@sjcrh/proteinpaint-client 2.213.0 → 2.214.0

package/dist/cellTypeBubbleHeatmap-KJSNP4A3.js

@@ -1,278 +0,0 @@
-import {
-  LegendCircleReference,
-  PlotBase,
-  addGeneSearchbox
-} from "./chunk-QI6X4V43.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-7HPICVA4.js";
-import {
-  Menu
-} from "./chunk-7XZA2XR2.js";
-import "./chunk-DD3DWHUY.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import {
-  dofetch3
-} from "./chunk-YU7CVG4B.js";
-import "./chunk-HH5JKOE6.js";
-import "./chunk-RU2UHH7M.js";
-import "./chunk-57Z4VYLM.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import {
-  linear,
-  sqrt
-} from "./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/cellTypeBubbleHeatmap.ts
-var defaultConfig = { chartType: "cellTypeBubbleHeatmap" };
-var CELL_W = 84;
-var CELL_H = 60;
-var ROW_LABEL_W = 74;
-var GROUP_LABEL_H = 22;
-var GENO_LABEL_H = 40;
-var COL_LABEL_H = GROUP_LABEL_H + GENO_LABEL_H;
-var MIN_DOT_R = 8;
-var MAX_DOT_R = 22;
-var NEG_LOG_FDR_CAP = 10;
-var COLOR_NEG = "#762a83";
-var COLOR_ZERO = "#f7f7f7";
-var COLOR_POS = "#2166ac";
-var CellTypeBubbleHeatmap = class _CellTypeBubbleHeatmap extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.currentIsoform = "";
-    this.type = _CellTypeBubbleHeatmap.type;
-  }
-  static {
-    this.type = "cellTypeBubbleHeatmap";
-  }
-  async init() {
-    const holder = this.opts.holder.append("div").style("padding", "10px");
-    this.dom = {
-      holder,
-      body: holder.append("div"),
-      tip: new Menu({ padding: "" }),
-      header: this.opts.header
-    };
-    if (this.dom.header) this.dom.header.html("Cell-type Bubble Heatmap");
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) throw `No plot with id='${this.id}' found`;
-    return { config };
-  }
-  async main() {
-    const gene = this.state.config?.gene;
-    if (!gene) throw new Error("cellTypeBubbleHeatmap: gene is missing");
-    if (this.dom.header) this.dom.header.text(`Cell-type Bubble Heatmap: ${gene}`);
-    const body = {
-      genome: this.app.opts.state.vocab.genome,
-      dslabel: this.app.opts.state.vocab.dslabel,
-      gene
-    };
-    const data = await dofetch3("termdb/cellTypeBubbleHeatmap", { body });
-    if (data.error) throw data.error;
-    this.data = data;
-    this.dom.body.selectAll("*").remove();
-    const isoformIds = Object.keys(data.isoforms);
-    if (isoformIds.length === 0) {
-      this.dom.body.append("div").style("padding", "20px").style("color", "#666").text(`No data found for gene "${gene}" in any cohort DAPfile.`);
-      return;
-    }
-    this.currentIsoform = isoformIds[0];
-    const isoBlock = this.dom.body.append("div").style("margin-bottom", "12px");
-    isoBlock.append("span").style("font-weight", "bold").text("Isoform: ");
-    if (isoformIds.length > 1) {
-      const sel = isoBlock.append("select").style("margin-left", "5px").style("padding", "3px 6px").on("change", () => {
-        this.currentIsoform = sel.node().value;
-        this.renderGrid();
-      });
-      sel.selectAll("option").data(isoformIds).enter().append("option").attr("value", (d) => d).text((d) => `${data.isoforms[d].gene_name} \u2014 ${d}`);
-    } else {
-      isoBlock.append("span").style("margin-left", "5px").text(`${data.isoforms[this.currentIsoform].gene_name} \u2014 ${this.currentIsoform}`);
-    }
-    this.gridHolder = this.dom.body.append("div");
