@sjcrh/proteinpaint-client 2.219.1 → 2.220.0

package/dist/Disco-ME53U25C.js

@@ -1,3384 +0,0 @@
-import {
-  InvalidDataUI,
-  PlotBase,
-  configUiInit,
-  fillbar,
-  getMaxLabelWidth,
-  getNormalRoot,
-  renderTable,
-  svgLegend,
-  table2col
-} from "./chunk-BKW35Z4U.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-ETXOEP4N.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import "./chunk-5NI77Z3O.js";
-import "./chunk-TVJOSRCH.js";
-import {
-  topBarInit
-} from "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import {
-  dofetch3
-} from "./chunk-CJHNPYFQ.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-NR6WFCPF.js";
-import "./chunk-GN2A5NL5.js";
-import {
-  arc_default,
-  bplen,
-  dtcnv,
-  dtfusionrna,
-  dtitd,
-  dtloh,
-  dtsnvindel,
-  dtsv,
-  line_default,
-  mclass,
-  mclassitd,
-  pie_default,
-  ribbon_default
-} from "./chunk-ME3HB3V6.js";
-import {
-  copyMerge,
-  getCompInit,
-  multiInit
-} from "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import {
-  linear,
-  ticks
-} from "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  pointer_default,
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// plots/disco/arc/FullArcRenderer.ts
-var FullArcRenderer = class {
-  constructor(radius, width, color) {
-    this.radius = radius;
-    this.width = width;
-    this.color = color;
-  }
-  render(holder) {
-    const donutGenerator = arc_default();
-    const arc = {
-      startAngle: 0,
-      endAngle: Math.PI * 2,
-      innerRadius: this.radius,
-      outerRadius: this.radius + this.width,
-      color: this.color,
-      text: "No label"
-    };
-    const array = [];
-    array.push(arc);
-    const donutArc = holder.append("g");
-    donutArc.selectAll("path").data(array).enter().append("path").attr("d", (d) => donutGenerator(d)).attr("fill", (d) => d.color);
-  }
-};
-
-// plots/disco/menu/MenuProvider.ts
-var MenuProvider = class {
-  static create() {
-    const menu = new Menu({ padding: 5 });
-    menu.d.style("border", "1px solid #FFF").style("position", "absolute").style("z-index", 1001);
-    return menu;
-  }
-};
-
-// plots/disco/fusion/FusionColorProvider.ts
-var FusionColorProvider = class {
-  static getColor(chrA, chrB) {
-    if (chrA != chrB) {
-      return "#6A3D9A" /* Interchromosomal */.valueOf();
-    } else {
-      return "#1B9E77" /* Intrachromosomal */.valueOf();
-    }
-  }
-};
-
-// plots/disco/fusion/FusionRenderer.ts
-var FusionRenderer = class {
-  constructor(genome) {
-    this.genome = genome;
-  }
-  render(holder, fusions, opacity = 1) {
-    let radius = 0;
-    const fusionsWithTarget = fusions.filter((f) => f.target);
-    if (fusionsWithTarget.length > 0) {
-      radius = fusionsWithTarget[0].target.radius;
-      const fullArcRenderer = new FullArcRenderer(radius, 2, "#6464641A");
-      fullArcRenderer.render(holder);
-    } else return;
-    const ribbon = ribbon_default().radius(radius);
-    const ribbons = holder.selectAll(".chord").data(fusions);
-    const menu = MenuProvider.create();
-    const createTooltip = this.createTooltip.bind(this);
-    const genome = this.genome;
-    ribbons.enter().append("path").attr("class", "chord").attr("d", ribbon).attr("fill", (fusion) => {
-      return FusionColorProvider.getColor(
-        fusion.source.positionInChromosome.chromosome,
-        fusion.target.positionInChromosome.chromosome
-      );
-    }).style("opacity", opacity).each(function(d) {
-      const path = select_default(this);
-      const tip = MenuProvider.create();
-      path.on("click", async function(event) {
-        tip.clear().show(event.x, event.y);
-        const div = tip.d.append("div");
-        await makeSvgraph(d, div, genome);
-      });
