@sjcrh/proteinpaint-client 2.166.0 → 2.167.1

package/dist/grin2-I6GJF35U.js

@@ -1,882 +0,0 @@
-import {
-  PlotBase
-} from "./chunk-I2GCD26Y.js";
-import {
-  axisstyle,
-  get$id,
-  getNormalRoot,
-  make_one_checkbox,
-  renderTable,
-  sayerror,
-  table2col,
-  to_svg
-} from "./chunk-UT6W4ZZL.js";
-import "./chunk-HJ6L54YS.js";
-import {
-  dofetch3
-} from "./chunk-5TDKRZN5.js";
-import "./chunk-RYRCMHYR.js";
-import {
-  dt2lesion,
-  dtcnv,
-  dtfusionrna,
-  dtsnvindel,
-  dtsv,
-  mclass,
-  proteinChangingMutations
-} from "./chunk-ECKWM4HB.js";
-import {
-  Menu
-} from "./chunk-NXOWHUR4.js";
-import {
-  icons
-} from "./chunk-5MWX5HUZ.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-ICNJQHQZ.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-FYTZCTJC.js";
-import "./chunk-7NTZWOJV.js";
-import "./chunk-OMO754MK.js";
-import "./chunk-RA5EXEHB.js";
-import "./chunk-PMZS3SHH.js";
-import {
-  axisLeft
-} from "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import {
-  linear
-} from "./chunk-W2IWHXLL.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-UJUXE42U.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/manhattan/manhattan.ts
-function plotManhattan(div, data, settings, app) {
-  settings = {
-    ...settings
-  };
-  div.style("position", "relative");
-  const geneTip = new Menu({ padding: "" });
-  const svg = div.append("svg").attr("data-testid", "sjpp-manhattan").attr("width", settings.plotWidth + 2 * settings.pngDotRadius + settings.yAxisX + settings.yAxisSpace).attr("height", settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY * 4);
-  const yPlot = linear().domain([data.plotData.y_min, data.plotData.y_max]).range([settings.plotHeight + 2 * settings.pngDotRadius, 0]);
-  const yAxisScale = linear().domain([0, data.plotData.y_max - settings.pngDotRadius]).range([yPlot(0), yPlot(data.plotData.y_max - settings.pngDotRadius)]);
-  const axisG = svg.append("g").attr("transform", `translate(${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("-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},${settings.yAxisY})`);
-    pointsLayer.selectAll("circle").data(data.plotData.points).enter().append("circle").attr("cx", (d) => d.pixel_x / devicePixelRatio).attr("cy", (d) => d.pixel_y / devicePixelRatio).attr("r", settings.interactiveDotRadius).attr("fill-opacity", 0).attr("stroke", "black").attr("stroke-width", settings.interactiveDotStrokeWidth).attr("stroke-opacity", 0).on("mouseover", (event, d) => {
-      event.target.setAttribute("stroke-opacity", 1);
-      geneTip.clear().show(event.clientX, event.clientY);
-      const table = table2col({
-        holder: geneTip.d.append("div"),
-        margin: "10px"
-      });
-      table.addRow("Gene", d.gene);
-      table.addRow("Position", `${d.chrom}:${d.start}-${d.end}`);
-      const [t1, t2] = table.addRow();
-      t1.text("Type");
-      t2.html(`<span style="color:${d.color}">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`);
-      table.addRow("-log\u2081\u2080(q-value)", d.y.toFixed(3));
-      table.addRow("Subject count", d.nsubj);
-    }).on("mouseout", (event) => {
-      event.target.setAttribute("stroke-opacity", 0);
-      geneTip.hide();
-    }).on("click", (event, d) => {
-      if (app) createLollipopFromGene(d.gene, app);
-    });
-  }
-  if (data.plotData.chrom_data) {
-    const chromLabelY = settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY;
-    Object.entries(data.plotData.chrom_data).forEach(([chrom, chromData]) => {
-      const chromLabel = chrom.replace("chr", "");
-      if (chromLabel === "M") return;
-      const centerPos = settings.yAxisX + settings.yAxisSpace + xScale(chromData.center);
-      svg.append("text").attr("x", centerPos).attr("y", chromLabelY).attr("text-anchor", "middle").attr("font-size", `${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);
-}
-
-// plots/grin2/grin2.ts
-var GRIN2 = class extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.type = "grin2";
-    // 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 });
-      this.dom.snvindel_minTotalDepth = this.addOptionRowToTable(
-        t2,
-        "Min Total Depth",
-        this.state.config.settings?.snvindelOptions?.minTotalDepth ?? 10,
-        // default. Getting from state and defaulting to 10 if not available
-        0,
-        // min
-        1e6,
