@sjcrh/proteinpaint-client 2.184.0 → 2.185.0

package/dist/grin2-P2UO22D2.js

@@ -1,1031 +0,0 @@
-import {
-  PlotBase,
-  axisstyle,
-  controlsInit,
-  filterInit,
-  get$id,
-  getCombinedTermFilter,
-  getNormalRoot,
-  make_one_checkbox,
-  renderTable,
-  sayerror,
-  table2col,
-  to_svg
-} from "./chunk-KBYRXJ6Y.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-Y7S3EY6T.js";
-import "./chunk-RCYTUKAJ.js";
-import {
-  Menu
-} from "./chunk-A6TQGNDQ.js";
-import "./chunk-HYZG6OPC.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-LSEFWW72.js";
-import {
-  icons
-} from "./chunk-B2F23ESD.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-UCLS2SVB.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-MVTCBVSX.js";
-import "./chunk-F6V4AYWP.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-JOT4WDJE.js";
-import "./chunk-OTCYJP7G.js";
-import "./chunk-GXINX3WK.js";
-import "./chunk-SOED2SLH.js";
-import {
-  dt2lesion,
-  dtcnv,
-  dtfusionrna,
-  dtsnvindel,
-  dtsv,
-  mclass,
-  proteinChangingMutations
-} from "./chunk-XRVBHNCW.js";
-import "./chunk-BEWDIM6H.js";
-import {
-  quadtree
-} from "./chunk-IH7ILDJS.js";
-import {
-  axisLeft
-} from "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import {
-  linear
-} from "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/manhattan/manhattan.ts
-function findPointsInRadius(quadtree2, mx, my, hitRadius) {
-  const candidates = [];
-  quadtree2.visit((node, x1, y1, x2, y2) => {
-    if (x1 > mx + hitRadius || x2 < mx - hitRadius || y1 > my + hitRadius || y2 < my - hitRadius) {
-      return true;
-    }
-    if (!node.length) {
-      let current = node;
-      while (current) {
-        const point = current.data;
-        if (point) {
-          const px = point.pixel_x;
-          const py = point.pixel_y;
-          const distance = Math.sqrt((mx - px) ** 2 + (my - py) ** 2);
-          if (distance <= hitRadius) {
-            candidates.push({ point, distance });
-          }
-        }
-        current = current.next;
-      }
-    }
-    return false;
-  });
-  return candidates;
-}
-function updateSelectionTracking(currentSelectionOrder, selectedIndices, dataSource) {
-  const newlySelected = selectedIndices.filter((idx) => !currentSelectionOrder.includes(idx));
-  const updatedSelectionOrder = currentSelectionOrder.filter((idx) => selectedIndices.includes(idx));
-  updatedSelectionOrder.push(...newlySelected);
-  let lastTouchedGene = null;
-  let buttonText = "Lollipop";
-  if (updatedSelectionOrder.length > 0) {
-    const lastSelectedIdx = updatedSelectionOrder[updatedSelectionOrder.length - 1];
-    const dataItem = dataSource[lastSelectedIdx];
-    if (Array.isArray(dataItem)) {
-      lastTouchedGene = dataItem[0]?.value || null;
-    } else {
-      lastTouchedGene = dataItem.gene;
-    }
-    buttonText = `Lollipop (${lastTouchedGene})`;
-  }
-  return {
-    selectionOrder: updatedSelectionOrder,
-    lastTouchedGene,
-    buttonText,
-    buttonDisabled: lastTouchedGene === null
-  };
-}
-function plotManhattan(div, data, settings, app) {
-  settings = {
-    ...settings
-  };
-  let interactivePoints = data.plotData.points;
-  if (data.plotData.points.length > settings.interactiveDotsCap) {
-    interactivePoints = data.plotData.points.sort((a, b) => b.y - a.y).slice(0, settings.interactiveDotsCap);
-  }
-  div.style("position", "relative");
-  const geneTip = new Menu({ padding: "" });
-  let clickMenuIsShown = false;
-  const clickMenu = new Menu({
-    padding: "",
-    onHide: () => {
-      clickMenuIsShown = false;
-    }
-  });
-  const svg = div.append("svg").attr("data-testid", "sjpp-manhattan").attr("width", settings.plotWidth + 2 * settings.pngDotRadius + settings.yAxisX + settings.yAxisSpace).attr("height", settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY * 4);
-  const yPlot = linear().domain([data.plotData.y_min, data.plotData.y_max]).range([settings.plotHeight + 2 * settings.pngDotRadius, 0]);
-  const yAxisScale = linear().domain([0, data.plotData.y_max - settings.pngDotRadius]).range([yPlot(0), yPlot(data.plotData.y_max - settings.pngDotRadius)]);
-  const axisG = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace - settings.yAxisPad},${settings.yAxisY})`);
-  axisG.call(
-    axisLeft(yAxisScale).tickSizeOuter(0)
-    // removes top/bottom cap lines for clean look
-  );
-  axisstyle({
-    axis: axisG,
-    color: settings.axisColor,
-    fontsize: settings.fontSize + 2,
-    showline: settings.showYAxisLine
-  });
-  svg.append("text").attr("x", -((settings.plotHeight + 2 * settings.pngDotRadius) / 2) - settings.yAxisY).attr("y", settings.yAxisX / 2).attr("transform", "rotate(-90)").attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 4}px`).attr("fill", "black").text(data.plotData.has_capped_points ? "-log\u2081\u2080(q-value) [capped]" : "-log\u2081\u2080(q-value)");
