `Showing ${cnvFiles.length.toLocaleString()} CNV files.`;
-    }
-    wait.html(`
-			${statusMessage}<br>
-			${filteringMessage ? `<span style="color: #666; font-style: italic;">${filteringMessage}</span>` : ""}
-		`);
-    const dynamicTableColumns = [
-      { label: "Case", sortable: true },
-      { label: "Project", sortable: true }
-    ];
-    if (obj.dataTypeStates.maf) {
-      dynamicTableColumns.push({ label: "MAF Sample", sortable: false }, {
-        label: "MAF File Size",
-        barplot: { tickFormat: "~s" },
-        sortable: true
-      });
-    }
-    if (obj.dataTypeStates.cnv) {
-      dynamicTableColumns.push({ label: "CNV File ID", sortable: true }, { label: "CNV Sample", sortable: false }, {
-        label: "CNV File Size",
-        barplot: { tickFormat: "~s" },
-        sortable: true
-      });
-    }
-    if (obj.dataTypeStates.fusion) {
-      dynamicTableColumns.push(
-        { label: "Fusion File ID", sortable: true },
-        { label: "Fusion Sample", sortable: false },
-        { label: "Fusion File Size", barplot: { tickFormat: "~s" }, sortable: true }
-      );
-    }
-    const rows = [];
-    for (const f of filteredFiles) {
-      const row = [];
-      row.push(
-        {
-          html: `<a href=https://portal.gdc.cancer.gov/files/${f.id} target=_blank>${f.case_submitter_id}</a>`,
-          value: f.case_submitter_id
-        },
-        { value: f.project_id }
-      );
-      if (obj.dataTypeStates.maf) {
-        row.push(
-          {
-            html: f.sample_types.map((i) => {
-              return '<span class="sja_mcdot" style="padding:1px 8px;background:#ddd;color:black;white-space:nowrap">' + i + "</span>";
-            }).join(" ")
-          },
-          { value: f.file_size }
-        );
-      }
-      if (obj.dataTypeStates.cnv) {
-        const cnvFile = cnvFilesByCase.get(f.case_submitter_id);
-        if (cnvSelected && !cnvFile) {
-          console.warn(`Expected CNV file for case ${f.case_submitter_id} but not found`);
-        }
-        row.push(
-          {
-            html: cnvFile ? `<a href=https://portal.gdc.cancer.gov/files/${cnvFile.id} target=_blank>${cnvFile.id}</a>` : '<span style="color: #dc3545; font-weight: 500;">Missing CNV file</span>',
-            value: cnvFile ? cnvFile.id : "Missing CNV file"
-          },
-          {
-            html: cnvFile && cnvFile.sample_types ? cnvFile.sample_types.map((i) => {
-              return '<span class="sja_mcdot" style="padding:1px 8px;background:#ddd;color:black;white-space:nowrap">' + i + "</span>";
-            }).join(" ") : '<span style="color: #dc3545;">No CNV sample</span>',
-            value: cnvFile && cnvFile.sample_types ? cnvFile.sample_types.join(" ") : "No CNV sample"
-          },
-          {
-            value: cnvFile ? cnvFile.file_size : 0
-          }
-        );
-      }
-      if (obj.dataTypeStates.fusion) {
-        row.push(
-          { html: '<span style="color: #6c757d;">No Fusion file</span>', value: "No Fusion file" },
-          { html: '<span style="color: #6c757d;">No Fusion sample</span>', value: "No Fusion sample" },
-          { value: 0 }
-        );
-      }
-      rows.push(row);
-    }
-    obj.mafTableArg = {
-      rows,
-      columns: dynamicTableColumns,
-      resize: false,
-      div: obj.tableDiv.append("div"),
-      selectAll: true,
-      dataTestId: "sja_FileTable",
-      header: { allowSort: true },
-      selectedRows: [],
-      buttons: [
-        {
-          text: "Run GRIN2 Analysis",
-          onChange: (lst, button) => updateButtonBySelectionChange(lst, button, filteredFiles),
-          callback: (lst, button) => runGRIN2Analysis(lst, button, obj, filteredFiles)
-        }
-      ]
-    };
-    renderTable(obj.mafTableArg);
-  } catch (e) {
-    wait.text(e instanceof Error ? e.message : String(e));
-    if (e instanceof Error && e.stack) console.log(e.stack);
-  }
-  function updateButtonBySelectionChange(lst, button, filteredFiles) {
-    if (obj.busy) {
-      button.property("disabled", true);
-      return;
-    }
-    let sum = 0;
-    for (const i of lst) sum += filteredFiles[i].file_size;
