@sjcrh/proteinpaint-client 2.194.0 → 2.195.0

package/dist/grin2-DR7XJIAS.js

@@ -1,968 +0,0 @@
-import {
-  DataPointInteractions,
-  PlotBase,
-  axisstyle,
-  controlsInit,
-  createLollipopFromGene,
-  filterInit,
-  getCombinedTermFilter,
-  getNormalRoot,
-  make_one_checkbox,
-  make_radios,
-  sayerror,
-  showResultsTable,
-  table2col,
-  to_svg
-} from "./chunk-RHGAE6PY.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-7K6LTROG.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-LQJMCE7G.js";
-import "./chunk-FN5XPUPH.js";
-import {
-  icons
-} from "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-KM4JBR26.js";
-import "./chunk-COYULNJF.js";
-import "./chunk-6G4YOMWW.js";
-import "./chunk-7IYJZZQI.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-I73KUUYG.js";
-import "./chunk-IVXCWCKS.js";
-import {
-  dt2lesion,
-  dtcnv,
-  dtfusionrna,
-  dtsnvindel,
-  dtsv,
-  mclass,
-  proteinChangingMutations
-} from "./chunk-7KRS7L4U.js";
-import "./chunk-BKPDYW5T.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-TJYRBEBK.js";
-import {
-  axisLeft
-} from "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import {
-  linear
-} from "./chunk-SOTB4FRE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/grin2/model/GRIN2Model.ts
-var GRIN2Model = class {
-  constructor(vocabApi) {
-    this.vocabApi = vocabApi;
-  }
-  async fetchGrin2Data(requestData, signal) {
-    return this.vocabApi.getGrin2Data(requestData, signal);
-  }
-};
-
-// plots/grin2/viewModel/GRIN2ViewModel.ts
-var GRIN2ViewModel = class {
-  constructor(response, manhattanSettings, dtUsage) {
-    this.viewData = {
-      manhattan: response.pngImg ? { plotData: response, settings: manhattanSettings } : null,
-      topGenes: this.buildTopGenes(response, manhattanSettings, dtUsage),
-      statsSections: response.stats?.lst || []
-    };
-  }
-  buildTopGenes(response, manhattanSettings, dtUsage) {
-    if (!response.topGeneTable || !response.stats?.lst) return null;
-    const totalGenes = response.stats.lst[0].rows.find((r) => r[0] === "Total Genes")?.[1] ?? "?";
-    const headerText = `Top Genes (showing ${response.topGeneTable.rows.length.toLocaleString()} of ${totalGenes})`;
-    const qValueEntries = this.buildQValueEntries(response.topGeneTable.columns, dtUsage);
-    const lesionTypeCircleCache = this.buildCircleCache(manhattanSettings.lesionTypeColors);
-    const qValueThreshold = manhattanSettings.qValueThreshold;
-    const rows = response.topGeneTable.rows.map((row) => {
-      const circles = qValueEntries.filter(({ colIndex }) => {
-        const qValue = row[colIndex]?.value;
-        return typeof qValue === "number" && qValue < qValueThreshold;
-      }).map(({ type }) => lesionTypeCircleCache.get(type));
-      return [{ value: "", html: circles.join("") }, ...row];
-    });
-    return {
-      headerText,
-      columns: [{ label: "", width: "20px" }, ...response.topGeneTable.columns],
-      rows,
-      dataItems: response.topGeneTable.rows
-    };
-  }
-  buildQValueEntries(columns, dtUsage) {
-    const dtMapping = {};
-    Object.entries(dt2lesion).forEach(([dt, cfg]) => {
-      dtMapping[dt] = cfg.lesionTypes.map((lt) => ({
-        col: `Q-value (${lt.name})`,
-        type: lt.lesionType
-      }));
-    });
-    const entries = [];
-    Object.entries(dtUsage).forEach(([key, info]) => {
-      const isChecked = typeof info === "object" ? info?.checked : !!info;
-      if (isChecked && dtMapping[key]) {
-        dtMapping[key].forEach(({ col, type }) => {
-          const colIndex = columns.findIndex((c) => c.label === col);
-          if (colIndex !== -1) entries.push({ colIndex, type });
-        });
-      }
-    });
-    return entries;
-  }
-  buildCircleCache(lesionTypeColors) {
-    return new Map(
-      Object.entries(lesionTypeColors).map(([type, color]) => [
-        type,
