@sjcrh/proteinpaint-client 2.212.0 → 2.213.0

package/dist/grin2-5TH4EBVQ.js

@@ -1,949 +0,0 @@
-import {
-  manhattanLayoutDefaults,
-  plotManhattan
-} from "./chunk-QWCKIRW2.js";
-import {
-  PlotBase,
-  controlsInit,
-  filterInit,
-  getCombinedTermFilter,
-  getNormalRoot,
-  make_one_checkbox,
-  make_radios,
-  sayerror,
-  showResultsTable,
-  table2col
-} from "./chunk-VHDYIOWU.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-5WIA4KFA.js";
-import "./chunk-7XZA2XR2.js";
-import "./chunk-DD3DWHUY.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-RMUK3TLD.js";
-import "./chunk-HH5JKOE6.js";
-import "./chunk-RU2UHH7M.js";
-import {
-  dt2lesion,
-  dtcnv,
-  dtfusionrna,
-  dtitd,
-  dtsnvindel,
-  dtsv,
-  mclass,
-  mclasscnvAmp,
-  mclasscnvHomozygousDel,
-  mclasscnvgain,
-  mclasscnvloh,
-  mclasscnvloss,
-  proteinChangingMutations
-} from "./chunk-57Z4VYLM.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.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:${color};margin-right:3px;"></span>`
-      ])
-    );
-  }
-};
-
-// plots/grin2/view/GRIN2ResultsView.ts
-var sectionMargin = "20px 0";
-var btnMargin = "10px";
-var headerMargin = "0 10px 0 0";
-var headerFontSize = 14;
-var statsTableFontWeight = "bold";
-var backgroundColor = "#f8f8f8";
-var GRIN2ResultsView = class {
-  constructor(holder, app) {
-    this.holder = holder;
-    this.app = app;
-  }
-  clear() {
-    this.holder.selectAll("*").remove();
-  }
-  render(viewData) {
-    if (viewData.manhattan) {
-      plotManhattan(this.holder, viewData.manhattan.plotData, viewData.manhattan.settings, this.app);
-    }
-    if (viewData.topGenes) {
-      const { headerText, columns, rows, dataItems } = viewData.topGenes;
-      const tableContainer = this.holder.append("div").style("margin", sectionMargin);
-      const headerDiv = tableContainer.append("div").style("display", "flex").style("align-items", "center").style("margin", btnMargin);
-      headerDiv.append("h3").style("margin", headerMargin).style("font-size", `${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 SNVINDEL_HYPERMUTATOR_FALLBACK = 8e3;
-var CNV_HYPERMUTATOR_FALLBACK = 0;
-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: {
-      /* The layout the Manhattan component draws by, from its own module rather than restated
-      here: these 22 keys were a second copy, so a spacing tweak for one plot silently left
-      the other rendering differently. GRIN2's own knobs follow. */
-      ...manhattanLayoutDefaults,
-      // Max genes to show in table
-      maxGenesToShow: 500,
-      // Q-value threshold for significance indicators in the table, tooltips, and for determining which dots become interactive
-      qValueThreshold: 0.05,
-      // Colors for lesion types, derived from the shared dt2lesion source of truth so every data
-      // type (incl. itd and any future dt) is covered without a parallel hardcoded list. Used for
-      // table significance indicators and passed to the Manhattan renderer as dot colors.