-    if (sum == 0) {
-      button.innerHTML = "No file selected";
-      button.disabled = true;
-      return;
-    }
-    select_default(button.parentElement).style("float", "left");
-    button.disabled = false;
-    const mafMaxSize = result.mafFiles ? result.mafFiles.maxTotalSizeCompressed : Infinity;
-    const cnvMaxSize = result.cnvFiles ? result.cnvFiles.maxTotalSizeCompressed : Infinity;
-    const maxSize = Math.min(mafMaxSize, cnvMaxSize);
-    button.innerHTML = sum < maxSize ? `Run GRIN2 Analysis` : `Run GRIN2 Analysis (Large Files)`;
-  }
-  async function runGRIN2Analysis(lst, button, obj2, filteredFiles = result.files) {
-    const mafSelected = obj2.dataTypeStates.maf;
-    const cnvSelected = obj2.dataTypeStates.cnv;
-    const caseFiles = {
-      caseFiles: {}
-    };
-    if (mafSelected) {
-      const soTerms = [];
-      for (const mclassCode of obj2.mafOptions.consequences) {
-        const soTermsForCode = class2SOterm.get(mclassCode) || [];
-        soTerms.push(...soTermsForCode);
-      }
-      caseFiles.mafOptions = {
-        minTotalDepth: obj2.mafOptions.minTotalDepth,
-        minAltAlleleCount: obj2.mafOptions.minAltAlleleCount,
-        consequences: soTerms,
-        hyperMutator: obj2.mafOptions.hyperMutator
-      };
-    }
-    if (cnvSelected) {
-      caseFiles.cnvOptions = {
-        dataType: obj2.cnvOptions.dataType,
-        lossThreshold: obj2.cnvOptions.lossThreshold,
-        gainThreshold: obj2.cnvOptions.gainThreshold,
-        segLength: obj2.cnvOptions.segLength,
-        hyperMutator: obj2.cnvOptions.hyperMutator
-      };
-    }
-    const cnvFilesByCase = /* @__PURE__ */ new Map();
-    if (result.cnvFiles && result.cnvFiles.files) {
-      for (const cnvFile of result.cnvFiles.files) {
-        const caseId = cnvFile.case_submitter_id;
-        if (!cnvFilesByCase.has(caseId)) {
-          cnvFilesByCase.set(caseId, cnvFile);
-        }
-      }
-    }
-    for (const i of lst) {
-      const file = filteredFiles[i];
-      const caseId = file.case_submitter_id;
-      if (!caseFiles.caseFiles[caseId]) {
-        caseFiles.caseFiles[caseId] = {};
-      }
-      const mafSelected2 = obj2.dataTypeStates.maf;
-      const cnvSelected2 = obj2.dataTypeStates.cnv;
-      if (mafSelected2) {
-        caseFiles.caseFiles[caseId].maf = file.id;
-      }
-      if (cnvSelected2) {
-        const cnvFile = cnvFilesByCase.get(caseId);
-        if (cnvFile) {
-          caseFiles.caseFiles[caseId].cnv = cnvFile.id;
-        }
-      }
-    }
-    if (Object.keys(caseFiles.caseFiles).length === 0) return;
-    const oldText = button.innerHTML;
-    button.innerHTML = "Analyzing... Please wait";
-    button.disabled = true;
-    if (obj2.downloadButtonDiv) {
-      obj2.downloadButtonDiv.selectAll("*").remove();
-      obj2.downloadButtonDiv.style("display", "none");
-    }
-    obj2.resultDiv.selectAll("*").remove();
-    try {
-      obj2.busy = true;
-      const response = await dofetch3("gdc/runGRIN2", { body: caseFiles });
-      if (!response) throw "invalid response";
-      if (response.error) throw response.error;
-      console.log("GRIN2 response:", response);
-      if (response.rustResult) {
-      } else {
-        console.log("[GRIN2] No rustResult in response");
-      }
-      const rustData = response.rustResult;
-      let failedFilesInfo = null;
-      let parsedRustResult;
-      let processedData = [];
-      try {
-        parsedRustResult = typeof rustData === "string" ? JSON.parse(rustData) : rustData;
-        if (parsedRustResult) {
-          if (parsedRustResult.successful_data && parsedRustResult.summary) {
-            processedData = parsedRustResult.successful_data;
-            console.log(`[GRIN2] parsedRustResult structure:`, parsedRustResult);
-            if (parsedRustResult.failed_files && parsedRustResult.failed_files.length > 0) {
-              failedFilesInfo = {
-                count: parsedRustResult.failed_files.length,
-                files: parsedRustResult.failed_files,
-                // Create table data for UI display (similar to your deduplication/filter tables)