-    }).on("mouseover", async function(mouseEvent, fusion) {
-      const table = table2col({ holder: menu.d });
-      createTooltip(table, fusion);
-      menu.show(mouseEvent.x, mouseEvent.y);
-    }).on("mouseout", () => {
-      menu.clear();
-      menu.hide();
-    });
-  }
-  createTooltip(table, fusion) {
-    {
-      const [td1, td2] = table.addRow();
-      td1.text("Data type");
-      td2.append("span").style("margin-left", "5px").text("Fusion transcript");
-    }
-    {
-      const positionInChromosomeSource = fusion.source.positionInChromosome;
-      const positionInChromosomeTarget = fusion.target.positionInChromosome;
-      const [td1, td2] = table.addRow();
-      td1.text("Position");
-      td2.append("span").style("margin-left", "5px").text(
-        ` ${fusion.source.gene || ""} ${positionInChromosomeSource.chromosome}:${positionInChromosomeSource.position} ${fusion.source.strand === "+" ? "forward" : "reverse"} >  ${fusion.target.gene || ""} ${positionInChromosomeTarget.chromosome}:${positionInChromosomeTarget.position} ${fusion.target.strand === "+" ? "forward" : "reverse"} `
-      );
-    }
-  }
-};
-async function makeSvgraph(fusion, div, genome) {
-  const wait = div.append("div").text("Loading...");
-  const svpair = {
-    a: {
-      chr: fusion.source.positionInChromosome.chromosome,
-      position: fusion.source.positionInChromosome.position,
-      strand: fusion.source.strand
-    },
-    b: {
-      chr: fusion.target.positionInChromosome.chromosome,
-      position: fusion.target.positionInChromosome.position,
-      strand: fusion.target.strand
-    }
-  };
-  await getGm(svpair.a, genome.name, fusion.source.gene);
-  await getGm(svpair.b, genome.name, fusion.target.gene);
-  wait.remove();
-  const _ = await import("./svgraph-2SL2SJVU.js");
-  _.default({
-    pairlst: [svpair],
-    genome,
-    holder: div
-  });
-}
-async function getGm(p, genome, name) {
-  const d = await dofetch3("isoformbycoord", {
-    body: { genome, chr: p.chr, pos: p.position }
-  });
-  if (d.error) throw d.error;
-  const u = d.lst.find((i) => i.isdefault && name === i.name) || d.lst[0];
-  if (u) {
-    p.name = u.name;
-    p.gm = { isoform: u.isoform };
-  }
-}
-
-// plots/disco/DiscoRenderer.ts
-var DiscoRenderer = class {
-  constructor(renders, legendRenderer, genome) {
-    this.renders = renders;
-    this.legendRenderer = legendRenderer;
-    this.fusionRenderer = new FusionRenderer(genome);
-  }
-  render(holder, viewModel, onCnvSourceSelect) {
-    const svgDiv = holder.append("div").style("display", "inline-block").style("font-family", "Arial");
-    const svg = svgDiv.append("svg").attr("id", "sjpp_disco_plot").attr("data-testid", "sjpp_disco_plot").attr("width", viewModel.width).attr("height", viewModel.height + viewModel.legendHeight);
-    const mainG = svg.append("g").attr("class", "mainG").attr(
-      "transform",
-      `translate(${viewModel.settings.rings.labelLinesInnerRadius + viewModel.settings.rings.labelsToLinesDistance + 100},${viewModel.height / 2})`
-    );
-    for (const [ringType, renderer] of this.renders) {
-      const elements = viewModel.getElements(ringType);
-      const collisions = viewModel.getCollisions(ringType);
-      renderer.render(mainG, elements, collisions);
-    }
-    this.fusionRenderer.render(mainG, viewModel.fusions, viewModel.settings.Disco.fusionOpacity);
-    if (viewModel.settings.Disco.centerText) {
-      const chrRingBbox = mainG.select('[data-testid="sjpp_chromosomes_arc_group"]').node().getBBox();
-      const text = viewModel.settings.Disco.centerText.length > 20 ? viewModel.settings.Disco.centerText.slice(0, 20) + "..." : viewModel.settings.Disco.centerText;
-      const textElem = mainG.append("text").attr("class", "sjpp-disco-center-text").text(text);