-      lesionTypeColors: Object.fromEntries(
-        Object.values(dt2lesion).flatMap((d) => d.lesionTypes.map((lt) => [lt.lesionType, lt.color]))
-      ),
-      // 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 CNV_CLASS_ORDER = [mclasscnvgain, mclasscnvAmp, mclasscnvloss, mclasscnvHomozygousDel, mclasscnvloh];
-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 checkboxRowLabelWidth = "110px";
-var GRIN2ControlsView = class {
-  constructor(opts) {
-    this.snvindelCheckbox = null;
-    this.cnvCheckbox = null;
-    this.fusionCheckbox = null;
-    this.svCheckbox = null;
-    this.itdCheckbox = null;
-    this.runButton = null;
-    this.consequenceCheckboxes = {};
-    this.snvindelSelectAllBtn = null;
-    this.snvindelClearAllBtn = null;
-    this.snvindelDefaultBtn = null;
-    // one checkbox per supported categorical cnv-segment class (populated only for ds.queries.cnv.type='category')
-    this.cnvCategoryCheckboxes = {};
-    this.cnv_lossThreshold = null;
-    this.cnv_gainThreshold = null;
-    this.cnv_maxSegLength = null;
-    this.cnv_hyperMutator = null;
-    this.snvindel_hyperMutator = 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.actionsHolder = opts.actionsHolder;
-    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);
-    if (queries.itd) this.addItdRow(table);
-    this.addExcludeRow(table);
-    this.runButton = this.actionsHolder.append("button").attr("data-testid", "sjpp-grin2-run-button").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");
-    if (dtUsage[dtitd]) dtUsage[dtitd].checked = this.itdCheckbox.property("checked");
-    return dtUsage;
-  }
-  getConfigValues(dtUsage) {
-    const requestConfig = {};
-    if (dtUsage[dtsnvindel]?.checked) {
-      requestConfig.snvindelOptions = {
-        consequences: this.getSelectedConsequences()
-      };
-      if (this.snvindel_hyperMutator) {
-        const v = parseFloat(this.snvindel_hyperMutator.property("value"));
-        requestConfig.snvindelOptions.hyperMutator = Number.isFinite(v) ? v : SNVINDEL_HYPERMUTATOR_FALLBACK;
-      }
-      if (this.snvindelMafFilter) {
-        requestConfig.snvindelOptions.mafFilter = this.snvindelMafFilter;
-      }
-    }
-    if (dtUsage[dtcnv]?.checked) {
-      requestConfig.cnvOptions = {
-        maxSegLength: parseFloat(this.cnv_maxSegLength.property("value"))
-      };
-      if (this.cnv_hyperMutator) {
-        const v = parseFloat(this.cnv_hyperMutator.property("value"));
-        requestConfig.cnvOptions.hyperMutator = Number.isFinite(v) ? v : CNV_HYPERMUTATOR_FALLBACK;
-      }
-      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 (Object.keys(this.cnvCategoryCheckboxes).length) {
-        requestConfig.cnvOptions.cnvCategories = this.getSelectedCnvCategories();
-      }
-    }
-    if (dtUsage[dtfusionrna]?.checked) requestConfig.fusionOptions = {};
-    if (dtUsage[dtsv]?.checked) requestConfig.svOptions = {};
-    if (dtUsage[dtitd]?.checked) requestConfig.itdOptions = {};
-    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 anyEffective = Object.entries(dtUsage).some(([dt, info]) => {
-      if (!info.checked) return false;
-      if (Number(dt) === dtsnvindel && Object.keys(this.consequenceCheckboxes).length > 0) {
-        return this.getSelectedConsequences().length > 0;
-      }
-      if (Number(dt) === dtcnv && Object.keys(this.cnvCategoryCheckboxes).length > 0) {
-        return this.getSelectedCnvCategories().length > 0;
-      }
-      return true;
-    });
-    this.runButton?.property("disabled", !anyEffective);
-  }
-  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").style("min-width", checkboxRowLabelWidth);
-      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);
-    }
-    this.snvindel_hyperMutator = this.addOptionRowToTable(
-      t2,
-      "Hypermutator Cutoff",
-      this.config.settings?.snvindelOptions?.hyperMutator ?? SNVINDEL_HYPERMUTATOR_FALLBACK,
-      0,
-      void 0,
-      1
-    ).attr("title", "Exclude a sample from SNV/indel when it has more than this many records. 0 disables.");
-    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];
-    this.cnvCategoryCheckboxes = {};
-    if (cfg.hideThresholds) {
-      this.cnv_lossThreshold = null;
-      this.cnv_gainThreshold = null;
-      this.createCnvCategoryCheckboxes(holder, savedCnv);
-    }
-    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
-      );
-    }
-    this.cnv_maxSegLength = this.addOptionRowToTable(
-      t2,
-      "Max Segment Length",
-      savedCnv?.maxSegLength ?? cnvQuery?.cnvMaxLength ?? CNV_MAX_SEG_LENGTH_FALLBACK,
-      0,
-      1e9,
-      1e3
-    );
-    this.cnv_hyperMutator = this.addOptionRowToTable(
-      t2,
-      "Hypermutator Cutoff",
-      savedCnv?.hyperMutator ?? CNV_HYPERMUTATOR_FALLBACK,
-      0,
-      void 0,
-      1