-        `<span style="display:inline-block;width:8px;height:8px;border-radius:50%;background-color:${color};margin-right:3px;"></span>`
-      ])
-    );
-  }
-};
-
-// plots/manhattan/manhattan.ts
-function plotManhattan(div, data, settings, app) {
-  settings = {
-    ...settings
-  };
-  let interactivePoints = data.plotData.points;
-  if (data.plotData.points.length > settings.interactiveDotsCap) {
-    interactivePoints = data.plotData.points.sort((a, b) => b.y - a.y).slice(0, settings.interactiveDotsCap);
-  }
-  div.style("position", "relative");
-  const geneTip = new Menu({ padding: "" });
-  const svg = div.append("svg").attr("data-testid", "sjpp-manhattan").attr("width", settings.plotWidth + 2 * settings.pngDotRadius + settings.yAxisX + settings.yAxisSpace).attr("height", settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY * 4);
-  const yPlot = linear().domain([data.plotData.y_min, data.plotData.y_max]).range([settings.plotHeight + 2 * settings.pngDotRadius, 0]);
-  const yAxisScale = linear().domain([0, data.plotData.y_max - settings.pngDotRadius]).range([yPlot(0), yPlot(data.plotData.y_max - settings.pngDotRadius)]);
-  const axisG = svg.append("g").attr("transform", `translate(${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,${data.pngImg || data.png}`);
-  const xScale = linear().domain([-data.plotData.x_buffer, data.plotData.total_genome_length + data.plotData.x_buffer]).range([0, settings.plotWidth + 2 * settings.pngDotRadius]);
-  if (settings.showInteractiveDots && data.plotData.points && data.plotData.points.length > 0) {
-    const hoverLayer = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).style("pointer-events", "none");
-    const cover = select_default(svg.node().parentNode).append("div").style("position", "absolute").style("left", `${settings.yAxisX + settings.yAxisSpace}px`).style("top", `${settings.yAxisY}px`).style("width", `${settings.plotWidth + 2 * settings.pngDotRadius}px`).style("height", `${settings.plotHeight + 2 * settings.pngDotRadius}px`).style("pointer-events", "all");
-    const circlePath = (r) => `M${r},0 A${r},${r} 0 1,1 ${-r},0 A${r},${r} 0 1,1 ${r},0 Z`;
-    const interactions = new DataPointInteractions({
-      cover,
-      hoverLayer,
-      hoverTip: geneTip,
-      points: interactivePoints,
-      getX: (d) => d.pixel_x,
-      getY: (d) => d.pixel_y,
-      hitRadius: settings.pngDotRadius + 3,
-      toHoverSpec: (d) => ({
-        path: circlePath(settings.pngDotRadius),
-        transform: `translate(${d.pixel_x},${d.pixel_y})`,
-        fill: "none",
-        stroke: "black",
-        strokeWidth: settings.interactiveDotStrokeWidth
-      }),
-      maxTooltipRows: settings.maxTooltipGenes,
-      itemNoun: "gene",
-      renderSingleHoverTooltip: (d, container) => {
-        const table = table2col({ holder: container.append("div"), margin: "10px" });
-        table.addRow("Gene", d.gene);
-        table.addRow("Position", `${d.chrom}:${d.start}-${d.end}`);
-        const [t1, t2] = table.addRow();
-        t1.text("Type");
-        t2.html(`<span style="color:${d.color}">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`);
-        table.addRow("Q-value", d.q_value.toPrecision(3));
-        table.addRow("Subject count", d.nsubj);
-      },
-      buildMultiHitTableData: (dots) => ({
-        columns: [
-          { label: "Gene" },
-          { label: "Position" },
-          { label: "Type" },
-          { label: "Q-value", sortable: true },
-          { label: "Subject count", sortable: true }
-        ],
-        rows: dots.map((d) => [
-          { value: d.gene },
-          { value: `${d.chrom}:${d.start}-${d.end}` },
-          {
-            html: `<span style="color:${d.color}">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`
-          },
-          { value: d.q_value.toPrecision(3) },
-          { value: d.nsubj }
-        ])
-      }),
-      // Manhattan single-click goes straight to a lollipop launch — no menu.