-                tableData: {
-                  headers: ["Case ID", "Data Type", "Error Type", "Error Details", "Attempts"],
-                  rows: parsedRustResult.failed_files.map((file) => [
-                    file.case_id,
-                    file.data_type,
-                    file.error_type,
-                    file.error_details,
-                    file.attempts_made.toString()
-                  ])
-                },
-                // Error summary for the popup
-                errorSummary: {
-                  connectionErrors: parsedRustResult.failed_files.filter((f) => f.error_type === "connection_error").length,
-                  timeoutErrors: parsedRustResult.failed_files.filter((f) => f.error_type === "timeout_error").length,
-                  serverErrors: parsedRustResult.failed_files.filter((f) => f.error_type === "server_error").length,
-                  otherErrors: parsedRustResult.failed_files.filter(
-                    (f) => !["connection_error", "timeout_error", "server_error"].includes(f.error_type)
-                  ).length
-                }
-              };
-            }
-          }
-          console.log(`[GRIN2] Final processed data contains ${processedData.length.toLocaleString()} characters`);
-        }
-      } catch (parseError) {
-        console.error("[GRIN2] Error parsing Rust result:", parseError);
-        processedData = [];
-        failedFilesInfo = null;
-      }
-      if (!response.resultData.png) throw "png missing";
-      const resultContainer = obj2.resultDiv.append("div").style("text-align", "left").style("margin", "0 auto").style("margin-top", "40px");
-      const plotData = response.resultData;
-      const plotDiv = resultContainer.append("div");
-      plotManhattanGDC(plotDiv, plotData, { yAxisSpace: 0 });
-      resultContainer.node().onerror = () => {
-        resultContainer.select("img").remove();
-        sayerror(resultContainer, "Failed to load image result.");
-      };
-      if (response.topGeneTable && response.topGeneTable.rows && response.topGeneTable.rows.length > 0) {
-        const tableTitle = resultContainer.append("h4").style("margin-bottom", "15px").style("text-align", "left");
-        if (response.totalGenes && response.showingTop) {
-          tableTitle.text(`Top ${response.showingTop} Genes`);
-          resultContainer.append("p").html(
-            `Showing top <strong>${response.showingTop}</strong> genes out of <strong>${response.totalGenes.toLocaleString()}</strong> total genes analyzed.`
-          ).style("color", "#495057").style("font-size", "14px").style("margin", "10px 0 20px 0");
-        } else {
-          tableTitle.text("Top Genes");
-          resultContainer.append("p").style("color", "#495057").style("font-size", "14px").style("margin", "10px 0 20px 0");
-        }
-        const tableContainer = resultContainer.append("div").style("margin-bottom", "20px").style("display", "flex").style("flex", "2");
-        const statsContainer = resultContainer.append("div").style("flex", "1").style("min-width", "250px").style("max-width", "350px");
-        const transformedRows = transformRows(response.topGeneTable.rows, response.topGeneTable.columns);
-        renderTable({
-          div: tableContainer,
-          rows: transformedRows,
-          columns: response.topGeneTable.columns,
-          showLines: true,
-          striped: true,
-          showHeader: true,
-          maxHeight: "500px",
-          maxWidth: "100%",
-          resize: false,
-          header: {
-            allowSort: true,
-            style: {
-              "background-color": "#f8f9fa",
-              "font-weight": "bold",
-              "border-bottom": "2px solid #dee2e6"
-            }
-          },
-          download: {
-            // Enable table download functionality
-            fileName: `GRIN2_TopGenes.tsv`
-          }
-        });
-        if (parsedRustResult?.summary) {
-          const statsPanel = statsContainer.append("div").style("background-color", "#f8f9fa").style("border", "1px solid #dee2e6").style("border-radius", "8px").style("padding", "20px").style("box-shadow", "0 2px 4px rgba(0,0,0,0.1)");