-    ).attr("title", "Exclude a sample from CNV when it has more than this many segments. 0 disables.");
-  }
-  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();
-      }
-    });
-  }
-  addItdRow(table) {
-    const [left, right] = table.addRow();
-    const t2 = table2col({ holder: right });
-    const isChecked = this.config.settings.dtUsage[dtitd].checked;
-    t2.table.style("display", isChecked ? "" : "none");
-    this.itdCheckbox = make_one_checkbox({
-      holder: left,
-      labeltext: dt2lesion[dtitd].uilabel,
-      checked: isChecked,
-      testid: "sjpp-grin2-checkbox-itd",
-      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` },
-        // clearing every consequence includes nothing, which can disable the run button (see
-        // updateRunButtonFromCheckboxes), so re-evaluate it on each toggle
-        callback: () => this.updateRunButtonFromCheckboxes()
-      });
-      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.updateRunButtonFromCheckboxes();
-    });
-    this.snvindelClearAllBtn.on("click", () => {
-      Object.values(this.consequenceCheckboxes).forEach((cb) => cb.property("checked", false));
-      this.updateRunButtonFromCheckboxes();
-    });
-    this.snvindelDefaultBtn.on("click", () => {
-      Object.entries(this.consequenceCheckboxes).forEach(([classKey, checkbox]) => {
-        checkbox.property("checked", canonicalDefault.has(classKey));
-      });
-      this.updateRunButtonFromCheckboxes();
-    });
-  }
-  getSelectedCnvCategories() {
-    const categories = [];
-    Object.entries(this.cnvCategoryCheckboxes).forEach(([classKey, checkbox]) => {
-      if (checkbox.property("checked")) categories.push(classKey);
-    });
-    return categories;
-  }
-  /** One checkbox per categorical cnv-segment class supported by this dataset, all checked by default —
-   * the cnv analog of the snvindel consequence checkboxes. The supported classes are the CNV entries the
-   * dataset declares in termdbConfig.mclass (e.g. GDC: Gain / Heterozygous Deletion / Amplification /
-   * Homozygous Deletion), identified via the global mclass dt; labels prefer the dataset override. Rendered
-   * in its own table2col with a fixed label width so the checkbox box aligns with "Consequences" above. */
-  createCnvCategoryCheckboxes(holder, savedCnv) {
-    const dsMclass = this.vocabApi.termdbConfig?.mclass || {};
-    const cnvClasses = Object.keys(dsMclass).filter((key) => mclass[key]?.dt === dtcnv).map((key) => ({ key, label: dsMclass[key]?.label || mclass[key]?.label || key, desc: mclass[key]?.desc || "" })).sort((a, b) => {
-      const ia = CNV_CLASS_ORDER.indexOf(a.key);
-      const ib = CNV_CLASS_ORDER.indexOf(b.key);
-      return (ia === -1 ? Infinity : ia) - (ib === -1 ? Infinity : ib);
-    });
-    this.cnvCategoryCheckboxes = {};
-    if (!cnvClasses.length) return;
-    const saved = savedCnv?.cnvCategories;
-    const useSaved = this.config.settings.runAnalysis === true && Array.isArray(saved);
-    const initialChecked = useSaved ? new Set(saved) : new Set(cnvClasses.map((c) => c.key));
-    const t2 = table2col({ holder });
-    const [labelCell, containerCell] = t2.addRow();
-    labelCell.text("Classes").style("padding-top", "8px").style("min-width", checkboxRowLabelWidth);
-    const controlDiv = containerCell.append("div").style("margin-bottom", "6px").style("display", "flex").style("gap", controlGap);
-    const selectAllBtn = controlDiv.append("button").style("font-size", `${tableFontSize}px`).text("Select All");
-    const clearAllBtn = controlDiv.append("button").style("font-size", `${tableFontSize}px`).text("Clear All");
-    const checkboxContainer = containerCell.append("div").style("max-height", checkboxContainerMaxHeight).style("overflow-y", "auto").style("border", checkboxContainerBorder).style("margin-bottom", "6px");
-    cnvClasses.forEach((c) => {
-      const checkboxDiv = checkboxContainer.append("div").style("margin-bottom", checkboxMarginBottom);
-      const checkbox = make_one_checkbox({
-        holder: checkboxDiv,
-        labeltext: c.label,
-        checked: initialChecked.has(c.key),
-        divstyle: { "font-size": `${tableFontSize}px` },
-        // clearing every class excludes all cnv, which can disable the run button (see
-        // updateRunButtonFromCheckboxes), so re-evaluate it on each toggle
-        callback: () => this.updateRunButtonFromCheckboxes()
-      });
-      if (c.desc) checkboxDiv.select("label").attr("title", c.desc);
-      this.cnvCategoryCheckboxes[c.key] = checkbox;
-    });
-    selectAllBtn.on("click", () => {
-      Object.values(this.cnvCategoryCheckboxes).forEach((cb) => cb.property("checked", true));
-      this.updateRunButtonFromCheckboxes();
-    });
-    clearAllBtn.on("click", () => {
-      Object.values(this.cnvCategoryCheckboxes).forEach((cb) => cb.property("checked", false));
-      this.updateRunButtonFromCheckboxes();