-      // Release hover-suppression immediately so the cursor's next move re-engages.
-      onSingleClick: (d, _event, ctx) => {
-        ctx.dismiss();
-        if (app) createLollipopFromGene(d.gene, app);
-      },
-      // Manhattan multi-click shows showResultsTable directly with `app + clickMenu`
-      // so the table renders inline Matrix/Lollipop buttons. Reuses the module's
-      // clickMenu so its onHide cleanup (clear flag, clear hover) fires on dismiss.
-      // Content is built BEFORE show2 so Menu can measure the populated rect for
-      // its right-edge clamp — otherwise the wide table is placed at cursor+offsetX
-      // and extends off the right edge of the viewport.
-      onMultiClick: (dots, event, ctx) => {
-        if (!app) {
-          ctx.dismiss();
-          return;
-        }
-        ctx.clickMenu.clear();
-        const holder = ctx.clickMenu.d.append("div").style("margin", "10px");
-        showResultsTable({ tableDiv: holder, hits: dots, app, clickMenu: ctx.clickMenu });
-        ctx.clickMenu.show2(event.clientX, event.clientY);
-      }
-    });
-    interactions.attach();
-  }
-  if (data.plotData.chrom_data) {
-    const chromLabelY = settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + 10;
-    Object.entries(data.plotData.chrom_data).forEach(([chrom, chromData]) => {
-      const chromLabel = chrom.replace("chr", "");
-      if (chromLabel === "M") return;
-      const centerPos = settings.yAxisX + settings.yAxisSpace + xScale(chromData.center);
-      svg.append("text").attr("x", centerPos).attr("y", chromLabelY).attr("text-anchor", "middle").attr("font-size", `${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", `${settings.legendFontSize + 2}px`).text(item.type);
-    });
-  }
-}
-
-// plots/grin2/view/GRIN2ResultsView.ts
-var sectionMargin = "20px 0";
-var btnMargin = "10px";
-var headerMargin = "0 10px 0 0";
-var headerFontSize = 14;
-var statsTableFontWeight = "bold";
-var backgroundColor = "#f8f8f8";
-var GRIN2ResultsView = class {
-  constructor(holder, app) {
-    this.holder = holder;
-    this.app = app;
-  }
-  clear() {
-    this.holder.selectAll("*").remove();
-  }
-  render(viewData) {
-    if (viewData.manhattan) {
-      plotManhattan(this.holder, viewData.manhattan.plotData, viewData.manhattan.settings, this.app);
-    }
-    if (viewData.topGenes) {
-      const { headerText, columns, rows, dataItems } = viewData.topGenes;
-      const tableContainer = this.holder.append("div").style("margin", sectionMargin);
-      const headerDiv = tableContainer.append("div").style("display", "flex").style("align-items", "center").style("margin", btnMargin);
-      headerDiv.append("h3").style("margin", headerMargin).style("font-size", `${headerFontSize}px`).text(headerText);
-      showResultsTable({
-        tableDiv: tableContainer.append("div"),
-        app: this.app,
-        columns,
-        rows,
-        dataItems,
-        getRowKey: (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_${(/* @__PURE__ */ new Date()).toISOString().replace(/[:.]/g, "-").slice(0, -5)}.tsv`
-        },
-        header: {
-          allowSort: true,
-          style: {
-            "font-weight": statsTableFontWeight,
-            "background-color": backgroundColor
-          }
-        }
-      });
-    }
-    if (viewData.statsSections.length > 0) {
-      const tablesContainer = this.holder.append("div").style("margin-top", "50px");
-      for (const section of viewData.statsSections) {
-        tablesContainer.append("h4").style("margin", headerMargin).style("margin-top", "15px").style("font-size", `${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);
-        }
-      }
-    }
-  }
-};
-
-// plots/grin2/settings/defaults.ts
-var CNV_LOSS_THRESHOLD_FALLBACK = -0.4;