-    this.renderGrid();
-  }
-  renderGrid() {
-    const data = this.data;
-    const selectedIsoform = this.currentIsoform;
-    const threshold = data.fdrThreshold;
-    this.gridHolder.selectAll("*").remove();
-    const container = this.gridHolder.append("div").style("display", "flex").style("gap", "24px").style("align-items", "flex-start").style("flex-wrap", "wrap");
-    const isoformData = data.isoforms[selectedIsoform];
-    if (!isoformData) return;
-    const columns = data.columns;
-    const rows = data.rows;
-    const nCols = columns.length;
-    const nRows = rows.length;
-    const negLogFdr = (fdr) => fdr > 0 ? Math.min(-Math.log10(fdr), NEG_LOG_FDR_CAP) : NEG_LOG_FDR_CAP;
-    const cellOf = (colKey, rowKey) => isoformData.data[colKey]?.[rowKey];
-    let maxAbs = 0;
-    const thresholdNegLog = negLogFdr(threshold);
-    let maxNegLog = thresholdNegLog;
-    for (const col of columns) {
-      for (const row of rows) {
-        const s = cellOf(col.key, row.key);
-        if (!s) continue;
-        const v = Math.abs(s.log2FC);
-        if (v > maxAbs) maxAbs = v;
-        const nl = negLogFdr(s.fdr);
-        if (nl > maxNegLog) maxNegLog = nl;
-      }
-    }
-    if (maxAbs === 0) maxAbs = 1;
-    if (maxNegLog <= thresholdNegLog) maxNegLog = thresholdNegLog + 1;
-    const colorScale = linear().domain([-maxAbs, 0, maxAbs]).range([COLOR_NEG, COLOR_ZERO, COLOR_POS]).clamp(true);
-    const sizeScale = sqrt().domain([thresholdNegLog, maxNegLog]).range([MIN_DOT_R, MAX_DOT_R]).clamp(true);
-    const gridW = ROW_LABEL_W + nCols * CELL_W + 20;
-    const gridH = COL_LABEL_H + nRows * CELL_H + 20;
-    const svg = container.append("svg").attr("width", gridW).attr("height", gridH).style("flex", "0 0 auto");
-    const grid = svg.append("g");
-    let c = 0;
-    while (c < nCols) {
-      const cellType = columns[c].cellType;
-      let end = c;
-      while (end + 1 < nCols && columns[end + 1].cellType === cellType) end++;
-      const xStart = ROW_LABEL_W + c * CELL_W;
-      const xEnd = ROW_LABEL_W + (end + 1) * CELL_W;
-      const xMid = (xStart + xEnd) / 2;
-      grid.append("text").attr("x", xMid).attr("y", GROUP_LABEL_H - 7).attr("text-anchor", "middle").attr("font-size", "13px").attr("font-weight", "bold").text(cellType);
-      grid.append("line").attr("x1", xStart + 4).attr("y1", GROUP_LABEL_H - 3).attr("x2", xEnd - 4).attr("y2", GROUP_LABEL_H - 3).attr("stroke", "#bbb").attr("stroke-width", 1);
-      c = end + 1;
-    }
-    for (let col = 0; col < nCols; col++) {
-      const cx = ROW_LABEL_W + col * CELL_W + CELL_W / 2;
-      grid.append("text").attr("x", cx).attr("y", COL_LABEL_H - 14).attr("text-anchor", "middle").attr("font-size", "12px").attr("font-weight", "600").text(columns[col].genotype);
-    }
-    for (let r = 0; r < nRows; r++) {
-      const cy = COL_LABEL_H + r * CELL_H + CELL_H / 2;
-      grid.append("text").attr("x", ROW_LABEL_W - 12).attr("y", cy).attr("text-anchor", "end").attr("dominant-baseline", "central").attr("font-size", "13px").attr("font-weight", "bold").text(rows[r].label);
-    }
-    for (let r = 0; r < nRows; r++) {
-      for (let col = 0; col < nCols; col++) {
-        const x0 = ROW_LABEL_W + col * CELL_W;
-        const y0 = COL_LABEL_H + r * CELL_H;
-        grid.append("rect").attr("x", x0).attr("y", y0).attr("width", CELL_W).attr("height", CELL_H).attr("fill", "none").attr("stroke", "#eee").attr("stroke-width", 1);