-        // max
-        1
-        // step
-      );
-      this.dom.snvindel_minAltAlleleCount = this.addOptionRowToTable(
-        t2,
-        "Min Alt Allele Count",
-        this.state.config.settings?.snvindelOptions?.minAltAlleleCount ?? 2,
-        // default. Getting from state and defaulting to 2 if not available
-        0,
-        1e6,
-        1
-      );
-      {
-        const [labelCell, containerCell] = t2.addRow();
-        labelCell.text("Consequences").style("font-size", `${this.optionsTextFontSize}px`).style("font-weight", "600").style("padding-top", "8px");
-        this.createConsequenceCheckboxes(containerCell);
-      }
-      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: "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: "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: "grin2-checkbox-sv",
-        callback: (checked) => {
-          t2.table.style("display", checked ? "" : "none");
-          this.updateRunButtonFromCheckboxes();
-        }
-      });
-    };
-    this.opts = opts;
-    opts.holder.classed("sjpp-grin2-main", true);
-    this.dom = {
-      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");
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    return {
-      config
-    };
-  }
-  // Enable the run button only if at least one data type is checked
-  updateRunButtonState(dtu) {
-    const dtUsage = dtu || this.state.config.settings.dtUsage;
-    const anyChecked = Object.values(dtUsage).some((info) => info.checked);
-    this.dom.runButton.property("disabled", !anyChecked);
-  }
-  createConfigTable() {
-    this.dom.controls.append("div").style("margin", "15px").html(
-      "GRIN2 stands for Genomic Random Interval (GRIN) statistical model. For details, see <a href=https://pubmed.ncbi.nlm.nih.gov/23842812/ target=_blank>Pounds, S. et al. Bioinformatics 2013</a>."
-    );
-    const table = table2col({ holder: this.dom.controls, disableScroll: true });
-    const queries = this.app.vocabApi.termdbConfig.queries;
-    if (queries.snvindel) {
-      this.addSnvindelRow(table);
-    }
-    if (queries.cnv) {
-      this.addCnvRow(table);
-    }
-    if (queries.svfusion?.dtLst?.includes(dtfusionrna)) {
-      this.addFusionRow(table);
-    }
-    if (queries.svfusion?.dtLst?.includes(dtsv)) {
-      this.addSvRow(table);
-    }
-    this.dom.runButton = this.dom.controls.append("button").attr("data-testid", "grin2-run-button").style("margin-left", "100px").text("Run GRIN2").on("click", () => {
-      this.runAnalysis();
-    });
-    if (this.state.config.settings.runAnalysis) {
-      this.runAnalysis();
-    } else {
-      this.updateRunButtonState();
-    }
-  }
-  // Helper method to add option rows to table2col instances
-  addOptionRowToTable(table, label, defaultValue, min, max, step) {
-    const [labelCell, inputCell] = table.addRow();
-    labelCell.text(label).style("font-size", `${this.optionsTextFontSize}px`);
-    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 (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 = {
-        genome: this.app.vocabApi.vocab.genome,
-        dslabel: this.app.vocabApi.vocab.dslabel,
-        filter: getNormalRoot(this.app.vocabApi.state.termfilter.filter),
-        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,
-        ...configValues
-      };
-      const response = await dofetch3("/grin2", {
-        body: requestData
-      });
-      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) {
-      sayerror(this.dom.div, `Error running GRIN2: ${error instanceof Error ? error.message : error}`);
-    } finally {
-      this.dom.controls.style("pointer-events", "auto").style("opacity", "1");
-      this.dom.runButton.property("disabled", false).text("Run GRIN2");
-    }
-  }
-  async init() {
-  }
-  async main() {
-    const config = structuredClone(this.state.config);
-    if (config.childType != this.type && config.chartType != this.type) return;
-    if (!this.dom.runButton) {
-      this.createConfigTable();
-    }
-  }
-  renderResults(result) {
-    if (result.pngImg) {
-      const plotData = result;
-      const plotDiv = this.dom.div;
-      const manhattanSettings = this.state.config.settings.manhattan;
-      plotManhattan(plotDiv, plotData, manhattanSettings, this.app);
-    }
-    if (result.topGeneTable) {