-var CNV_GAIN_THRESHOLD_FALLBACK = 0.4;
-var CNV_MAX_SEG_LENGTH_FALLBACK = 2e6;
-var CNV_TYPE_CONFIG = {
-  log2ratio: {
-    lossDefault: CNV_LOSS_THRESHOLD_FALLBACK,
-    gainDefault: CNV_GAIN_THRESHOLD_FALLBACK,
-    lossMin: -5,
-    lossMax: 0,
-    gainMin: 0,
-    gainMax: 5,
-    step: 0.05,
-    hideThresholds: false,
-    unitLabel: "log2 ratio"
-  },
-  segmean: {
-    lossDefault: CNV_LOSS_THRESHOLD_FALLBACK,
-    gainDefault: CNV_GAIN_THRESHOLD_FALLBACK,
-    lossMin: -5,
-    lossMax: 0,
-    gainMin: 0,
-    gainMax: 5,
-    step: 0.05,
-    hideThresholds: false,
-    unitLabel: "segment mean"
-  },
-  copyNumber: {
-    lossDefault: 1,
-    gainDefault: 3,
-    lossMin: 0,
-    lossMax: 2,
-    gainMin: 2,
-    gainMax: 20,
-    step: 1,
-    hideThresholds: false,
-    unitLabel: "copy number"
-  },
-  category: {
-    lossDefault: 0,
-    gainDefault: 0,
-    lossMin: 0,
-    lossMax: 0,
-    gainMin: 0,
-    gainMax: 0,
-    step: 1,
-    hideThresholds: true,
-    unitLabel: ""
-  }
-};
-var EXCLUDE_OVERLAP_FRAC_FALLBACK = 0.5;
-function getDefaultGRIN2Settings(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);
-}
-
-// plots/grin2/view/GRIN2ControlsView.ts
-var optionsTextFontSize = 12;
-var tableFontSize = 11;
-var inputWidth = "80px";
-var inputPadding = "2px 4px";
-var inputBorderColor = "#ddd";
-var inputBorderRadius = "2px";
-var checkboxContainerMaxHeight = "150px";
-var checkboxContainerBorder = "1px solid #ddd";
-var controlGap = "8px";
-var checkboxMarginBottom = "2px";
-var GRIN2ControlsView = class {
-  constructor(opts) {
-    this.snvindelCheckbox = null;
-    this.cnvCheckbox = null;
-    this.fusionCheckbox = null;
-    this.svCheckbox = null;
-    this.runButton = null;
-    this.consequenceCheckboxes = {};
-    this.snvindelSelectAllBtn = null;
-    this.snvindelClearAllBtn = null;
-    this.snvindelDefaultBtn = null;
-    this.cnv_lossThreshold = null;
-    this.cnv_gainThreshold = null;
-    this.cnv_maxSegLength = null;
-    /** how this ds quantifies cnv values; from the selected cnv type or ds.queries.cnv.type, default 'log2ratio' */
-    this.cnvType = "log2ratio";
-    /** id of the user-selected cnv file type, when the ds exposes singleSampleMutation.cnvTypes (else null) */
-    this.cnvSelectedTypeId = null;
-    // one checkbox per genome-declared blacklist source, keyed by source name
-    this.excludeCheckboxes = {};
-    this.exclude_overlapFrac = null;
-    this.snvindelMafFilter = null;
-    this.headerHolder = opts.headerHolder;
-    this.controlsHolder = opts.controlsHolder;
-    this.config = opts.config;
-    this.vocabApi = opts.vocabApi;
-    this.genome = opts.genome;
-    this.callbacks = opts.callbacks;
-  }
-  build() {
-    this.headerHolder.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.controlsHolder, disableScroll: true });
-    const queries = this.vocabApi.termdbConfig.queries;
-    if (queries.snvindel) this.addSnvindelRow(table);
-    if (queries.cnv || queries.singleSampleMutation?.cnvTypes?.length) this.addCnvRow(table);
-    if (queries.svfusion?.dtLst?.includes(dtfusionrna)) this.addFusionRow(table);
-    if (queries.svfusion?.dtLst?.includes(dtsv)) this.addSvRow(table);
-    this.addExcludeRow(table);
-    this.runButton = this.controlsHolder.append("button").attr("data-testid", "sjpp-grin2-run-button").style("margin-left", "100px").text("Run GRIN2").on("click", () => this.callbacks.onRun());
-    this.updateRunButtonFromCheckboxes();
-  }
-  getDtUsage() {
-    const dtUsage = structuredClone(this.config.settings.dtUsage);
-    if (dtUsage[dtsnvindel]) dtUsage[dtsnvindel].checked = this.snvindelCheckbox.property("checked");
-    if (dtUsage[dtcnv]) dtUsage[dtcnv].checked = this.cnvCheckbox.property("checked");
-    if (dtUsage[dtfusionrna]) dtUsage[dtfusionrna].checked = this.fusionCheckbox.property("checked");