-      const textBbox = textElem.node().getBBox();
-      textElem.attr("transform", `translate(${chrRingBbox.x + chrRingBbox.width / 2 - textBbox.width / 2},0)`);
-    }
-    this.legendRenderer.render(
-      mainG,
-      viewModel.legend,
-      -1 * (viewModel.settings.rings.labelLinesInnerRadius + viewModel.settings.rings.labelsToLinesDistance + 75),
-      viewModel.width,
-      viewModel.height / 2,
-      viewModel,
-      onCnvSourceSelect
-    );
-  }
-};
-
-// plots/disco/interactions/DiscoInteractions.ts
-var DiscoInteractions = class {
-  constructor(discoApp) {
-    this.discoApp = discoApp;
-    this.downloadClickListener = (svg) => {
-      const downloadImgName = this.discoApp.state.settings.downloadImgName || "disco.plot";
-      const a = document.createElement("a");
-      document.body.appendChild(a);
-      a.addEventListener(
-        "click",
-        () => {
-          const serializer = new XMLSerializer();
-          const svg_blob = new Blob([serializer.serializeToString(svg)], {
-            type: "image/svg+xml"
-          });
-          a.download = downloadImgName + ".svg";
-          a.href = URL.createObjectURL(svg_blob);
-          document.body.removeChild(a);
-        },
-        false
-      );
-      a.click();
-    };
-    this.geneClickListener = async (gene, mnames) => {
-      const { filter, filter0 } = this.discoApp.app.getState().termfilter;
-      const arg = {
-        holder: this.discoApp.app.opts.holder,
-        genome: this.discoApp.app.opts.state.args.genome,
-        nobox: true,
-        query: gene,
-        tklst: [
-          {
-            type: "mds3",
-            dslabel: this.discoApp.app.opts.state.vocab.dslabel,
-            hlaachange: mnames.join(","),
-            filter0,
-            filterObj: getNormalRoot(filter)
-            // must not pass filter as frozen. pass unfrozen, normalized copy so mds3 code will work
-          }
-        ]
-      };
-      const _ = await import("./block.init-2Y6CNK7H.js");
-      await _.default(arg);
-    };
-    this.colorScaleNumericInputsCallback = async (obj) => {
-      const callAppDispatch = (settings) => {
-        this.discoApp.app.dispatch({
-          type: "plot_edit",
-          id: this.discoApp.id,
-          config: { settings: { Disco: Object.assign({ cnvCutoffMode: obj.cutoffMode }, settings) } }
-        });
-      };
-      if (obj.cutoffMode == "auto") {
-        if (obj.min == null || obj.max == null)
-          throw new Error('Color scale must return min and max if cutoffMode "auto"');
-        callAppDispatch({
-          cnvCapping: this.discoApp.state.settings.cnv.capping,
-          cnvPercentile: this.discoApp.state.settings.cnv.percentile
-        });
-      } else if (obj.cutoffMode == "fixed") {
-        if (obj.min == null || obj.max == null)
-          throw new Error('Color scale must return min and max if cutoffMode "fixed"');
-        const diffValue = obj.max !== this.discoApp.state.settings.cnv.capping ? obj.max : Math.abs(obj.min);
-        callAppDispatch({
-          cnvCapping: diffValue
-        });
-      } else if (obj.cutoffMode == "percentile") callAppDispatch({ cnvPercentile: obj.percentile });
-      else throw new Error("Unknown cutoff mode returned from dom/ColorScale");
-    };
-    this.onMutationWaterfallColorChange = (color) => {
-      this.discoApp.app.dispatch({
-        type: "plot_edit",
-        id: this.discoApp.id,
-        config: { settings: { Disco: { mutationWaterfallColor: color } } }
-      });
-    };
-  }
-};
-
-// plots/disco/chromosome/Reference.ts
-var Reference = class {
-  /**
-   * Creates a Reference object that contains information about chromosomes.