-      const tableContainer = this.dom.div.append("div").style("margin", this.sectionMargin);
-      const headerDiv = tableContainer.append("div").style("display", "flex").style("align-items", "center").style("margin", this.btnMargin);
-      headerDiv.append("h3").style("margin", this.headerMargin).style("font-size", `${this.headerFontSize}px`).text(`Top Genes (showing ${result.showingTop?.toLocaleString()} of ${result.totalGenes?.toLocaleString()})`);
-      const matrixBtn = headerDiv.append("button").text("Matrix (0 genes selected)").property("disabled", true).on("click", () => {
-        matrixBtn.property("disabled", true);
-        this.createMatrixFromGenes(selectedGenes);
-      });
-      const lollipopBtn = headerDiv.append("button").text("Lollipop").property("disabled", true).on("click", () => {
-        if (lastTouchedGene) {
-          lollipopBtn.property("disabled", true);
-          createLollipopFromGene(lastTouchedGene, this.app);
-        }
-      });
-      const tableDiv = tableContainer.append("div");
-      const selectedGenes = [];
-      let lastTouchedGene = null;
-      const lesionTypeColors = this.state.config.settings.manhattan.lesionTypeColors;
-      const qValueThreshold = this.state.config.settings.manhattan.qValueThreshold;
-      const columns = result.topGeneTable.columns;
-      const dtMapping = {};
-      Object.entries(dt2lesion).forEach(([dt, config]) => {
-        dtMapping[dt] = config.lesionTypes.map((lt) => ({
-          col: `Q-value (${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:${color};margin-right:3px;"></span>`
-        ])
-      );
-      const processedRows = result.topGeneTable.rows.map((row) => {
-        const circles = qValueEntries.filter(({ colIndex }) => {
-          const qValue = row[colIndex]?.value;
-          return typeof qValue === "number" && qValue < qValueThreshold;
-        }).map(({ type }) => lesionTypeCircleCache.get(type));
-        return [{ value: "", html: circles.join("") }, ...row];
-      });
-      renderTable({
-        columns: modifiedColumns,
-        rows: processedRows,
-        div: tableDiv,
-        maxHeight: "400px",
-        maxWidth: "100%",
-        dataTestId: "grin2-top-genes-table",
-        noButtonCallback: (rowIndex, checkboxNode) => {
-          const geneName = result.topGeneTable.rows[rowIndex][0]?.value;
-          if (checkboxNode.checked) {
-            selectedGenes.push(geneName);
-            lastTouchedGene = geneName;
-          } else {
-            selectedGenes.splice(selectedGenes.indexOf(geneName), 1);
-            lastTouchedGene = selectedGenes.length > 0 ? selectedGenes[selectedGenes.length - 1] : null;
-          }
-          if (selectedGenes.length > 0) {
-            lollipopBtn.text(`Lollipop (${lastTouchedGene})`);
-            lollipopBtn.property("disabled", false);
-          } else {
-            lollipopBtn.text("Lollipop");
-            lollipopBtn.property("disabled", true);
-          }
-          matrixBtn.text(`Matrix (${selectedGenes.length} genes selected)`).property("disabled", !selectedGenes.length);
-        },
-        selectAll: false,
-        download: {
-          fileName: `grin2_top_genes_${(/* @__PURE__ */ new Date()).toISOString().replace(/[:.]/g, "-").slice(0, -5)}.tsv`
-        },
-        header: {
-          allowSort: true,
-          style: {
-            "font-weight": this.statsTableFontWeight,
-            "background-color": this.backgroundColor
-          }
-        }
-      });
-    }
-    if (result.processingSummary) {
-      const headerDiv = this.dom.div.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("GRIN2 Processing Summary");
-      const tablesContainer = this.dom.div.append("div");
-      const generalTable = table2col({
-        holder: tablesContainer.append("div")
-      });
-      generalTable.addRow("Total Samples", result.processingSummary.totalSamples.toLocaleString());
-      generalTable.addRow("Processed Samples", result.processingSummary.processedSamples.toLocaleString());
-      generalTable.addRow("Unprocessed Samples", (result.processingSummary.unprocessedSamples ?? 0).toLocaleString());
-      generalTable.addRow("Failed Samples", result.processingSummary.failedSamples.toLocaleString());
-      generalTable.addRow(
-        "Failed Files",
-        result.processingSummary.failedFiles?.length ? result.processingSummary.failedFiles.map((f) => f.sampleName).join(", ") : "0"