-  svg.append("image").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).attr("width", settings.plotWidth + 2 * settings.pngDotRadius).attr("height", settings.plotHeight + 2 * settings.pngDotRadius).attr("href", `data:image/png;base64,${data.pngImg || data.png}`);
-  const xScale = linear().domain([-data.plotData.x_buffer, data.plotData.total_genome_length + data.plotData.x_buffer]).range([0, settings.plotWidth + 2 * settings.pngDotRadius]);
-  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})`);
-    const cover = select_default(svg.node().parentNode).append("div").style("position", "absolute").style("left", `${settings.yAxisX + settings.yAxisSpace}px`).style("top", `${settings.yAxisY}px`).style("width", `${settings.plotWidth + 2 * settings.pngDotRadius}px`).style("height", `${settings.plotHeight + 2 * settings.pngDotRadius}px`).style("pointer-events", "all");
-    let highlightedDots = [];
-    const normalizedPoints = interactivePoints;
-    const pointQuadtree = quadtree().x((d) => d.pixel_x).y((d) => d.pixel_y).addAll(normalizedPoints);
-    cover.on("mousemove", (event) => {
-      if (clickMenuIsShown) return;
-      const rect = cover.node().getBoundingClientRect();
-      const mx = event.clientX - rect.left;
-      const my = event.clientY - rect.top;
-      const hitRadius = settings.pngDotRadius + 3;
-      const candidates = findPointsInRadius(pointQuadtree, mx, my, hitRadius);
-      candidates.sort((a, b) => a.distance - b.distance);
-      const nearbyDots = candidates.slice(0, settings.maxTooltipGenes).map((c) => c.point);
-      const additionalCount = candidates.length - settings.maxTooltipGenes;
-      pointsLayer.selectAll(".hover-circle").remove();
-      if (nearbyDots.length > 0) {
-        nearbyDots.forEach((d) => {
-          pointsLayer.append("circle").attr("class", "hover-circle").attr("cx", d.pixel_x).attr("cy", d.pixel_y).attr("r", settings.pngDotRadius).attr("fill", "none").attr("stroke", "black").attr("stroke-width", settings.interactiveDotStrokeWidth);
-        });
-        highlightedDots = nearbyDots;
-        geneTip.clear().show(event.clientX, event.clientY);
-        if (nearbyDots.length > 1) {
-          const holder = geneTip.d.append("div").style("margin", "10px");
-          showGrin2ResultTable({ tableDiv: holder, hits: nearbyDots });
-          if (additionalCount > 0) {
-            holder.append("div").style("font-size", "0.85em").style("color", "#666").style("font-style", "italic").text(`and ${additionalCount} more gene${additionalCount > 1 ? "s" : ""}...`);
-          }
-        } else {
-          const d = nearbyDots[0];
-          const table = table2col({
-            holder: geneTip.d.append("div"),
-            margin: "10px"
-          });
-          table.addRow("Gene", d.gene);
-          table.addRow("Position", `${d.chrom}:${d.start}-${d.end}`);
-          const [t1, t2] = table.addRow();
-          t1.text("Type");
-          t2.html(`<span style="color:${d.color}">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`);
-          table.addRow("Q-value", d.q_value.toPrecision(3));
-          table.addRow("Subject count", d.nsubj);
-        }
-      } else {
-        highlightedDots = [];
-        geneTip.hide();
-      }
-    }).on("mouseleave", () => {
-      pointsLayer.selectAll(".hover-circle").remove();
-      highlightedDots = [];
-      geneTip.hide();
-    }).on("click", (event) => {
-      if (highlightedDots.length === 0 || !app) return;
-      geneTip.hide();
-      const rect = cover.node().getBoundingClientRect();
-      const mx = event.clientX - rect.left;
-      const my = event.clientY - rect.top;
-      const hitRadius = settings.pngDotRadius + 3;
-      const allCandidates = findPointsInRadius(pointQuadtree, mx, my, hitRadius);
-      allCandidates.sort((a, b) => a.distance - b.distance);
-      const allNearbyDots = allCandidates.map((c) => c.point);
-      if (allNearbyDots.length === 1) {
-        createLollipopFromGene(allNearbyDots[0].gene, app);
-      } else if (allNearbyDots.length > 1) {
-        clickMenu.clear().show(event.clientX, event.clientY);
-        clickMenuIsShown = true;
-        const holder = clickMenu.d.append("div").style("margin", "10px");
-        showGrin2ResultTable({ tableDiv: holder, hits: allNearbyDots, app, clickMenu });
-      }
-    });
-  }
-  if (data.plotData.chrom_data) {
-    const chromLabelY = settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + 10;
-    Object.entries(data.plotData.chrom_data).forEach(([chrom, chromData]) => {
-      const chromLabel = chrom.replace("chr", "");
-      if (chromLabel === "M") return;
-      const centerPos = settings.yAxisX + settings.yAxisSpace + xScale(chromData.center);
-      svg.append("text").attr("x", centerPos).attr("y", chromLabelY).attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 2}px`).text(chromLabel);