-          statsPanel.append("h5").text("Analysis Summary").style("margin", "0 0 15px 0").style("color", "#343a40").style("font-weight", "bold").style("border-bottom", "2px solid #dee2e6").style("padding-bottom", "8px");
-          if (parsedRustResult && parsedRustResult.summary) {
-            const downloadStats = statsPanel.append("div").style("margin-bottom", "20px");
-            downloadStats.append("h6").text("File Download & Processing").style("margin", "0 0 10px 0").style("color", "#495057").style("font-size", "14px").style("font-weight", "bold");
-            const downloadStatsGrid = downloadStats.append("div").style("display", "grid").style("grid-template-columns", "1fr 1fr").style("gap", "8px").style("font-size", "13px");
-            const totalAttempted = parsedRustResult.summary.total_files;
-            const successful = parsedRustResult.summary.successful_files;
-            const failed = parsedRustResult.summary.failed_files;
-            downloadStatsGrid.append("div").style("color", "#6c757d").text("Total Attempted:");
-            downloadStatsGrid.append("div").style("font-weight", "bold").text(totalAttempted || 0);
-            downloadStatsGrid.append("div").style("color", "#28a745").text("Successfully Downloaded:");
-            downloadStatsGrid.append("div").style("font-weight", "bold").style("color", "#28a745").text(successful || 0);
-            downloadStatsGrid.append("div").style("color", "#dc3545").text("Failed Downloads:");
-            downloadStatsGrid.append("div").style("font-weight", "bold").style("color", "#dc3545").text(failed || 0);
-            if (failedFilesInfo && failedFilesInfo.count > 0) {
-              addExpandableFailedFilesToStats(downloadStats, failedFilesInfo);
-            }
-          }
-          if (response.timing) {
-            const timingStats = statsPanel.append("div").style("margin-bottom", "20px");
-            timingStats.append("h6").text("Timings").style("margin", "0 0 10px 0").style("color", "#495057").style("font-size", "14px").style("font-weight", "bold");
-            const timingStatsGrid = timingStats.append("div").style("display", "grid").style("grid-template-columns", "1fr 1fr").style("gap", "8px").style("font-size", "13px");
-            if (response.timing.rustProcessingTime !== void 0) {
-              timingStatsGrid.append("div").style("color", "#6c757d").text("GDC API Data Query and Parsing (s):");
-              timingStatsGrid.append("div").style("font-weight", "bold").style("color", "black").text(response.timing.rustProcessingTime);
-            }
-            if (response.timing.grin2ProcessingTime !== void 0) {
-              timingStatsGrid.append("div").style("color", "#6c757d").text("GRIN2 Analysis (s):");
-              timingStatsGrid.append("div").style("font-weight", "bold").style("color", "black").text(response.timing.grin2ProcessingTime);
-            }
-            if (response.timing.totalTime !== void 0) {
-              timingStatsGrid.append("div").style("color", "#6c757d").text("Total Processing Time (s):");
-              timingStatsGrid.append("div").style("font-weight", "bold").style("color", "black").text(response.timing.totalTime);
-            }
-          }
-          if (response.rustResult.summary && (response.rustResult.summary.filtered_records !== void 0 || response.rustResult.summary.filtered_maf_records !== void 0 || response.rustResult.summary.filtered_cnv_records !== void 0)) {
-            const filterStats = statsPanel.append("div").style("margin-bottom", "20px");
-            filterStats.append("h6").text("Data Filtering").style("margin", "0 0 10px 0").style("color", "#495057").style("font-size", "14px").style("font-weight", "bold");
-            const filterStatsGrid = filterStats.append("div").style("display", "grid").style("grid-template-columns", "1fr 1fr").style("gap", "8px").style("font-size", "13px");
-            if (response.rustResult.summary.filtered_records !== void 0) {
-              filterStatsGrid.append("div").style("color", "#6c757d").text("Total Number of Excluded Records:");