-        const s = cellOf(columns[col].key, rows[r].key);
-        if (!s) continue;
-        const cx = x0 + CELL_W / 2;
-        const cy = y0 + CELL_H / 2;
-        grid.append("circle").attr("cx", cx).attr("cy", cy).attr("r", sizeScale(negLogFdr(s.fdr))).attr("fill", colorScale(s.log2FC)).attr("stroke", "#888").attr("stroke-width", 0.8).style("opacity", s.significant ? 1 : 0.35).on(
-          "mouseover",
-          (event) => this.showCellTip(event, isoformData.gene_name, selectedIsoform, columns[col], rows[r], s)
-        ).on("mouseout", () => this.dom.tip.hide());
-      }
-    }
-    this.renderLegend(container, colorScale, maxAbs, threshold, maxNegLog);
-  }
-  fmtFdr(v) {
-    return v >= 1e-4 ? v.toFixed(4) : v.toExponential(2);
-  }
-  showCellTip(event, geneName, isoform, col, row, s) {
-    this.dom.tip.clear().show(event.clientX, event.clientY);
-    const t = this.dom.tip.d.append("div").style("padding", "8px").style("font-size", "13px");
-    t.append("div").style("font-weight", "bold").style("margin-bottom", "4px").text(`${geneName} \u2014 ${isoform}`);
-    t.append("div").text(`Cell type: ${col.cellType}`);
-    t.append("div").text(`Genotype: ${col.genotype}`);
-    t.append("div").text(`Timepoint: ${row.label}`);
-    t.append("div").text(`Protein: ${s.id}`);
-    t.append("div").text(`log\u2082FC: ${s.log2FC.toFixed(3)}`);
-    t.append("div").text(`FDR: ${this.fmtFdr(s.fdr)}${s.significant ? "" : " (n.s.)"}`);
-    t.append("div").style("color", "#666").style("margin-top", "4px").text("Color = log\u2082FC (blue up / purple down). Size = \u2212log\u2081\u2080 FDR.");
-  }
-  renderLegend(container, colorScale, maxAbs, threshold, maxNegLog) {
-    const legend = container.append("div").style("display", "flex").style("flex-direction", "column").style("gap", "16px").style("padding", "8px 0").style("min-width", "180px").style("max-width", "260px");
-    const colorBlock = legend.append("div");
-    colorBlock.append("div").style("font-weight", "bold").style("font-size", "13px").style("margin-bottom", "6px").text("log\u2082FC");
-    const cW = 22;
-    const cH = 130;
-    const cSvg = colorBlock.append("svg").attr("width", cW + 80).attr("height", cH + 16);
-    const gid = `ctbh-grad-${this.id}`;
-    const grad = cSvg.append("defs").append("linearGradient").attr("id", gid).attr("x1", "0").attr("y1", "0").attr("x2", "0").attr("y2", "1");
-    const steps = 10;
-    for (let i = 0; i <= steps; i++) {
-      const t = i / steps;
-      grad.append("stop").attr("offset", `${t * 100}%`).attr("stop-color", colorScale(maxAbs * (1 - 2 * t)));
-    }
-    cSvg.append("rect").attr("x", 0).attr("y", 8).attr("width", cW).attr("height", cH).style("fill", `url(#${gid})`).attr("stroke", "#999");
-    const cScale = linear().domain([maxAbs, -maxAbs]).range([8, cH + 8]);
-    for (const tick of [maxAbs, maxAbs / 2, 0, -maxAbs / 2, -maxAbs]) {
-      const y = cScale(tick);
-      cSvg.append("line").attr("x1", cW).attr("y1", y).attr("x2", cW + 5).attr("y2", y).attr("stroke", "#666");
-      cSvg.append("text").attr("x", cW + 8).attr("y", y).attr("dominant-baseline", "central").attr("font-size", "10px").text(`${tick > 0 ? "+" : ""}${tick.toFixed(2)}`);
-    }
-    colorBlock.append("div").style("font-size", "11px").style("color", "#666").style("margin-top", "2px").text("blue = up (+), purple = down (\u2212)");