-    });
-  }
-  svg.append("text").attr("x", settings.yAxisX + settings.yAxisSpace + (settings.plotWidth + 2 * settings.pngDotRadius) / 2).attr("y", settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + settings.xAxisLabelPad).attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 4}px`).attr("fill", "black").text("Chromosomes");
-  svg.append("text").attr("x", settings.yAxisX + settings.yAxisSpace).attr("y", settings.yAxisY / 2).attr("font-weight", "bold").attr("font-size", `${settings.fontSize + 2}px`).text("Manhattan Plot");
-  if (settings.showDownload) {
-    const downloadDiv = div.append("div").style("position", "absolute").style("top", "5px").style("left", `${settings.yAxisX + settings.yAxisSpace + 108}px`);
-    icons["download"](downloadDiv, {
-      width: 16,
-      height: 16,
-      title: "Download Manhattan plot",
-      handler: () => {
-        const svgNode = svg.node();
-        const clone = svgNode.cloneNode(true);
-        const bbox = svgNode.getBBox();
-        clone.setAttribute("width", bbox.width.toString());
-        clone.setAttribute("height", bbox.height.toString());
-        clone.setAttribute("viewBox", `${bbox.x} ${bbox.y} ${bbox.width} ${bbox.height}`);
-        to_svg(clone, `manhattan_plot_${(/* @__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 + (settings.plotWidth + 2 * settings.pngDotRadius) - 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);
-      svg.append("text").attr("x", x + 8 + settings.legendTextOffset).attr("y", legendY + settings.legendVerticalOffset).attr("font-size", `${settings.legendFontSize + 2}px`).text(item.type);
-    });
-  }
-}
-function createLollipopFromGene(geneSymbol, app) {
-  const cfg = {
-    type: "plot_create",
-    config: {
-      chartType: "genomeBrowser",
-      snvindel: { shown: true },
-      // always set snvindel.shown=true so the mds3 tk is always shown; since grin2 works for this ds, it doesn't matter whether snvindel/cnv/svfusion any is present; all will be shown in mds3 tk
-      geneSearchResult: { geneSymbol }
-    }
-  };
-  if (app.vocabApi.termdbConfig.queries.trackLst?.activeTracks) {
-    cfg.config.trackLst = structuredClone(app.vocabApi.termdbConfig.queries.trackLst);
-    cfg.config.trackLst.activeTracks = [];
-  }
-  app.dispatch(cfg);
-}
-async function createMatrixFromGenes(geneSymbols, app) {
-  const MAX_GENES = 100;
-  const genesToUse = geneSymbols.slice(0, MAX_GENES);
-  try {
-    const termwrappers = await Promise.all(
-      genesToUse.map(async (gene) => {
-        const term = {
-          type: "geneVariant",
-          gene,
-          name: gene
-        };
-        const minTwCopy = app.vocabApi.getTwMinCopy({ term, q: {} });
-        return {
-          $id: await get$id(minTwCopy),
-          term,
-          q: {}
-        };
-      })
-    );
-    app.dispatch({
-      type: "plot_create",
-      config: {
-        chartType: "matrix",
-        dataType: "geneVariant",
-        termgroups: [
-          {
-            name: "Genomic Alterations",
-            lst: termwrappers
-          }
-        ]
-      }
-    });
-  } catch (error) {
-    sayerror(app.dom.div, `Error creating matrix: ${error instanceof Error ? error.message : error}`);
-  }
-}
-
-// plots/grin2/grin2.ts
-function showGrin2ResultTable(opts) {
-  const {
-    tableDiv,
-    hits,
-    app,
-    clickMenu,
-    columns: prebuiltColumns,
-    rows: prebuiltRows,
-    dataItems: prebuiltDataItems,
-    getGene = (item) => item.gene,
-    matrixButtonFormat = "Matrix ({n})",
-    ...renderTableOpts
-  } = opts;
-  const dataItems = prebuiltDataItems || hits;
-  if (!dataItems || dataItems.length === 0) return;
-  const columns = prebuiltColumns || [
-    { label: "Gene" },
-    { label: `${hits[0].chrom.charAt(0).toUpperCase()}${hits[0].chrom.slice(1).toLowerCase()} pos` },
-    { label: "Type" },
-    { label: "Q-value", sortable: true },
-    { label: "Subject count", sortable: true }
-  ];
-  const rows = prebuiltRows || hits.map((d) => [
-    { value: d.gene },
-    { html: `<span style="font-size:.8em">${d.start}-${d.end}</span>` },
-    { html: `<span style="color:${d.color}">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}` },
-    { value: d.q_value.toPrecision(3) },
-    { value: d.nsubj }
-  ]);
-  const tableOptions = {
-    div: tableDiv,
-    columns,
-    rows,
-    showLines: false,
-    showHeader: true,
-    striped: true,
-    resize: "both",
-    header: { allowSort: true },
-    ...renderTableOpts
-  };
-  if (app) {
-    let lastTouchedGene = null;
-    let selectionOrder = [];
-    tableOptions.buttonsToLeft = true;
-    tableOptions.buttons = [
-      {
-        text: matrixButtonFormat.replace("{n}", "0"),
-        callback: (selectedIndices, buttonNode) => {
-          if (selectedIndices.length > 0) {
-            buttonNode.disabled = true;