-   * @param settings State settings
-   * @param chromosomes Chromosome order. This function formats into an obj with `chr` removed.
-   * @param chromosomeOverride Obj of chromsome keys and sizes. Filtered to remove hidden chromosomes in settings.
-   */
-  constructor(settings, chromosomes, chromosomeOverride) {
-    this.chromosomes = [];
-    this.chromosomesOrder = [];
-    this.keysArray = [];
-    this.totalSizeArray = [];
-    this.chrSizesArray = [];
-    const chrSizes = chromosomeOverride || chromosomes;
-    this.settings = settings;
-    this.chromosomesOrder = [];
-    let totalSize = 0;
-    this.totalPadAngle = Object.keys(chrSizes).length * this.settings.padAngle;
-    this.totalChromosomesAngle = 2 * Math.PI - this.totalPadAngle;
-    for (const chr in chrSizes) {
-      const key = chr.slice(0, 3) === "chr" ? chr.slice(3) : chr;
-      this.chromosomesOrder.push(chr);
-      this.keysArray.push(key);
-      this.totalSizeArray.push(totalSize);
-      this.chrSizesArray.push(chrSizes[chr]);
-      totalSize += chrSizes[chr];
-    }
-    this.totalSize = totalSize;
-    let lastAngle = 0;
-    for (let i = 0; i < this.keysArray.length; i++) {
-      const chromosomeAngle = this.totalChromosomesAngle * (this.chrSizesArray[i] / totalSize);
-      const startAngle = i == 0 ? this.settings.padAngle / 2 : lastAngle + this.settings.padAngle;
-      const endAngle = i == 0 ? this.settings.padAngle / 2 + chromosomeAngle : lastAngle + this.settings.padAngle + chromosomeAngle;
-      const chromosome = {
-        start: this.totalSizeArray[i],
-        size: this.chrSizesArray[i],
-        factor: 1,
-        startAngle,
-        endAngle,
-        angle: (startAngle + endAngle) / 2,
-        innerRadius: this.settings.rings.chromosomeInnerRadius,
-        outerRadius: this.settings.rings.chromosomeInnerRadius + this.settings.rings.chromosomeWidth,
-        color: "#AAA",
-        text: this.keysArray[i]
-      };
-      this.chromosomes.push(chromosome);
-      if (chromosome.endAngle != null) {
-        lastAngle = chromosome.endAngle;
-      }
-    }
-  }
-};
-
-// plots/disco/data/DataObjectMapper.ts
-var DataObjectMapper = class {
-  constructor(sampleName, prioritizedGenes) {
-    this.sampleName = sampleName;
-    this.prioritizedGenes = prioritizedGenes;
-  }
-  map(dObject) {
-    return {
-      dt: dObject.dt,
-      mname: dObject.mname,
-      mClass: dObject.class,
-      gene: dObject.gene,
-      chr: dObject.chr,
-      ref: dObject.ref,
-      alt: dObject.alt,
-      vafs: dObject.vafs,
-      position: dObject.pos ? dObject.pos : dObject.position,
-      poschr: dObject.poschr,
-      posbins: dObject.posbins,
-      poslabel: dObject.poslabel,
-      sampleName: this.sampleName,
-      ssm_id: dObject.ssm_id,
-      start: dObject.start,
-      stop: dObject.stop,
-      value: dObject.value,
-      segmean: dObject.segmean,
-      isPrioritized: this.prioritizedGenes.some((cancerGene) => cancerGene == dObject.gene),
-      chrA: dObject.chrA,
-      chrB: dObject.chrB,
-      geneA: dObject.geneA,
-      geneB: dObject.geneB,
-      posA: dObject.posA,
-      posB: dObject.posB,
-      strandA: dObject.strandA,
-      strandB: dObject.strandB
-    };
-  }
-};
-
-// plots/disco/data/PercentileMapper.ts
-var PercentileMapper = class {
-  map(data, percentile) {
-    return this.calculatePercentileForPositivesAndNegatives(data, percentile);
-  }
-  calculatePercentileForPositivesAndNegatives(data, percentile) {
-    const positives = data.filter((x) => x > 0);