-              filterStatsGrid.append("div").style("font-weight", "bold").style("color", "black").text(response.rustResult.summary.filtered_records.toLocaleString());
-            }
-            const mafRecords = response.rustResult.summary.included_maf_records || 0;
-            const cnvRecords = response.rustResult.summary.included_cnv_records || 0;
-            const totalIncludedRecords = mafRecords + cnvRecords;
-            filterStatsGrid.append("div").style("color", "#6c757d").text("Total Number of Included Records:");
-            filterStatsGrid.append("div").style("font-weight", "bold").style("color", "black").text(totalIncludedRecords.toLocaleString());
-            if (response.rustResult.summary.filtered_maf_records !== void 0) {
-              filterStatsGrid.append("div").style("color", "#6c757d").text("MAF Records Excluded:");
-              filterStatsGrid.append("div").style("font-weight", "bold").style("color", "black").text(response.rustResult.summary.filtered_maf_records.toLocaleString());
-            }
-            if (response.rustResult.summary.included_maf_records !== void 0) {
-              filterStatsGrid.append("div").style("color", "#6c757d").text("MAF Records Included:");
-              filterStatsGrid.append("div").style("font-weight", "bold").style("color", "black").text(response.rustResult.summary.included_maf_records.toLocaleString());
-            }
-            if (response.rustResult.summary.filtered_cnv_records !== void 0) {
-              filterStatsGrid.append("div").style("color", "#6c757d").text("CNV Records Excluded:");
-              filterStatsGrid.append("div").style("font-weight", "bold").style("color", "black").text(response.rustResult.summary.filtered_cnv_records.toLocaleString());
-            }
-            if (response.rustResult.summary.included_cnv_records !== void 0) {
-              filterStatsGrid.append("div").style("color", "#6c757d").text("CNV Records Included:");
-              filterStatsGrid.append("div").style("font-weight", "bold").style("color", "black").text(response.rustResult.summary.included_cnv_records.toLocaleString());
-            }
-            if (response.rustResult.summary.filtered_records_by_case !== void 0) {
-              const { columns, rows } = parseRecordsByCaseData(
-                response.rustResult.summary.filtered_records_by_case,
-                response.rustResult.summary.excluded_by_max_record
-              );
-              const recordsByCaseContainer = filterStats.append("div").style("grid-column", "1 / -1").style("margin-top", "15px");
-              const expandableHeader = recordsByCaseContainer.append("div").style("display", "flex").style("align-items", "center").style("gap", "8px").style("cursor", "pointer").style("padding", "8px").style("border-radius", "4px").style("transition", "background-color 0.2s").style("background-color", "rgba(0, 123, 255, 0.1)").style("border", "1px solid rgba(0, 123, 255, 0.2)").on("mouseenter", function() {
-                select_default(this).style("background-color", "rgba(0, 123, 255, 0.15)");
-              }).on("mouseleave", function() {
-                select_default(this).style("background-color", "rgba(0, 123, 255, 0.1)");
-              });
-              const expandIcon = expandableHeader.append("span").style("font-size", "12px").style("color", "#007bff").style("transition", "transform 0.2s").text("\u25B6");
-              expandableHeader.append("span").style("color", "#007bff").style("text-decoration", "underline").style("font-size", "13px").style("font-weight", "500").text(
-                `View detailed statistics for ${Object.keys(response.rustResult.summary.filtered_records_by_case).length} cases`
-              );
-              const expandableContent = recordsByCaseContainer.append("div").style("display", "none").style("margin-top", "12px");
-              const tableContainer2 = expandableContent.append("div").style("max-height", "400px").style("overflow-y", "auto").style("border", "1px solid #dee2e6").style("border-radius", "4px");
-              renderTable({
-                div: tableContainer2,
-                columns,