-            const selectedGenes = selectedIndices.map((idx) => getGene(dataItems[idx]));
-            clickMenu?.hide();
-            createMatrixFromGenes(selectedGenes, app);
-          }
-        },
-        onChange: (selectedIndices, buttonNode) => {
-          buttonNode.textContent = matrixButtonFormat.replace("{n}", String(selectedIndices.length));
-          buttonNode.disabled = selectedIndices.length === 0;
-        }
-      },
-      {
-        text: "Lollipop",
-        callback: (_selectedIndices, buttonNode) => {
-          if (lastTouchedGene) {
-            buttonNode.disabled = true;
-            clickMenu?.hide();
-            createLollipopFromGene(lastTouchedGene, app);
-          }
-        },
-        onChange: (selectedIndices, buttonNode) => {
-          const result = updateSelectionTracking(selectionOrder, selectedIndices, dataItems);
-          selectionOrder = result.selectionOrder;
-          lastTouchedGene = result.lastTouchedGene;
-          buttonNode.textContent = result.buttonText;
-          buttonNode.disabled = result.buttonDisabled;
-        }
-      }
-    ];
-  }
-  renderTable(tableOptions);
-}
-var GRIN2 = class extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.type = "grin2";
-    // active MAF filter state, updated by filterInit UI
-    // Colors
-    this.borderColor = "#eee";
-    this.backgroundColor = "#f8f8f8";
-    this.optionsTextColor = "#666";
-    this.btnBackgroundColor = "#f0f0f0";
-    this.btnBorderColor = "#ccc";
-    this.btnTextColor = "#333";
-    this.btnHoverBackgroundColor = "#e0e0e0";
-    // Typography
-    this.optionsTextFontSize = 12;
-    this.btnFontSize = 12;
-    this.headerFontSize = 14;
-    this.headerFontWeight = 600;
-    this.tableFontSize = 11;
-    this.statsTableFontWeight = "bold";
-    // Spacing & Layout
-    this.btnPadding = "8px 16px";
-    this.btnSmallPadding = "2px 8px";
-    // for Select All/Clear All
-    this.btnBorderRadius = "3px";
-    this.btnMargin = "10px";
-    this.tableCellPadding = "8px";
-    this.controlsMargin = "5px";
-    this.controlsPadding = "10px";
-    // Input fields
-    this.inputWidth = "80px";
-    this.inputPadding = "2px 4px";
-    this.inputBorderColor = "#ddd";
-    this.inputBorderRadius = "2px";
-    // Containers
-    this.checkboxContainerMaxHeight = "150px";
-    this.checkboxContainerBackground = "#fafafa";
-    this.checkboxContainerBorder = "1px solid #ddd";
-    this.checkboxContainerPadding = "4px";
-    this.checkboxContainerBorderRadius = "3px";
-    // Interactive states
-    this.disabledOpacity = "0.6";
-    this.enabledOpacity = "1";
-    // Gaps and offsets
-    this.controlGap = "8px";
-    this.checkboxMarginBottom = "2px";
-    this.headerMargin = "0 10px 0 0";
-    this.sectionMargin = "20px 0";
-    this.addSnvindelRow = (table) => {
-      const [left, right] = table.addRow();
-      const t2 = table2col({ holder: right });
-      {
-        const [labelCell, containerCell] = t2.addRow();
-        labelCell.text("Consequences").style("padding-top", "8px");
-        this.createConsequenceCheckboxes(containerCell);
-      }
-      const mafFilterConfig = this.app.vocabApi.termdbConfig.queries?.snvindel?.mafFilter;
-      if (mafFilterConfig) {
-        this.snvindelMafFilter = structuredClone(
-          this.state.config.settings?.snvindelOptions?.mafFilter || mafFilterConfig.filter
-        );
-        const [td1, td2] = t2.addRow();
-        td1.text("MAF filter");
-        filterInit({
-          emptyLabel: "+",
-          holder: td2,
-          header_mode: "hide_search",
-          vocab: { terms: mafFilterConfig.terms },
-          callback: async (filter) => {
-            this.snvindelMafFilter = filter;
-          }
-        }).main(this.snvindelMafFilter);
-      }
-      const isChecked = this.state.config.settings.dtUsage[dtsnvindel].checked;
-      t2.table.style("display", isChecked ? "" : "none");
-      this.dom.snvindelCheckbox = make_one_checkbox({
-        holder: left,
-        labeltext: dt2lesion[dtsnvindel].uilabel,
-        checked: isChecked,
-        testid: "sjpp-grin2-checkbox-snvindel",
-        callback: (checked) => {
-          t2.table.style("display", checked ? "" : "none");
-          this.updateRunButtonFromCheckboxes();
-        }
-      });
-    };
-    // Add CNV row
-    this.addCnvRow = (table) => {
-      const [left, right] = table.addRow();
-      const t2 = table2col({ holder: right });
-      const useSaved = this.state.config.settings.runAnalysis === true;
-      const savedCnv = useSaved ? this.state.config.settings.cnvOptions : void 0;
-      this.dom.cnv_lossThreshold = this.addOptionRowToTable(
-        t2,
-        "Loss Threshold",
-        savedCnv?.lossThreshold ?? this.app.vocabApi.termdbConfig.queries.cnv?.cnvLossCutoff ?? -0.4,