-    const negatives = data.filter((x) => x < 0).map((x) => -1 * x);
-    let positive = NaN;
-    let negative = NaN;
-    if (positives.length > 0) {
-      positive = this.calculatePercentile(positives, percentile);
-    }
-    if (negatives.length > 0) {
-      negative = -1 * this.calculatePercentile(negatives, percentile);
-    }
-    return { positive, negative };
-  }
-  calculatePercentile(data, percentile) {
-    if (data.length === 0) {
-      throw new Error("Array must contain at least one element.");
-    }
-    const sortedValues = data.sort((a, b) => a - b);
-    const index = percentile / 100 * (sortedValues.length - 1);
-    const lowerIndex = Math.floor(index);
-    const upperIndex = Math.ceil(index);
-    const fraction = index - lowerIndex;
-    if (lowerIndex === upperIndex) {
-      return sortedValues[lowerIndex];
-    }
-    return sortedValues[lowerIndex] + fraction * (sortedValues[upperIndex] - sortedValues[lowerIndex]);
-  }
-};
-
-// plots/disco/snv/vafTooltip.ts
-function getIntegerCount(v) {
-  if (Number.isInteger(v)) return v;
-  if (typeof v == "string" && /^-?\d+$/.test(v)) {
-    const n = Number(v);
-    if (Number.isInteger(n)) return n;
-  }
-  return null;
-}
-function getReadCounts(refCountValue, altCountValue, totalCountValue) {
-  const altCount = getIntegerCount(altCountValue);
-  if (altCount == null || altCount < 0) return null;
-  const totalCount = getIntegerCount(totalCountValue);
-  if (totalCount != null) {
-    if (totalCount <= 0 || totalCount < altCount) return null;
-    return { altCount, refCount: totalCount - altCount, totalCount };
-  }
-  const refCount = getIntegerCount(refCountValue);
-  if (refCount == null || refCount < 0 || refCount + altCount <= 0) return null;
-  return { altCount, refCount, totalCount: refCount + altCount };
-}
-function hasValidReadCounts(refCountValue, altCountValue, totalCountValue) {
-  return getReadCounts(refCountValue, altCountValue, totalCountValue) != null;
-}
-function getVafEntries(vafs) {
-  const entries = [];
-  if (Array.isArray(vafs)) {
-    for (const vaf of vafs) {
-      const label = vaf?.id || vaf?.name;
-      const refCount = vaf?.refCount;
-      const totalCount = vaf?.totalCount;
-      const altCount = vaf?.altCount;
-      if (!label || altCount == null || refCount == null && totalCount == null) continue;
-      const entry = { label, altCount };
-      if (refCount != null) entry.refCount = refCount;
-      if (totalCount != null) entry.totalCount = totalCount;
-      entries.push(entry);
-    }
-  }
-  return entries;
-}
-function getNumericFraction(v) {
-  if (typeof v != "number" && typeof v != "string") return null;
-  const n = Number(v);
-  return Number.isFinite(n) && n >= 0 && n <= 1 ? n : null;
-}
-function getMutationFractions(vafs) {
-  const fractions = [];
-  if (!Array.isArray(vafs)) return fractions;
-  for (const vaf of vafs) {
-    const explicitFraction = getNumericFraction(vaf?.fraction ?? vaf?.mutationFraction);
-    if (explicitFraction != null) {
-      fractions.push(explicitFraction);
-      continue;
-    }
-    const counts = getReadCounts(vaf?.refCount, vaf?.altCount, vaf?.totalCount);
-    if (!counts) continue;
-    fractions.push(counts.altCount / counts.totalCount);
-  }
-  return fractions;
-}
-function getMaxMutationFraction(vafs) {
-  const fractions = getMutationFractions(vafs);
-  return fractions.length ? Math.max(...fractions) : null;
-}
-function hasAnyValidVafEntry(vafs) {
-  return getVafEntries(vafs).some((vaf) => hasValidReadCounts(vaf.refCount, vaf.altCount, vaf.totalCount));