-    const sizeBlock = legend.append("div");
-    sizeBlock.append("div").style("font-weight", "bold").style("font-size", "13px").style("margin-bottom", "6px").text("Dot size: significance (\u2212log\u2081\u2080 FDR)");
-    const sSvg = sizeBlock.append("svg");
-    const sG = sSvg.append("g");
-    new LegendCircleReference({
-      g: sG,
-      inputMin: 0,
-      inputMax: MAX_DOT_R * 2,
-      minRadius: MIN_DOT_R,
-      maxRadius: MAX_DOT_R,
-      minLabel: Number(Math.min(-Math.log10(threshold), NEG_LOG_FDR_CAP).toFixed(1)),
-      maxLabel: Number(maxNegLog.toFixed(1))
-    });
-    const sPad = 4;
-    const sBox = sG.node().getBBox();
-    sG.attr("transform", `translate(${sPad - sBox.x}, ${sPad - sBox.y})`);
-    sSvg.attr("width", Math.ceil(sBox.width + 2 * sPad)).attr("height", Math.ceil(sBox.height + 2 * sPad));
-    const notes = legend.append("div").style("font-size", "11px").style("color", "#666").style("line-height", "1.5").style("max-width", "240px").style("overflow-wrap", "break-word");
-    notes.append("div").text(
-      `Color = log\u2082FC (blue up, purple down). Dot size = significance, \u2212log\u2081\u2080 FDR; the smallest size marks the FDR < ${threshold} cutoff. Non-significant dots (FDR \u2265 ${threshold}) are faded.`
-    );
-    notes.append("div").style("margin-top", "4px").text("An empty cell means the cohort was not assayed (e.g. OPC has no 4m) or the protein was not detected.");
-  }
-};
-var componentInit = getCompInit(CellTypeBubbleHeatmap);
-async function getPlotConfig(opts) {
-  const config = structuredClone(defaultConfig);
-  if (!opts.gene) throw new Error("cellTypeBubbleHeatmap requires opts.gene");
-  return copyMerge(config, opts);
-}
-function makeChartBtnMenu(holder, chartsInstance) {
-  const row = holder.append("div").style("padding", "5px");
-  row.append("span").style("font-weight", "bold").text("Enter a gene name:");
-  const geneSearch = addGeneSearchbox({
-    row,
-    genome: chartsInstance.app.opts.genome,
-    tip: new Menu({ padding: "0px" }),
-    searchOnly: "gene",
-    callback: async () => {
-      if (!geneSearch.geneSymbol) throw new Error("A valid gene selection is required");
-      chartsInstance.dom.tip.hide();
-      chartsInstance.app.dispatch({
-        type: "plot_create",
-        config: {
-          chartType: "cellTypeBubbleHeatmap",
-          gene: geneSearch.geneSymbol
-        }
-      });
-    }
-  });
-}
-export {
-  componentInit,
-  getPlotConfig,
-  makeChartBtnMenu
-};
-//# sourceMappingURL=cellTypeBubbleHeatmap-KJSNP4A3.js.map

package/dist/chunk-2WKGE7BO.js

@@ -1,54 +0,0 @@
-import {
-  getColors
-} from "./chunk-57Z4VYLM.js";
-
-// termdb/handlers/junction.customTerm.ts
-var junctionCustomTermSource = "junction";
-function makeJunctionCustomTerm(junctions, eventlabel) {
-  if (!junctions.length) throw new Error("junctions[] is empty");
-  if (!eventlabel) {
-    const term = junctions[0];
-    return {
-      id: `junction:${term.id}`,
-      name: term.name,
-      source: junctionCustomTermSource,
-      tw: {
-        term,
-        q: { mode: "continuous" }
-      }
-    };
-  }
-  const termlst = [...new Map(junctions.map((term) => [term.id, term])).values()];
-  const colorScale = getColors(termlst.length);
-  const termIds = termlst.map((term) => term.id);
-  return {
-    id: `junction-event:${eventlabel}`,
-    name: eventlabel,