-    if (dtUsage[dtsv]) dtUsage[dtsv].checked = this.svCheckbox.property("checked");
-    return dtUsage;
-  }
-  getConfigValues(dtUsage) {
-    const requestConfig = {};
-    if (dtUsage[dtsnvindel]?.checked) {
-      requestConfig.snvindelOptions = {
-        consequences: this.getSelectedConsequences()
-      };
-      if (this.snvindelMafFilter) {
-        requestConfig.snvindelOptions.mafFilter = this.snvindelMafFilter;
-      }
-    }
-    if (dtUsage[dtcnv]?.checked) {
-      requestConfig.cnvOptions = {
-        maxSegLength: parseFloat(this.cnv_maxSegLength.property("value"))
-      };
-      if (this.cnvSelectedTypeId) requestConfig.cnvOptions.cnvType = this.cnvSelectedTypeId;
-      if (this.cnv_lossThreshold && this.cnv_gainThreshold) {
-        requestConfig.cnvOptions.lossThreshold = parseFloat(this.cnv_lossThreshold.property("value"));
-        requestConfig.cnvOptions.gainThreshold = parseFloat(this.cnv_gainThreshold.property("value"));
-      }
-    }
-    if (dtUsage[dtfusionrna]?.checked) requestConfig.fusionOptions = {};
-    if (dtUsage[dtsv]?.checked) requestConfig.svOptions = {};
-    if (Object.keys(this.excludeCheckboxes).length > 0) {
-      const blacklists = Object.entries(this.excludeCheckboxes).filter(([, cb]) => cb.property("checked")).map(([name]) => name);
-      const overlapFracRaw = this.exclude_overlapFrac ? parseFloat(this.exclude_overlapFrac.property("value")) : EXCLUDE_OVERLAP_FRAC_FALLBACK;
-      requestConfig.excludeOptions = {
-        blacklists,
-        overlapFrac: Number.isFinite(overlapFracRaw) ? overlapFracRaw : EXCLUDE_OVERLAP_FRAC_FALLBACK
-      };
-    }
-    return requestConfig;
-  }
-  setBusy(busy) {
-    this.controlsHolder?.style("pointer-events", busy ? "none" : "auto").style("opacity", busy ? "0.5" : "1");
-    this.runButton?.property("disabled", busy).text(busy ? "Running GRIN2..." : "Run GRIN2");
-  }
-  updateRunButtonFromCheckboxes() {
-    const dtUsage = this.snvindelCheckbox ? this.getDtUsage() : this.config.settings.dtUsage;
-    const anyChecked = Object.values(dtUsage).some((info) => info.checked);
-    this.runButton?.property("disabled", !anyChecked);
-  }
-  getSelectedConsequences() {
-    const consequences = [];
-    Object.entries(this.consequenceCheckboxes).forEach(([classKey, checkbox]) => {
-      if (checkbox.property("checked")) consequences.push(classKey);
-    });
-    return consequences;
-  }
-  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.vocabApi.termdbConfig.queries?.snvindel?.mafFilter;
-    if (mafFilterConfig) {
-      this.snvindelMafFilter = structuredClone(
-        this.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.config.settings.dtUsage[dtsnvindel].checked;
-    t2.table.style("display", isChecked ? "" : "none");
-    this.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();
-      }
-    });
-  }
-  addCnvRow(table) {
-    const [left, right] = table.addRow();
-    const cnvBody = right.append("div");
-    const useSaved = this.config.settings.runAnalysis === true;
-    const savedCnv = useSaved ? this.config.settings.cnvOptions : void 0;
-    const cnvQuery = this.vocabApi.termdbConfig.queries.cnv;
-    const cnvTypes = this.vocabApi.termdbConfig.queries.singleSampleMutation?.cnvTypes;
-    const radioHolder = cnvTypes?.length ? cnvBody.append("div").style("margin-bottom", "6px") : null;
-    const thresholdHolder = cnvBody.append("div");
-    if (cnvTypes?.length) {
-      const savedId = savedCnv?.cnvType;
-      this.cnvSelectedTypeId = savedId && cnvTypes.find((t) => t.id === savedId)?.id || cnvTypes[0].id;
-      make_radios({
-        holder: radioHolder,
-        options: cnvTypes.map((t) => ({
-          label: t.label,
-          value: t.id,