-        // default. We first check if we have saved state, then we check the ds specific value, if that is undefined we fall back to the hardcoded default value
-        -5,
-        // min
-        0,
-        // max
-        0.05
-        // step
-      );
-      this.dom.cnv_gainThreshold = this.addOptionRowToTable(
-        t2,
-        "Gain Threshold",
-        savedCnv?.gainThreshold ?? this.app.vocabApi.termdbConfig.queries.cnv?.cnvGainCutoff ?? 0.4,
-        // default. We first check if we have saved state, then we check the ds specific value, if that is undefined we fall back to the hardcoded default value
-        0,
-        // min
-        5,
-        // max
-        0.05
-        // step
-      );
-      this.dom.cnv_maxSegLength = this.addOptionRowToTable(
-        t2,
-        "Max Segment Length",
-        savedCnv?.maxSegLength ?? this.app.vocabApi.termdbConfig.queries.cnv?.cnvMaxLength ?? 2e6,
-        // default 2Mb. We first check if we have saved state, then we check the ds specific value, if that is undefined we fall back to the hardcoded default value
-        0,
-        // min
-        1e9,
-        // max
-        1e3
-        // step
-      );
-      const dtUsage = this.state.config.settings.dtUsage;
-      const isChecked = useSaved && dtUsage[dtcnv]?.checked !== void 0 ? dtUsage[dtcnv].checked : !!this.app.vocabApi.termdbConfig.queries.cnv;
-      t2.table.style("display", isChecked ? "" : "none");
-      this.dom.cnvCheckbox = make_one_checkbox({
-        holder: left,
-        labeltext: dt2lesion[dtcnv].uilabel,
-        checked: isChecked,
-        testid: "sjpp-grin2-checkbox-cnv",
-        callback: (checked) => {
-          t2.table.style("display", checked ? "" : "none");
-          this.updateRunButtonFromCheckboxes();
-        }
-      });
-    };
-    // Add Fusion row
-    this.addFusionRow = (table) => {
-      const [left, right] = table.addRow();
-      const t2 = table2col({ holder: right });
-      const isChecked = this.state.config.settings.dtUsage[dtfusionrna].checked;
-      t2.table.style("display", isChecked ? "" : "none");
-      this.dom.fusionCheckbox = make_one_checkbox({
-        holder: left,
-        labeltext: dt2lesion[dtfusionrna].uilabel,
-        checked: isChecked,
-        testid: "grin2-checkbox-fusion",
-        callback: (checked) => {
-          t2.table.style("display", checked ? "" : "none");
-          this.updateRunButtonFromCheckboxes();
-        }
-      });
-    };
-    // Add SV row
-    this.addSvRow = (table) => {
-      const [left, right] = table.addRow();
-      const t2 = table2col({ holder: right });
-      const isChecked = this.state.config.settings.dtUsage[dtsv].checked;
-      t2.table.style("display", isChecked ? "" : "none");
-      this.dom.svCheckbox = make_one_checkbox({
-        holder: left,
-        labeltext: dt2lesion[dtsv].uilabel,
-        checked: isChecked,
-        testid: "sjpp-grin2-checkbox-sv",
-        callback: (checked) => {
-          t2.table.style("display", checked ? "" : "none");
-          this.updateRunButtonFromCheckboxes();
-        }
-      });
-    };
-    this.opts = opts;
-    this.components = {
-      controls: {}
-    };
-    opts.holder.classed("sjpp-grin2-main", true);
-    this.dom = {
-      massControls: opts.holder.append("div").style("display", "inline-block"),
-      headerText: opts.holder.append("div").style("display", "inline-block"),
-      controls: opts.holder.append("div"),
-      // controls ui on top
-      div: opts.holder.append("div").style("margin", "20px"),
-      // result ui on bottom
-      tip: new Menu({ padding: "" }),
-      geneTip: new Menu({ padding: "" }),
-      snvindelCheckbox: null,
-      cnvCheckbox: null,
-      fusionCheckbox: null,
-      svCheckbox: null,
-      runButton: null,
-      consequenceCheckboxes: {},
-      snvindelSelectAllBtn: null,
-      snvindelClearAllBtn: null,
-      snvindelDefaultBtn: null
-    };
-    if (opts.header) this.dom.header = opts.header.text("GRIN2");
-  }
-  static {
-    this.type = "grin2";
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    const parentConfig = appState.plots.find((p) => p.id === this.parentId);
-    const termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter);
-    return {
-      config,
-      termfilter
-    };
-  }
-  // Enable the run button only if at least one data type is checked
-  updateRunButtonState(dtu) {
-    const dtUsage = dtu || this.state.config.settings.dtUsage;
-    const anyChecked = Object.values(dtUsage).some((info) => info.checked);
-    this.dom.runButton.property("disabled", !anyChecked);
-  }
-  createConfigTable() {
-    this.dom.headerText.style("margin", "15px").html(
-      "GRIN2 stands for Genomic Random Interval (GRIN) statistical model. For details, see <a href=https://pubmed.ncbi.nlm.nih.gov/23842812/ target=_blank>Pounds, S. et al. Bioinformatics 2013</a>."