-    source: junctionCustomTermSource,
-    eventlabel,
-    tw: {
-      term: {
-        type: "termCollection",
-        isCustom: true,
-        memberType: "numeric",
-        name: eventlabel,
-        termIds,
-        termlst,
-        propsByTermId: Object.fromEntries(termlst.map((term) => [term.id, { color: colorScale(term.id) }])),
-        isleaf: true
-      },
-      q: {
-        mode: "continuous",
-        type: "values",
-        lst: termIds,
-        numerators: termIds
-      }
-    }
-  };
-}
-
-export {
-  junctionCustomTermSource,
-  makeJunctionCustomTerm
-};
-//# sourceMappingURL=chunk-2WKGE7BO.js.map

package/dist/chunk-2Z2TFFLP.js

@@ -1,299 +0,0 @@
-import {
-  first_genetrack_tolist,
-  gmmode,
-  sayerror
-} from "./chunk-QI6X4V43.js";
-import {
-  dofetch3
-} from "./chunk-YU7CVG4B.js";
-import {
-  codon_stop,
-  nt2aa,
-  proteinDomainColorScale
-} from "./chunk-57Z4VYLM.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// common/snp.js
-async function string2snp(genome, str) {
-  const data = await dofetch3("snp", {
-    method: "POST",
-    body: JSON.stringify({ byName: true, genome: genome.name, lst: [str] })
-  });
-  if (data.error) throw data.error;
-  if (!data.results || data.results.length == 0) throw str + ": not a SNP";
-  for (const i of data.results) {
-    const chr = genome.chrlookup[i.chrom.toUpperCase()];
-    if (chr && chr.major) {
-      return {
-        chr: i.chrom,
-        start: i.chromStart,
-        stop: i.chromEnd
-      };
-    }
-  }
-  const r = data.results[0];
-  return {
-    chr: r.chrom,
-    start: r.chromStart,
-    stop: r.chromEnd
-  };
-}
-
-// src/block.init.js
-async function block_init_default(arg) {
-  if (!arg.holder) throw "No holder for block.init";
-  if (!arg.genome) throw "no genome";
-  if (arg.holder instanceof Element) arg.holder = select_default(arg.holder);
-  if (!arg.tklst) arg.tklst = [];
-  if (arg.query) {
-    await step1_findgm(arg);
-    return;
-  }
-  if (arg.model && arg.allmodels) {
-    await step2_getseq(arg);
-    return;
-  }
-}
-async function step1_findgm(arg) {
-  const wait = arg.holder.append("p").style("font-size", "2em").style("color", "#858585").text("Searching for " + arg.query + " ...");
-  const data = await dofetch3("genelookup", {
-    body: { deep: 1, input: arg.query, genome: arg.genome.name }
-  });
-  if (!data) throw "querying genes: server error";
-  if (data.error) throw "error querying genes: " + data.error;
-  if (!data.gmlst || data.gmlst.length == 0) {
-    if (arg.genome.hasSNP) {
-      try {
-        const r = await string2snp(arg.genome, arg.query);
-        wait.remove();
-        const par = {
-          genome: arg.genome,
-          holder: arg.holder,
-          chr: r.chr,
-          start: Math.max(0, r.start - 300),
-          stop: r.start + 300,
-          nobox: true,
-          tklst: arg.tklst,
-          debugmode: arg.debugmode
-        };
-        first_genetrack_tolist(arg.genome, par.tklst);
-        const b = await import("./block-PRB7FXIC.js");
-        const block = new b.Block(par);
-        block.addhlregion(r.chr, r.start, r.stop - 1);
-      } catch (e) {
-        wait.text("Not a gene or SNP: " + arg.query);
-      }
-    } else {
-      wait.text("No match to gene: " + arg.query);
-    }
-    return;
-  }
-  wait.remove();
-  arg.allmodels = data.gmlst;
-  for (const m of arg.allmodels) {