-          checked: t.id === this.cnvSelectedTypeId,
-          testid: `sjpp-grin2-cnvtype-${t.id}`
-        })),
-        styles: { display: "block" },
-        callback: (value) => {
-          this.cnvSelectedTypeId = value;
-          const def = cnvTypes.find((t) => t.id === value);
-          const savedForType = value === savedCnv?.cnvType ? savedCnv : void 0;
-          this.renderCnvThresholdRows(thresholdHolder, def?.valueType ?? "log2ratio", savedForType, cnvQuery);
-        }
-      });
-    } else {
-      this.cnvSelectedTypeId = null;
-    }
-    const initialValueType = (cnvTypes?.length ? cnvTypes.find((t) => t.id === this.cnvSelectedTypeId)?.valueType : cnvQuery?.type) ?? "log2ratio";
-    const initialSaved = !cnvTypes?.length || this.cnvSelectedTypeId === savedCnv?.cnvType ? savedCnv : void 0;
-    this.renderCnvThresholdRows(thresholdHolder, initialValueType, initialSaved, cnvQuery);
-    const dtUsage = this.config.settings.dtUsage;
-    const isChecked = useSaved && dtUsage[dtcnv]?.checked !== void 0 ? dtUsage[dtcnv].checked : !!(cnvQuery || cnvTypes?.length);
-    cnvBody.style("display", isChecked ? "" : "none");
-    this.cnvCheckbox = make_one_checkbox({
-      holder: left,
-      labeltext: dt2lesion[dtcnv].uilabel,
-      checked: isChecked,
-      testid: "sjpp-grin2-checkbox-cnv",
-      callback: (checked) => {
-        cnvBody.style("display", checked ? "" : "none");
-        this.updateRunButtonFromCheckboxes();
-      }
-    });
-  }
-  /** (Re)build the loss/gain/maxSeg inputs for a given cnv value type. Called on first render and whenever
-   *  the user switches cnv type — segmean/copyNumber/log2ratio have type-specific defaults and ranges, and
-   *  'category' is qualitative and hides the thresholds entirely. */
-  renderCnvThresholdRows(holder, valueType, savedCnv, cnvQuery) {
-    holder.selectAll("*").remove();
-    this.cnvType = valueType;
-    const cfg = CNV_TYPE_CONFIG[valueType];
-    const t2 = table2col({ holder });
-    if (!cfg.hideThresholds) {
-      this.cnv_lossThreshold = this.addOptionRowToTable(
-        t2,
-        cfg.unitLabel ? `Loss Threshold (${cfg.unitLabel})` : "Loss Threshold",
-        savedCnv?.lossThreshold ?? cnvQuery?.cnvLossCutoff ?? cfg.lossDefault,
-        cfg.lossMin,
-        cfg.lossMax,
-        cfg.step
-      );
-      this.cnv_gainThreshold = this.addOptionRowToTable(
-        t2,
-        cfg.unitLabel ? `Gain Threshold (${cfg.unitLabel})` : "Gain Threshold",
-        savedCnv?.gainThreshold ?? cnvQuery?.cnvGainCutoff ?? cfg.gainDefault,
-        cfg.gainMin,
-        cfg.gainMax,
-        cfg.step
-      );
-    } else {
-      this.cnv_lossThreshold = null;
-      this.cnv_gainThreshold = null;
-    }
-    this.cnv_maxSegLength = this.addOptionRowToTable(
-      t2,
-      "Max Segment Length",
-      savedCnv?.maxSegLength ?? cnvQuery?.cnvMaxLength ?? CNV_MAX_SEG_LENGTH_FALLBACK,
-      0,
-      1e9,
-      1e3
-    );
-  }
-  addFusionRow(table) {
-    const [left, right] = table.addRow();
-    const t2 = table2col({ holder: right });
-    const isChecked = this.config.settings.dtUsage[dtfusionrna].checked;
-    t2.table.style("display", isChecked ? "" : "none");
-    this.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();
-      }
-    });
-  }
-  addSvRow(table) {
-    const [left, right] = table.addRow();
-    const t2 = table2col({ holder: right });
-    const isChecked = this.config.settings.dtUsage[dtsv].checked;
-    t2.table.style("display", isChecked ? "" : "none");
-    this.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();
-      }
-    });
-  }
-  /** Artifact-region mask row. Renders one checkbox per blacklist source declared for the genome
-   * (Genome.blacklists, exposed to the client as {name}[]), plus the gene-overlap-fraction input.