-    );
-    const table = table2col({ holder: this.dom.controls, disableScroll: true });
-    const queries = this.app.vocabApi.termdbConfig.queries;
-    if (queries.snvindel) {
-      this.addSnvindelRow(table);
-    }
-    if (queries.cnv) {
-      this.addCnvRow(table);
-    }
-    if (queries.svfusion?.dtLst?.includes(dtfusionrna)) {
-      this.addFusionRow(table);
-    }
-    if (queries.svfusion?.dtLst?.includes(dtsv)) {
-      this.addSvRow(table);
-    }
-    this.dom.runButton = this.dom.controls.append("button").attr("data-testid", "sjpp-grin2-run-button").style("margin-left", "100px").text("Run GRIN2").on("click", () => {
-      this.runAnalysis();
-    });
-    if (this.state.config.settings.runAnalysis) {
-      this.runAnalysis();
-    } else {
-      this.updateRunButtonState();
-    }
-  }
-  // Helper method to add option rows to table2col instances
-  addOptionRowToTable(table, label, defaultValue, min, max, step) {
-    const [labelCell, inputCell] = table.addRow();
-    labelCell.text(label);
-    const input = inputCell.append("input").attr("type", "number").attr("value", defaultValue).style("width", this.inputWidth).style("padding", this.inputPadding).style("border", `1px solid ${this.inputBorderColor}`).style("border-radius", this.inputBorderRadius).style("font-size", `${this.optionsTextFontSize}px`);
-    if (min !== null && min !== void 0) input.attr("min", min);
-    if (max !== null && max !== void 0) input.attr("max", max);
-    if (step !== null && step !== void 0) input.attr("step", step);
-    return input;
-  }
-  createConsequenceCheckboxes(container) {
-    const snvIndelClasses = Object.entries(mclass).filter(
-      ([key, cls]) => cls.dt === dtsnvindel && key !== "Blank" && key !== "WT"
-    );
-    const saved = this.state.config.settings.snvindelOptions?.consequences;
-    const useSaved = this.state.config.settings.runAnalysis === true && !!saved && saved.length > 0;
-    const canonicalDefault = /* @__PURE__ */ new Set([...proteinChangingMutations, "StartLost", "StopLost"]);
-    const initialChecked = useSaved ? new Set(saved) : canonicalDefault;
-    const controlDiv = container.append("div").style("margin-bottom", "6px").style("display", "flex").style("gap", this.controlGap);
-    this.dom.snvindelSelectAllBtn = controlDiv.append("button").style("font-size", `${this.tableFontSize}px`).text("Select All");
-    this.dom.snvindelClearAllBtn = controlDiv.append("button").style("font-size", `${this.tableFontSize}px`).text("Clear All");
-    this.dom.snvindelDefaultBtn = controlDiv.append("button").style("font-size", `${this.tableFontSize}px`).text("Default");
-    const checkboxContainer = container.append("div").style("max-height", this.checkboxContainerMaxHeight).style("overflow-y", "auto").style("border", this.checkboxContainerBorder);
-    this.dom.consequenceCheckboxes = {};
-    snvIndelClasses.forEach(([classKey, classInfo]) => {
-      const checkboxDiv = checkboxContainer.append("div").style("margin-bottom", this.checkboxMarginBottom);
-      const checkbox = make_one_checkbox({
-        holder: checkboxDiv,
-        labeltext: classInfo.label,
-        checked: initialChecked.has(classKey),
-        divstyle: { "font-size": `${this.tableFontSize}px` },
-        callback: () => {
-        }
-      });
-      checkboxDiv.select("label").attr("title", classInfo.desc);
-      this.dom.consequenceCheckboxes[classKey] = checkbox;
-    });
-    this.dom.snvindelSelectAllBtn.on("click", () => {
-      Object.values(this.dom.consequenceCheckboxes).forEach((cb) => cb.property("checked", true));
-    });
-    this.dom.snvindelClearAllBtn.on("click", () => {
-      Object.values(this.dom.consequenceCheckboxes).forEach((cb) => cb.property("checked", false));
-    });
-    this.dom.snvindelDefaultBtn.on("click", () => {
-      Object.entries(this.dom.consequenceCheckboxes).forEach(([classKey, checkbox]) => {
-        checkbox.property("checked", canonicalDefault.has(classKey));
-      });
-    });
-  }
-  getConfigValues(dtUsage) {
-    const requestConfig = {};
-    const usage = dtUsage || this.state.config.settings.dtUsage;
-    if (usage[dtsnvindel]?.checked) {
-      requestConfig.snvindelOptions = {
-        // minTotalDepth: parseFloat(this.dom.snvindel_minTotalDepth.property('value')),
-        // minAltAlleleCount: parseFloat(this.dom.snvindel_minAltAlleleCount.property('value')),
-        consequences: this.getSelectedConsequences()
-      };
-      if (this.snvindelMafFilter) {
-        requestConfig.snvindelOptions.mafFilter = this.snvindelMafFilter;
-      }
-    }
-    if (usage[dtcnv]?.checked) {
-      requestConfig.cnvOptions = {
-        lossThreshold: parseFloat(this.dom.cnv_lossThreshold.property("value")),
-        gainThreshold: parseFloat(this.dom.cnv_gainThreshold.property("value")),
-        maxSegLength: parseFloat(this.dom.cnv_maxSegLength.property("value"))
-      };
-    }
-    if (usage[dtfusionrna]?.checked) {
-      requestConfig.fusionOptions = {};
-    }
-    if (usage[dtsv]?.checked) {
-      requestConfig.svOptions = {};
-    }
-    return requestConfig;
-  }
-  getDtUsageFromCheckboxes() {
-    const dtUsage = structuredClone(this.state.config.settings.dtUsage);
-    if (dtUsage[dtsnvindel]) {
-      dtUsage[dtsnvindel].checked = this.dom.snvindelCheckbox.property("checked");
-    }
-    if (dtUsage[dtcnv]) {
-      dtUsage[dtcnv].checked = this.dom.cnvCheckbox.property("checked");
-    }
-    if (dtUsage[dtfusionrna]) {
-      dtUsage[dtfusionrna].checked = this.dom.fusionCheckbox.property("checked");