-    if (m.isoform.toUpperCase() == (data.found_isoform ? data.found_isoform.toUpperCase() : arg.query.toUpperCase())) {
-      arg.model = m;
-      await step2_getseq(arg);
-      return;
-    }
-  }
-  const defaultisoforms = [];
-  for (const m of arg.allmodels) {
-    if (!m.isoform) throw "isoform missing from one gene model: " + JSON.stringify(m);
-    const n = m.isoform.toUpperCase();
-    if (arg.genome.isoformcache.has(n)) {
-      let nothas = true;
-      for (const m2 of arg.genome.isoformcache.get(n)) {
-        if (m2.chr == m.chr && m2.start == m.start && m2.stop == m.stop && m2.strand == m.strand) {
-          nothas = false;
-          break;
-        }
-      }
-      if (nothas) {
-        arg.genome.isoformcache.get(n).push(m);
-      }
-    } else {
-      arg.genome.isoformcache.set(n, [m]);
-    }
-    if (m.isoform.toUpperCase() == arg.query.toUpperCase()) {
-      defaultisoforms.push(m);
-      break;
-    }
-    if (m.isdefault) {
-      defaultisoforms.push(m);
-    }
-  }
-  if (defaultisoforms.length == 1) {
-    arg.model = defaultisoforms[0];
-  } else if (defaultisoforms.length > 1) {
-    for (const m of defaultisoforms) {
-      if (m.chr == "chrY") {
-        continue;
-      }
-      const chr = arg.genome.chrlookup[m.chr.toUpperCase()];
-      if (!chr) {
-        continue;
-      }
-      if (!chr.major) {
-        continue;
-      }
-      arg.model = m;
-      break;
-    }
-    if (!arg.model) {
-      arg.model = defaultisoforms[0];
-    }
-  }
-  if (!arg.model) {
-    arg.model = arg.allmodels[0];
-  }
-  await step2_getseq(arg);
-}
-async function step2_getseq(arg) {
-  if (arg.model.genomicseq) {
-    checker();
-    step2_getpdomain(arg);
-    return;
-  }
-  const par = {
-    genome: arg.genome.name,
-    coord: arg.model.chr + ":" + (arg.model.start + 1) + "-" + arg.model.stop
-  };
-  const data = await dofetch3("ntseq", { method: "POST", body: JSON.stringify(par) });
-  if (!data) throw "getting sequence: server error";
-  if (data.error) throw "getting sequence: " + data.error;
-  if (!data.seq) throw "no nt seq???";
-  arg.model.genomicseq = data.seq.toUpperCase();
-  arg.model.aaseq = nt2aa(arg.model);
-  checker();
-  await step2_getpdomain(arg);
-  function checker() {
-    if (arg.model.aaseq) {
-      const stop = arg.model.aaseq.indexOf(codon_stop);
-      const cdslen = arg.model.cdslen - (arg.model.startCodonFrame ? 3 - arg.model.startCodonFrame : 0);
-      if (stop != -1 && stop < cdslen / 3 - 1) {
-        sayerror(arg.holder, "Translating " + arg.model.isoform + " ends at " + stop + " AA, expecting " + cdslen / 3);
-      }
-    }
-  }
-}
-async function step2_getpdomain(arg) {
-  const isoform2gm = /* @__PURE__ */ new Map();
-  for (const m of arg.allmodels) {
-    if (!m.pdomains) {
-      m.pdomains = [];
-      m.domain_hidden = {};
-      if (!isoform2gm.has(m.isoform)) isoform2gm.set(m.isoform, []);
-      isoform2gm.get(m.isoform).push(m);
-    }
-  }
-  if (isoform2gm.size == 0) {
-    await step3(arg);
-    return;
-  }
-  const data = await dofetch3("pdomain", {
-    method: "POST",
-    body: JSON.stringify({ genome: arg.genome.name, isoforms: [...isoform2gm.keys()] })
-  });
-  if (data.error) throw "error getting protein domain: " + data.error;
-  if (!Array.isArray(data.lst)) throw ".lst[] not array";
-  for (const a of data.lst) {