-}
-function appendVafBar(td2, refCountValue, altCountValue, label = "VAF", totalCountValue) {
-  const counts = getReadCounts(refCountValue, altCountValue, totalCountValue);
-  if (!counts) return;
-  const fraction = counts.altCount / counts.totalCount;
-  const div = td2.append("div").style("margin-left", "5px").style("margin-top", "4px").style("display", "flex").style("align-items", "center").style("gap", "6px");
-  div.append("span").style("font-size", "0.8em").style("color", "#555").text(label);
-  fillbar(div, { f: fraction, v1: counts.altCount, v2: counts.totalCount });
-}
-function appendVafBars(td2, vafs) {
-  for (const vaf of getVafEntries(vafs)) {
-    if (!hasValidReadCounts(vaf.refCount, vaf.altCount, vaf.totalCount)) continue;
-    appendVafBar(td2, vaf.refCount, vaf.altCount, vaf.label, vaf.totalCount);
-  }
-}
-
-// plots/disco/data/DataMapper.ts
-var DataMapper = class _DataMapper {
-  constructor(settings, reference, sample, prioritizedGenes = []) {
-    // remove fields and extract filters to seperate classes
-    this.labelData = [];
-    this.nonExonicSnvData = [];
-    this.nonExonicInnerRadius = 0;
-    this.snvRingDataMap = /* @__PURE__ */ new Map();
-    this.snvInnerRadius = 0;
-    this.snvData = [];
-    this.bpx = 0;
-    this.onePxArcAngle = 0;
-    this.filteredSnvData = [];
-    this.filteredSnvCountByChr = /* @__PURE__ */ new Map();
-    this.lohData = [];
-    this.lohInnerRadius = 0;
-    this.cnvData = [];
-    this.cnvInnerRadius = 0;
-    this.fusionData = [];
-    this.fusionRadius = 0;
-    this.hasPrioritizedGenes = false;
-    this.hasWaterfallEligibleChromosome = false;
-    this.invalidEntries = [];
-    this.cnvLossMaxValue = 0;
-    this.cnvGainMaxValue = 0;
-    this.percentilePositive = 0;
-    this.percentileNegative = 0;
-    this.cnvMaxPercentileAbs = 0;
-    this.mutationWaterfallData = [];
-    this.hasMutationFractionData = false;
-    this.mutationWaterfallInnerRadius = 0;
-    this.mutationWaterfallRangeMin = Infinity;
-    this.mutationWaterfallRangeMax = -Infinity;
-    this.lohMaxValue = void 0;
-    this.lohMinValue = void 0;
-    this.snvFilter = (data) => data.dt == dtsnvindel;
-    this.fusionFilter = (data) => data.dt == dtfusionrna || data.dt == dtsv;
-    this.cnvFilter = (data) => data.dt == dtcnv || data.dt == dtitd;
-    this.lohFilter = (data) => data.dt == dtloh;
-    this.compareData = (a, b) => {
-      const chrDiff = this.reference.chromosomesOrder.indexOf(a.chr) - this.reference.chromosomesOrder.indexOf(b.chr);
-      if (chrDiff != 0) {
-        return chrDiff;
-      }
-      const aPos = a.pos ? a.pos : a.start;
-      const bPos = b.pos ? b.pos : b.start;
-      return aPos - bPos;
-    };
-    this.settings = settings;
-    this.reference = reference;
-    this.sample = sample;
-    this.excludedChromosomes = this.settings.Disco.hiddenChromosomes;
-    this.lastInnerRadious = this.settings.rings.chromosomeInnerRadius;
-    this.gainCapped = this.settings.Disco.cnvCapping;
-    this.lossCapped = -1 * this.settings.Disco.cnvCapping;
-    this.nonExonicFilter = (data) => {
-      if (prioritizedGenes.length > 0 && this.settings.Disco.prioritizeGeneLabelsByGeneSets) {
-        return prioritizedGenes.includes(data.gene) && settings.rings.nonExonicFilterValues.includes(ViewModelMapper.snvClassLayer[data.mClass]);
-      } else {
-        return settings.rings.nonExonicFilterValues.includes(ViewModelMapper.snvClassLayer[data.mClass]);
-      }
-    };
-    this.snvRingFilter = (data) => {