-    }
-    if (dtUsage[dtsv]) {
-      dtUsage[dtsv].checked = this.dom.svCheckbox.property("checked");
-    }
-    return dtUsage;
-  }
-  getSelectedConsequences() {
-    const consequences = [];
-    Object.entries(this.dom.consequenceCheckboxes).forEach(([classKey, checkbox]) => {
-      if (checkbox.property("checked")) {
-        consequences.push(classKey);
-      }
-    });
-    return consequences;
-  }
-  updateRunButtonFromCheckboxes() {
-    const dtUsage = this.getDtUsageFromCheckboxes();
-    this.updateRunButtonState(dtUsage);
-  }
-  async runAnalysis() {
-    this.dom.controls.style("pointer-events", "none").style("opacity", "0.5");
-    try {
-      const dtUsage = this.getDtUsageFromCheckboxes();
-      this.dom.runButton.property("disabled", true).text("Running GRIN2...");
-      this.dom.div.selectAll("*").remove();
-      const configValues = this.getConfigValues(dtUsage);
-      const requestData = {
-        filter: getNormalRoot(this.state.termfilter.filter),
-        filter0: this.state.termfilter.filter0,
-        width: this.state.config.settings.manhattan?.plotWidth,
-        height: this.state.config.settings.manhattan?.plotHeight,
-        pngDotRadius: this.state.config.settings.manhattan?.pngDotRadius,
-        devicePixelRatio: window.devicePixelRatio,
-        maxGenesToShow: this.state.config.settings?.manhattan?.maxGenesToShow,
-        lesionTypeColors: this.state.config.settings?.manhattan?.lesionTypeColors,
-        qValueThreshold: this.state.config.settings?.manhattan?.qValueThreshold,
-        maxCappedPoints: this.state.config.settings?.manhattan?.maxCappedPoints,
-        hardCap: this.state.config.settings?.manhattan?.hardCap,
-        binSize: this.state.config.settings?.manhattan?.binSize,
-        ...configValues
-      };
-      const response = await this.app.vocabApi.getGrin2Data(requestData, this.api.getAbortSignal());
-      if (response.status === "error") throw `GRIN2 analysis failed: ${response.error}`;
-      this.renderResults(response);
-      const updatedConfig = {
-        ...this.state.config,
-        settings: {
-          ...this.state.config.settings,
-          ...configValues,
-          dtUsage,
-          runAnalysis: true
-        }
-      };
-      this.app.dispatch({
-        type: "plot_edit",
-        id: this.id,
-        config: updatedConfig
-      });
-    } catch (error) {
-      if (this.dom.div) {
-        sayerror(this.dom.div, `Error running GRIN2: ${error instanceof Error ? error.message : error}`);
-      } else {
-      }
-    } finally {
-      this.dom.controls?.style("pointer-events", "auto").style("opacity", "1");
-      this.dom.runButton?.property("disabled", false).text("Run GRIN2");
-    }
-  }
-  async init() {
-    this.components.controls = await controlsInit({
-      app: this.app,
-      id: this.id,
-      holder: this.dom.massControls.style("display", "inline-block"),
-      inputs: []
-    });
-    const burgerMenu = this.dom.massControls.select("div > svg.bi.bi-copy");
-    if (burgerMenu) burgerMenu.remove();
-    const downloadBtn = this.dom.massControls.select("div > svg.bi.bi-download");
-    if (downloadBtn) downloadBtn.remove();
-    this.components.controls.on("helpClick.grin2", () => {
-      window.open("https://github.com/stjude/proteinpaint/wiki/Grin2");
-    });
-  }
-  async main() {
-    const config = structuredClone(this.state.config);
-    if (config.childType != this.type && config.chartType != this.type) return;
-    if (!this.dom.runButton) {
-      this.createConfigTable();
-    }
-  }
-  renderResults(result) {
-    if (result.pngImg) {
-      const plotData = result;
-      const plotDiv = this.dom.div;
-      const manhattanSettings = this.state.config.settings.manhattan;
-      plotManhattan(plotDiv, plotData, manhattanSettings, this.app);
-    }
-    if (result.topGeneTable) {
-      const tableContainer = this.dom.div.append("div").style("margin", this.sectionMargin);
-      const headerDiv = tableContainer.append("div").style("display", "flex").style("align-items", "center").style("margin", this.btnMargin);
-      headerDiv.append("h3").style("margin", this.headerMargin).style("font-size", `${this.headerFontSize}px`).text(`Top Genes (showing ${result.stats.lst[0].rows[1][1]} of ${result.stats.lst[0].rows[0][1]})`);
-      const tableDiv = tableContainer.append("div");
-      const lesionTypeColors = this.state.config.settings.manhattan.lesionTypeColors;
-      const qValueThreshold = this.state.config.settings.manhattan.qValueThreshold;
-      const columns = result.topGeneTable.columns;
-      const dtMapping = {};
-      Object.entries(dt2lesion).forEach(([dt, config]) => {
-        dtMapping[dt] = config.lesionTypes.map((lt) => ({
-          col: `Q-value (${lt.name})`,
-          type: lt.lesionType
-        }));
-      });
-      const qValueEntries = [];
-      Object.entries(this.state.config.settings.dtUsage).forEach(([key, isChecked]) => {
-        if (isChecked && dtMapping[key]) {
-          dtMapping[key].forEach(({ col, type }) => {
-            const colIndex = columns.findIndex((c) => c.label === col);
-            if (colIndex !== -1) qValueEntries.push({ colIndex, type });
-          });
-        }
-      });
-      const modifiedColumns = [{ label: "", width: "20px" }, ...result.topGeneTable.columns];
-      const lesionTypeCircleCache = new Map(
-        Object.entries(lesionTypeColors).map(([type, color]) => [
-          type,