-    for (const m of isoform2gm.get(a.name)) {
-      m.pdomains = a.pdomains;
-      if (arg.hidePdomain) {
-        for (const i of a.pdomains) {
-          m.domain_hidden[i.name + i.description] = 1;
-        }
-      }
-    }
-  }
-  if (arg.geneDomains) {
-    if (typeof arg.geneDomains != "object") throw "geneDomains not object";
-    for (const isoform in arg.geneDomains) {
-      const lst = isoform2gm.get(isoform);
-      if (!lst) throw `unknown isoform ${isoform} from geneDomains{}`;
-      for (const g of lst) {
-        if (!g.pdomains) g.pdomains = [];
-        if (!Array.isArray(arg.geneDomains[isoform])) throw `geneDomains[${isoform}] not array`;
-        for (const b of arg.geneDomains[isoform]) {
-          if (typeof b != "object") throw "element from geneDomains[] not object";
-          if (!Number.isInteger(b.start)) throw "start not integer from geneDomains[]";
-          if (!Number.isInteger(b.stop)) throw "stop not integer from geneDomains[]";
-          if (b.start > b.stop) throw "start>stop from geneDomains[]";
-          if (!b.name) b.name = "Custom domain";
-          if (!g.pdomains.find((a) => a.start == b.start && a.stop == b.stop && a.name == b.name)) g.pdomains.push(b);
-        }
-      }
-    }
-  }
-  const s = proteinDomainColorScale();
-  for (const lst of isoform2gm.values()) {
-    for (const g of lst) {
-      for (const d of g.pdomains || []) {
-        if (!d.color) d.color = s(d.name + d.description);
-      }
-    }
-  }
-  await step3(arg);
-}
-async function step3(arg) {
-  let mode = arg.gmmode;
-  if (!mode) {
-    if (arg.model.cdslen) {
-      mode = gmmode.protein;
-    } else {
-      mode = gmmode.exononly;
-    }
-  }
-  if (arg.dataset) {
-    if (!Array.isArray(arg.dataset)) throw "dataset is not array";
-    for (const dsname of arg.dataset) {
-      if (arg.genome.datasets[dsname] && !arg.genome.datasets[dsname].legacyDsIsUninitiated) continue;
-      const d = await dofetch3(`getDataset?genome=${arg.genome.name}&dsname=${dsname}`);
-      if (d.error) throw `invalid name from dataset[]: ${d.error}`;
-      if (!d.ds) throw ".ds missing";
-      const ds = arg.genome.datasets[d.ds.label];
-      Object.assign(ds, d.ds);
-      const _ = await import("./legacyDataset-IEFWFVS6.js");
-      _.validate_oldds(ds);
-      delete ds.legacyDsIsUninitiated;
-    }
-  }
-  const b = await import("./block-PRB7FXIC.js");
-  arg.__blockInstance = new b.Block({
-    genome: arg.genome,
-    holder: arg.holder,
-    nobox: true,
-    usegm: arg.model,
-    gmstackheight: 37,
-    allgm: arg.allmodels,
-    datasetlst: arg.dataset,
-    legacyDsFilter: arg.legacyDsFilter,
-    mset: arg.mset,
-    hlaachange: arg.hlaachange,
-    hlvariants: arg.hlvariants,
-    hlregions: arg.hlregions,
-    aarange: arg.aarange,
-    gmmode: mode,
-    hidedatasetexpression: arg.hidedatasetexpression,
-    hidegenecontrol: arg.hidegenecontrol,
-    hidegenelegend: arg.hidegenelegend,
-    variantPageCall_snv: arg.variantPageCall_snv,
-    datasetqueries: arg.datasetqueries,
-    samplecart: arg.samplecart,
-    debugmode: arg.debugmode,
-    tklst: arg.tklst,
-    mclassOverride: arg.mclassOverride,
-    hide_dsHandles: arg.hide_dsHandles,
-    onloadalltk_always: arg.onloadalltk_always,
-    onAddRemoveTk: arg.onAddRemoveTk
-  });
-}
-
-export {
-  string2snp,
-  block_init_default
-};
-//# sourceMappingURL=chunk-2Z2TFFLP.js.map