-      );
-      generalTable.addRow("Total Lesions", result.processingSummary.totalLesions.toLocaleString());
-      generalTable.addRow("Processed Lesions", result.processingSummary.processedLesions.toLocaleString());
-      if (result.processingSummary.lesionCounts?.byType) {
-        const typeLabels = {};
-        Object.values(dt2lesion).forEach((config) => {
-          config.lesionTypes.forEach((lt) => {
-            typeLabels[lt.lesionType] = lt.name;
-          });
-        });
-        const columns = [
-          { label: "Lesion Type" },
-          { label: "Count", sortable: true },
-          { label: "Samples", sortable: true },
-          { label: "Capped" }
-        ];
-        const rows = Object.entries(result.processingSummary.lesionCounts.byType).map(([type, typeData]) => {
-          const { count, capped, samples } = typeData;
-          return [
-            { value: typeLabels[type] || type },
-            { value: count.toLocaleString() },
-            { value: samples?.toLocaleString() ?? "0" },
-            { value: capped ? "Yes" : "No" }
-          ];
-        });
-        renderTable({
-          columns,
-          rows,
-          dataTestId: "grin2-lesion-counts-table",
-          div: tablesContainer.append("div"),
-          showLines: false,
-          striped: true,
-          maxHeight: "none",
-          maxWidth: "100%",
-          resize: false,
-          download: {
-            fileName: `grin2_lesion_stats_${(/* @__PURE__ */ new Date()).toISOString().replace(/[:.]/g, "-").slice(0, -5)}.tsv`
-          },
-          header: {
-            style: {
-              "font-weight": this.statsTableFontWeight,
-              "background-color": this.backgroundColor
-            },
-            allowSort: true
-          }
-        });
-      }
-    }
-    if (result.timing) {
-      this.dom.div.append("div").style("margin", this.sectionMargin).style("font-size", `${this.optionsTextFontSize}px`).style("color", this.optionsTextColor).text(
-        `Analysis completed in ${result.timing.totalTime} (Processing: ${result.timing.processingTime}, GRIN2: ${result.timing.grin2Time}, Plotting: ${result.timing.plottingTime})`
-      );
-    }
-    const expectedToProcessSamples = result.processingSummary.totalSamples - result.processingSummary.failedSamples;
-    if (result.processingSummary.processedSamples < expectedToProcessSamples) {
-      this.dom.div.append("div").style("margin", this.sectionMargin).style("font-size", `${this.optionsTextFontSize}px`).style("color", this.optionsTextColor).text(
-        `Note: Per-type lesion caps were reached before all samples could be processed. Analysis ran on ${result.processingSummary.processedSamples.toLocaleString()} of ${expectedToProcessSamples.toLocaleString()} samples.`
-      );
-    }
-  }
-  async createMatrixFromGenes(geneSymbols) {
-    try {
-      const termwrappers = await Promise.all(
-        geneSymbols.map(async (gene) => {
-          const term = {
-            type: "geneVariant",
-            gene,
-            name: gene
-          };
-          const minTwCopy = this.app.vocabApi.getTwMinCopy({ term });
-          return {
-            $id: await get$id(minTwCopy),
-            term,
-            q: {}
-          };
-        })
-      );
-      this.app.dispatch({
-        type: "plot_create",
-        config: {
-          chartType: "matrix",
-          dataType: "geneVariant",
-          termgroups: [
-            {
-              name: "Genomic alterations",
-              lst: termwrappers
-            }
-          ]
-        }
-      });
-    } catch (error) {
-      sayerror(this.dom.div, `Error creating matrix: ${error instanceof Error ? error.message : error}`);
-    }
-  }
-};
-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: 20,
-      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
-      maxGenesToShow: 500,
-      // Q-value threshold for significance indicators in the table
-      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
-      }
-    }
-  };
-  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
-    },
-    hidePlotFilter: true
-  };
-  return copyMerge(config, opts);
-}
-export {
-  componentInit,
-  getDefaultSettings,
-  getPlotConfig,
-  grin2Init
-};
-//# sourceMappingURL=grin2-I6GJF35U.js.map