-      if (prioritizedGenes.length > 0 && this.settings.Disco.prioritizeGeneLabelsByGeneSets) {
-        return prioritizedGenes.includes(data.gene) && settings.rings.snvRingFilters.includes(ViewModelMapper.snvClassLayer[data.mClass]);
-      } else {
-        return settings.rings.snvRingFilters.includes(ViewModelMapper.snvClassLayer[data.mClass]);
-      }
-    };
-    this.dataObjectMapper = new DataObjectMapper(sample, prioritizedGenes);
-  }
-  map(data) {
-    const dataArray = [];
-    this.filteredSnvCountByChr.clear();
-    this.hasWaterfallEligibleChromosome = false;
-    this.mutationWaterfallData = [];
-    this.mutationWaterfallInnerRadius = 0;
-    this.mutationWaterfallRangeMin = Infinity;
-    this.mutationWaterfallRangeMax = -Infinity;
-    this.hasMutationFractionData = false;
-    data.forEach((dObject) => {
-      if (dObject.dt == dtsnvindel && getMaxMutationFraction(dObject.vafs) != null) {
-        this.hasMutationFractionData = true;
-      }
-      const index = this.reference.chromosomesOrder.indexOf(dObject.chr);
-      const indexA = this.reference.chromosomesOrder.indexOf(dObject.chrA);
-      const indexB = this.reference.chromosomesOrder.indexOf(dObject.chrB);
-      if (dObject.dt == dtsnvindel) {
-        if (index != -1 && this.snvData.length < this.settings.snv.maxMutationCount) {
-          const pos = dObject.pos ?? dObject.position;
-          const chrSize = this.reference.chromosomes[index].size;
-          if (Number.isFinite(pos) && pos >= 0 && pos <= chrSize) {
-            this.addData(dObject, dataArray);
-          } else {
-            this.invalidEntries.push({ dataType: "SNV", reason: `Position ${pos} outside of ${dObject.chr}` });
-          }
-        } else if (index == -1) {
-          if (!this.excludedChromosomes.includes(dObject.chr)) {
-            this.invalidEntries.push({ dataType: "SNV", reason: `Unknown chr ${dObject.chr}` });
-          }
-        }
-      } else if (dObject.dt == dtfusionrna || dObject.dt == dtsv) {
-        if (indexA != -1 && indexB != -1) {
-          const posA = dObject.posA;
-          const posB = dObject.posB;
-          const chrSizeA = this.reference.chromosomes[indexA].size;
-          const chrSizeB = this.reference.chromosomes[indexB].size;
-          if (Number.isFinite(posA) && Number.isFinite(posB) && posA >= 0 && posA <= chrSizeA && posB >= 0 && posB <= chrSizeB) {
-            this.addData(dObject, dataArray);
-          } else {
-            const reasonParts = [];
-            if (!(Number.isFinite(posA) && posA >= 0 && posA <= chrSizeA))
-              reasonParts.push(`Position ${posA} outside of ${dObject.chrA}`);
-            if (!(Number.isFinite(posB) && posB >= 0 && posB <= chrSizeB))
-              reasonParts.push(`Position ${posB} outside of ${dObject.chrB}`);
-            this.invalidEntries.push({ dataType: "Fusion", reason: reasonParts.join("; ") });
-          }
-        } else {
-          const missing = [];
-          if (indexA == -1 && !this.excludedChromosomes.includes(dObject.chrA)) missing.push(dObject.chrA);
-          if (indexB == -1 && !this.excludedChromosomes.includes(dObject.chrB)) missing.push(dObject.chrB);
-          if (missing.length) this.invalidEntries.push({ dataType: "Fusion", reason: "Unknown chr in fusion" });
-        }
-      } else if ([dtcnv, dtloh, dtitd].includes(Number(dObject.dt))) {
-        const idx = this.reference.chromosomesOrder.indexOf(dObject.chr);
-        const dataType = dObject.dt == dtcnv ? "CNV" : dObject.dt == dtloh ? "LOH" : "ITD";
-        if (dObject.chr && idx != -1) {