-                rows,
-                showLines: true,
-                striped: true,
-                showHeader: true,
-                maxHeight: "380px",
-                resize: false,
-                header: {
-                  allowSort: true,
-                  style: {
-                    "background-color": "#f8f9fa",
-                    "font-weight": "bold",
-                    "border-bottom": "2px solid #dee2e6"
-                  }
-                }
-              });
-              expandableContent.append("div").style("margin-top", "12px").style("padding", "8px").style("background-color", "#f8f9fa").style("border-radius", "4px").style("font-size", "12px").style("color", "#495057").style("line-height", "1.4").text("This table shows analysis statistics per case.");
-              let isExpanded = false;
-              expandableHeader.on("click", function() {
-                isExpanded = !isExpanded;
-                if (isExpanded) {
-                  expandableContent.style("display", "block");
-                  expandIcon.style("transform", "rotate(90deg)").text("\u25BC");
-                } else {
-                  expandableContent.style("display", "none");
-                  expandIcon.style("transform", "rotate(0deg)").text("\u25B6");
-                }
-              });
-            }
-          }
-        }
-        console.log(`Displayed table with ${response.topGeneTable.rows.length} genes`);
-        if (response.totalGenes && response.showingTop && response.totalGenes > response.showingTop) {
-          resultContainer.append("div").style("margin-top", "15px").style("padding", "10px").style("background-color", "#e9ecef").style("border-radius", "4px").style("font-size", "14px").style("max-width", "100%").style("width", "fit-content").style("color", "#495057").html(`
-						<strong>Note:</strong> For performance reasons, only the top ${response.showingTop} 
-						most significant genes are displayed. The complete analysis identified 
-						${response.totalGenes.toLocaleString()} genes total.
-					`);
-        }
-      } else {
-        console.log("No table data received or empty results");
-        resultContainer.append("div").style("padding", "15px").style("background-color", "#fff3cd").style("border", "1px solid #ffeaa7").style("border-radius", "4px").style("margin", "15px 0").style("max-width", "100%").style("width", "fit-content").text("No significant genes found in the analysis.");
-      }
-    } catch (e) {
-      sayerror(obj2.errDiv, e.message || e);
-      if (e.stack) console.log(e.stack);
-    }
-    button.innerHTML = oldText;
-    button.disabled = false;
-    obj2.busy = false;
-  }
-}
-async function gdcGRIN2ui({ filter0, callbacks, debugmode = false }, holder) {
-  if (debugmode) {
-  }
-  try {
-    if (callbacks) {
-      delete callbacks.sjcharts;
-      for (const n in callbacks) {
-        if (typeof callbacks[n] != "function") throw `callbacks.${n} not function`;
-      }
-    }
-    update({ filter0 });
-  } catch (e) {
-    console.log(e);
-    sayerror(holder, e instanceof Error ? e.message : String(e));
-  }
-  async function update({ filter0: filter02 }) {
-    holder.selectAll("*").remove();
-    holder.style("width", "100%").style("max-width", "none");
-    const obj = {
-      errDiv: holder.append("div"),
-      controlDiv: holder.append("div"),
-      tableDiv: holder.append("div").style("width", "100%"),
-      deduplicationInfoDiv: holder.append("div"),
-      downloadButtonDiv: holder.append("div").style("margin-top", "10px").style("display", "none"),
-      resultDiv: holder.append("div").style("margin-top", "20px"),
-      opts: {
-        filter0: filter02,
-        experimentalStrategy: "WXS"
-      },
-      busy: false,
-      // when analyzing, set to true for disabling ui interactivity
-      mafTableArg: null,
-      expStrategyRadio: null
-    };
-    makeControls(obj);
-    await getFilesAndShowTable(obj);
-    callbacks?.postRender?.(publicApi);
-  }
-  const publicApi = { update };
-  return publicApi;
-}
-export {
-  gdcGRIN2ui
-};
-//# sourceMappingURL=grin2-LGI535FF.js.map