-          `<span style="display:inline-block;width:8px;height:8px;border-radius:50%;background-color:${color};margin-right:3px;"></span>`
-        ])
-      );
-      const processedRows = result.topGeneTable.rows.map((row) => {
-        const circles = qValueEntries.filter(({ colIndex }) => {
-          const qValue = row[colIndex]?.value;
-          return typeof qValue === "number" && qValue < qValueThreshold;
-        }).map(({ type }) => lesionTypeCircleCache.get(type));
-        return [{ value: "", html: circles.join("") }, ...row];
-      });
-      showGrin2ResultTable({
-        tableDiv,
-        app: this.app,
-        columns: modifiedColumns,
-        rows: processedRows,
-        dataItems: result.topGeneTable.rows,
-        getGene: (row) => row[0]?.value,
-        matrixButtonFormat: "Matrix ({n} genes selected)",
-        maxHeight: "400px",
-        maxWidth: "100%",
-        dataTestId: "sjpp-grin2-top-genes-table",
-        resize: "both",
-        selectAll: false,
-        allowRestoreRowOrder: true,
-        restoreButtonInFooter: true,
-        download: {
-          fileName: `grin2_top_genes_${(/* @__PURE__ */ new Date()).toISOString().replace(/[:.]/g, "-").slice(0, -5)}.tsv`
-        },
-        header: {
-          allowSort: true,
-          style: {
-            "font-weight": this.statsTableFontWeight,
-            "background-color": this.backgroundColor
-          }
-        }
-      });
-    }
-    if (result.stats?.lst) {
-      const tablesContainer = this.dom.div.append("div").style("margin-top", "50px");
-      for (const section of result.stats.lst.slice(1)) {
-        tablesContainer.append("h4").style("margin", this.headerMargin).style("margin-top", "15px").style("font-size", `${this.headerFontSize - 2}px`).text(section.name);
-        const table = table2col({ holder: tablesContainer.append("div"), margin: "2px 8px" });
-        for (const [k, v] of section.rows) {
-          table.addRow(k, v);
-        }
-      }
-    }
-  }
-};
-var grin2Init = getCompInit(GRIN2);
-var componentInit = grin2Init;
-function getDefaultSettings(opts) {
-  const defaults = {
-    manhattan: {
-      // Core plot dimensions
-      plotWidth: 1e3,
-      plotHeight: 400,
-      pngDotRadius: 2,
-      // Layout spacing
-      yAxisX: 70,
-      yAxisY: 40,
-      yAxisSpace: 20,
-      xAxisLabelPad: 30,
-      yAxisPad: 5,
-      axisColor: "#545454",
-      showYAxisLine: true,
-      // Typography
-      fontSize: 12,
-      // Legend settings
-      showLegend: true,
-      legendItemWidth: 80,
-      legendDotRadius: 3,
-      legendRightOffset: 15,
-      legendTextOffset: 12,
-      legendVerticalOffset: 4,
-      legendFontSize: 12,
-      // Interactive dots
-      showInteractiveDots: true,
-      interactiveDotRadius: 2,
-      interactiveDotStrokeWidth: 1,
-      // Download options
-      showDownload: true,
-      // Max genes to show in table, interactive dots cap, and tooltip genes
-      maxGenesToShow: 500,
-      interactiveDotsCap: 5e3,
-      maxTooltipGenes: 5,
-      // Q-value threshold for significance indicators in the table, tooltips, and for determining which dots become interactive
-      qValueThreshold: 0.05,
-      // Colors for lesion types (currently used for table significance indicators. Long term will also be used for the rust code colors)
-      lesionTypeColors: {
-        mutation: "#44AA44",
-        // green
-        loss: "#4444FF",
-        // blue
-        gain: "#FF4444",
-        // red
-        fusion: "#FFA500",
-        // orange
-        sv: "#9932CC"
-        // purple
-      },
-      // Threshold for the rust code when determining if we need to raise the cap value from the default
-      maxCappedPoints: 5,
-      // Bin size for cap calculations
-      binSize: 10,
-      // Hard cap regardless of data distribution
-      hardCap: 200
-    }
-  };
-  return Object.assign(defaults, opts?.overrides);
-}
-async function getPlotConfig(opts, app) {
-  const queries = app.vocabApi.termdbConfig.queries;
-  const defaultSettings = getDefaultSettings(opts);
-  const dtUsage = {};
-  if (queries?.snvindel) {
-    dtUsage[dtsnvindel] = { checked: true, label: dt2lesion[dtsnvindel].uilabel };
-  }
-  if (queries?.cnv) {
-    dtUsage[dtcnv] = { checked: true, label: dt2lesion[dtcnv].uilabel };
-  }
-  if (queries?.svfusion) {
-    if (queries.svfusion.dtLst.includes(dtfusionrna)) {
-      dtUsage[dtfusionrna] = { checked: false, label: dt2lesion[dtfusionrna].uilabel };
-    }
-    if (queries.svfusion.dtLst.includes(dtsv)) {
-      dtUsage[dtsv] = { checked: false, label: dt2lesion[dtsv].uilabel };
-    }
-  }
-  const config = {
-    chartType: "grin2",
-    settings: {
-      controls: {},
-      dtUsage,
-      runAnalysis: false,
-      manhattan: {
-        ...defaultSettings.manhattan,
-        ...opts?.manhattan
-      },
-      snvindelOptions: queries?.snvindel ? {
-        // minTotalDepth: 10,
-        // minAltAlleleCount: 2,
-        consequences: [],
-        hyperMutator: 1e3
-      } : void 0,
-      cnvOptions: queries?.cnv ? {
-        lossThreshold: -0.4,
-        gainThreshold: 0.3,
-        maxSegLength: 0,
-        hyperMutator: 500
-      } : void 0,
-      fusionOptions: queries?.svfusion?.dtLst?.includes(dtfusionrna) ? {} : void 0,
-      svOptions: queries?.svfusion?.dtLst?.includes(dtsv) ? {} : void 0
-    }
-  };
-  return copyMerge(config, opts);
-}
-export {
-  componentInit,
-  getDefaultSettings,
-  getPlotConfig,
-  grin2Init,
-  showGrin2ResultTable
-};
-//# sourceMappingURL=grin2-P2UO22D2.js.map