-    });
-  }
-};
-
-// plots/grin2/grin2.ts
-var GRIN2 = class _GRIN2 extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.controlsView = null;
-    this.controlsToggleButton = null;
-    this.hasResults = false;
-    this.inputPanelCollapsed = false;
-    this.cohortFilterSignature = null;
-    this.type = _GRIN2.type;
-    this.components = { controls: {} };
-    opts.holder.classed("sjpp-grin2-main", true);
-    const massControls = opts.holder.append("div").style("display", "inline-block");
-    const inputPanel = opts.holder.append("div").attr("data-testid", "sjpp-grin2-input-panel").style("display", "grid").style("grid-template-rows", "1fr").style("opacity", "1").style("transition", "grid-template-rows 250ms ease, opacity 200ms ease");
-    const inputPanelContent = inputPanel.append("div").style("min-height", "0").style("overflow", "hidden");
-    this.dom = {
-      massControls,
-      inputPanel,
-      headerText: inputPanelContent.append("div").style("display", "inline-block"),
-      controls: inputPanelContent.append("div"),
-      controlsToggle: opts.holder.append("div").style("display", "flex").style("align-items", "center").style("gap", "8px").style("margin", "10px 20px 10px 100px"),
-      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.controlsToggleButton = this.dom.controlsToggle.append("button").attr("type", "button").attr("data-testid", "sjpp-grin2-input-toggle").style("display", "none").on("click", () => {
-      if (!this.hasResults) return;
-      this.inputPanelCollapsed = !this.inputPanelCollapsed;
-      this.updateInputPanel();
-    });
-    this.updateInputPanel();
-    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;
-    const cohortFilterSignature = this.getCohortFilterSignature();
-    if (this.cohortFilterSignature === null) {
-      this.cohortFilterSignature = cohortFilterSignature;
-    } else if (this.cohortFilterSignature !== cohortFilterSignature) {
-      this.cohortFilterSignature = cohortFilterSignature;
-      this.clearResultsAndShowInputs();
-    }
-    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,
-        actionsHolder: this.dom.controlsToggle,
-        callbacks: { onRun: () => this.handleRun() }
-      });
-      this.controlsView.build();
-      if (this.state.config.settings.runAnalysis) this.handleRun();
-    }
-  }
-  async handleRun() {
-    if (!this.controlsView) return;
-    const runFilterSignature = this.cohortFilterSignature;
-    this.clearResultsAndShowInputs();
-    this.controlsView.setBusy(true);
-    try {
-      const dtUsage = this.controlsView.getDtUsage();
-      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}`;
-      if (runFilterSignature !== this.cohortFilterSignature) return;
-      const vm = new GRIN2ViewModel(response, manhattan, dtUsage);
-      this.resultsView.render(vm.viewData);
-      this.hasResults = true;
-      this.inputPanelCollapsed = true;
-      this.updateInputPanel();
-      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.app.isAbortError(error)) return;
-      if (this.dom.div) {
-        sayerror(this.dom.div, `Error running GRIN2: ${error instanceof Error ? error.message : error}`);
-      }
-    } finally {
-      this.controlsView?.setBusy(false);
-    }
-  }
-  getCohortFilterSignature() {
-    return JSON.stringify({
-      filter: this.state.termfilter?.filter ?? null,
-      filter0: this.state.termfilter?.filter0 ?? null
-    });
-  }
-  clearResultsAndShowInputs() {
-    this.resultsView.clear();
-    this.hasResults = false;
-    this.inputPanelCollapsed = false;
-    this.updateInputPanel();
-  }
-  updateInputPanel() {
-    this.dom.inputPanel.attr("aria-hidden", String(this.inputPanelCollapsed)).property("inert", this.inputPanelCollapsed).style("grid-template-rows", this.inputPanelCollapsed ? "0fr" : "1fr").style("opacity", this.inputPanelCollapsed ? "0" : "1").style("pointer-events", this.inputPanelCollapsed ? "none" : "auto");
-    this.controlsToggleButton?.style("display", this.hasResults ? null : "none");
-    this.dom.controlsToggle.select('[data-testid="sjpp-grin2-run-button"]').style("display", this.inputPanelCollapsed ? "none" : null);
-    this.controlsToggleButton?.attr("aria-expanded", String(!this.inputPanelCollapsed)).text(this.inputPanelCollapsed ? "Show input options" : "Hide input options");
-  }
-};
-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 };
-    }
-  }
-  if (queries?.itd) {
-    dtUsage[dtitd] = { checked: false, label: dt2lesion[dtitd].uilabel };
-  }
-  const config = {
-    chartType: "grin2",
-    settings: {
-      controls: {},
-      dtUsage,
-      runAnalysis: false,
-      manhattan: {
-        ...defaultSettings.manhattan,
-        ...opts?.manhattan
-      }
-    }
-  };
-  return copyMerge(config, opts);
-}
-export {
-  componentInit,
-  getPlotConfig,
-  grin2Init
-};
-//# sourceMappingURL=grin2-5TH4EBVQ.js.map