-   * Skipped entirely when the genome declares no blacklists. Unchecking all sources disables the
-   * mask (server resolves an empty source list to no masking). */
-  addExcludeRow(table) {
-    const blacklists = this.genome?.blacklists || [];
-    if (!blacklists.length) return;
-    const [left, right] = table.addRow();
-    left.text("Exclude genes overlapping").style("padding-top", "4px");
-    const savedExclude = this.config.settings.runAnalysis === true ? this.config.settings.excludeOptions : void 0;
-    const savedNames = savedExclude?.blacklists;
-    const isChecked = (name) => savedNames ? savedNames.includes(name) : true;
-    this.excludeCheckboxes = {};
-    const cbContainer = right.append("div").style("margin-bottom", "6px");
-    blacklists.forEach((bl) => {
-      const div = cbContainer.append("div").style("margin-bottom", checkboxMarginBottom);
-      this.excludeCheckboxes[bl.name] = make_one_checkbox({
-        holder: div,
-        labeltext: bl.name,
-        checked: isChecked(bl.name),
-        divstyle: { "font-size": `${tableFontSize}px` },
-        callback: () => {
-        }
-      });
-    });
-    const t2 = table2col({ holder: right });
-    this.exclude_overlapFrac = this.addOptionRowToTable(
-      t2,
-      "Min gene overlap",
-      savedExclude?.overlapFrac ?? EXCLUDE_OVERLAP_FRAC_FALLBACK,
-      0,
-      1,
-      0.05
-    );
-  }
-  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", inputWidth).style("padding", inputPadding).style("border", `1px solid ${inputBorderColor}`).style("border-radius", inputBorderRadius).style("font-size", `${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.config.settings.snvindelOptions?.consequences;
-    const useSaved = this.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", controlGap);
-    this.snvindelSelectAllBtn = controlDiv.append("button").style("font-size", `${tableFontSize}px`).text("Select All");
-    this.snvindelClearAllBtn = controlDiv.append("button").style("font-size", `${tableFontSize}px`).text("Clear All");
-    this.snvindelDefaultBtn = controlDiv.append("button").style("font-size", `${tableFontSize}px`).text("Default");
-    const checkboxContainer = container.append("div").style("max-height", checkboxContainerMaxHeight).style("overflow-y", "auto").style("border", checkboxContainerBorder);
-    this.consequenceCheckboxes = {};
-    snvIndelClasses.forEach(([classKey, classInfo]) => {
-      const checkboxDiv = checkboxContainer.append("div").style("margin-bottom", checkboxMarginBottom);
-      const checkbox = make_one_checkbox({
-        holder: checkboxDiv,
-        labeltext: classInfo.label,
-        checked: initialChecked.has(classKey),
-        divstyle: { "font-size": `${tableFontSize}px` },
-        callback: () => {
-        }
-      });
-      checkboxDiv.select("label").attr("title", classInfo.desc);
-      this.consequenceCheckboxes[classKey] = checkbox;
-    });
-    this.snvindelSelectAllBtn.on("click", () => {
-      Object.values(this.consequenceCheckboxes).forEach((cb) => cb.property("checked", true));
-    });
-    this.snvindelClearAllBtn.on("click", () => {
-      Object.values(this.consequenceCheckboxes).forEach((cb) => cb.property("checked", false));
-    });
-    this.snvindelDefaultBtn.on("click", () => {
-      Object.entries(this.consequenceCheckboxes).forEach(([classKey, checkbox]) => {
-        checkbox.property("checked", canonicalDefault.has(classKey));
-      });
-    });
-  }
-};
-
-// plots/grin2/grin2.ts
-var GRIN2 = class extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.type = "grin2";
-    this.controlsView = null;
-    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"),
-      div: opts.holder.append("div").style("margin", "20px")
-    };
-    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 };
-  }
-  async init() {
-    this.model = new GRIN2Model(this.app.vocabApi);
-    this.resultsView = new GRIN2ResultsView(this.dom.div, this.app);
-    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.controlsView) {
-      this.controlsView = new GRIN2ControlsView({
-        headerHolder: this.dom.headerText,
-        controlsHolder: this.dom.controls,
-        config: this.state.config,
-        vocabApi: this.app.vocabApi,
-        genome: this.app.opts.genome,
-        callbacks: { onRun: () => this.handleRun() }
-      });
-      this.controlsView.build();
-      if (this.state.config.settings.runAnalysis) this.handleRun();
-    }
-  }
-  async handleRun() {
-    if (!this.controlsView) return;
-    this.controlsView.setBusy(true);
-    try {
-      const dtUsage = this.controlsView.getDtUsage();
-      this.resultsView.clear();
-      const configValues = this.controlsView.getConfigValues(dtUsage);
-      const manhattan = this.state.config.settings.manhattan;
-      const requestData = {
-        filter: getNormalRoot(this.state.termfilter.filter),
-        filter0: this.state.termfilter.filter0,
-        width: manhattan?.plotWidth,
-        height: manhattan?.plotHeight,
-        pngDotRadius: manhattan?.pngDotRadius,
-        devicePixelRatio: window.devicePixelRatio,
-        maxGenesToShow: manhattan?.maxGenesToShow,
-        lesionTypeColors: manhattan?.lesionTypeColors,
-        qValueThreshold: manhattan?.qValueThreshold,
-        maxCappedPoints: manhattan?.maxCappedPoints,
-        hardCap: manhattan?.hardCap,
-        binSize: manhattan?.binSize,
-        ...configValues
-      };
-      const response = await this.model.fetchGrin2Data(requestData, this.api.getAbortSignal());
-      if (response.status === "error") throw `GRIN2 analysis failed: ${response.error}`;
-      const vm = new GRIN2ViewModel(response, manhattan, dtUsage);
-      this.resultsView.render(vm.viewData);
-      this.app.dispatch({
-        type: "plot_edit",
-        id: this.id,
-        config: {
-          ...this.state.config,
-          settings: {
-            ...this.state.config.settings,
-            ...configValues,
-            dtUsage,
-            runAnalysis: true
-          }
-        }
-      });
-    } catch (error) {
-      if (this.dom.div) {
-        sayerror(this.dom.div, `Error running GRIN2: ${error instanceof Error ? error.message : error}`);
-      }
-    } finally {
-      this.controlsView?.setBusy(false);
-    }
-  }
-};
-var grin2Init = getCompInit(GRIN2);
-var componentInit = grin2Init;
-async function getPlotConfig(opts, app) {
-  const queries = app.vocabApi.termdbConfig.queries;
-  const defaultSettings = getDefaultGRIN2Settings(opts);
-  const dtUsage = {};
-  if (queries?.snvindel) {
-    dtUsage[dtsnvindel] = { checked: true, label: dt2lesion[dtsnvindel].uilabel };
-  }
-  if (queries?.cnv || queries?.singleSampleMutation?.cnvTypes?.length) {
-    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
-      }
-    }
-  };
-  return copyMerge(config, opts);
-}
-export {
-  componentInit,
-  getPlotConfig,
-  grin2Init
-};
-//# sourceMappingURL=grin2-DR7XJIAS.js.map