-          const chrSize = this.reference.chromosomes[idx].size;
-          const start = dObject.start;
-          const stop = dObject.stop;
-          if (Number.isFinite(start) && Number.isFinite(stop) && start >= 0 && stop <= chrSize && start <= stop) {
-            this.addData(dObject, dataArray);
-          } else {
-            this.invalidEntries.push({
-              dataType,
-              reason: `Position ${start}-${stop} outside of ${dObject.chr}`
-            });
-          }
-        } else {
-          if (!this.excludedChromosomes.includes(dObject.chr)) {
-            this.invalidEntries.push({
-              dataType,
-              reason: `Unknown chr ${dObject.chr}`
-            });
-          }
-        }
-      } else {
-        throw Error("Unknown mutation type!");
-      }
-    });
-    const sortedData = dataArray.sort(this.compareData);
-    if (this.settings.rings.nonExonicRingEnabled) {
-      sortedData.forEach((data2) => {
-        this.filterNonExonicSnvData(data2);
-      });
-    }
-    if (this.nonExonicSnvData.length > 0) {
-      this.nonExonicInnerRadius = this.lastInnerRadious - this.settings.rings.nonExonicRingWidth;
-      this.lastInnerRadious = this.nonExonicInnerRadius;
-    }
-    sortedData.forEach((data2) => {
-      this.filterSnvs(data2);
-    });
-    this.hasWaterfallEligibleChromosome = Array.from(this.filteredSnvCountByChr.values()).some((count) => count >= 2);
-    if (this.settings.Disco.mutationWaterfallPlot && this.hasWaterfallEligibleChromosome) {
-      this.prepareMutationWaterfallData();
-    }
-    sortedData.forEach((data2) => {
-      this.filterLohs(data2);
-    });
-    if (this.lohData.length > 0) {
-      this.lohInnerRadius = this.lastInnerRadious - this.settings.rings.lohRingWidth;
-      this.lastInnerRadious = this.lohInnerRadius;
-    }
-    sortedData.forEach((data2) => {
-      this.filterCnvs(data2);
-    });
-    if (this.cnvData.length > 0) {
-      this.cnvInnerRadius = this.lastInnerRadious - this.settings.rings.cnvRingWidth;
-      this.lastInnerRadious = this.cnvInnerRadius;
-      this.cappedCnvMaxAbsValue = Math.min(
-        this.settings.Disco.cnvCapping,
-        Math.max(
-          Math.abs(_DataMapper.capMaxValue(this.cnvLossMaxValue, this.gainCapped, this.lossCapped)),
-          Math.abs(_DataMapper.capMaxValue(this.cnvGainMaxValue, this.gainCapped, this.lossCapped))
-        )
-      );
-      const cnvValues = this.cnvData.filter((data2) => data2.dt == dtcnv).map((data2) => data2.value);
-      if (cnvValues.length) {
-        const percentilePair = new PercentileMapper().map(cnvValues, this.settings.Disco.cnvPercentile);
-        this.percentilePositive = _DataMapper.capMaxValue(percentilePair.positive, this.gainCapped, this.lossCapped);
-        this.percentileNegative = _DataMapper.capMaxValue(percentilePair.negative, this.gainCapped, this.lossCapped);
-        this.cnvMaxPercentileAbs = Math.min(
-          this.settings.Disco.cnvCapping,
-          Math.max(this.percentilePositive, Math.abs(this.percentileNegative))
-        );
-      }
-    }
-    sortedData.forEach((data2) => {
-      this.filterFusion(data2);
-    });
-    if (this.fusionData.length > 0) {
-      this.fusionRadius = this.lastInnerRadious;
-    }
-    const dataHolder = {
-      labelData: this.labelData,
-      nonExonicSnvData: this.nonExonicSnvData,
-      nonExonicInnerRadius: this.nonExonicInnerRadius,
-      snvRingDataMap: this.snvRingDataMap,
-      snvInnerRadius: this.snvInnerRadius,
-      snvData: this.snvData,
-      bpx: this.bpx,
-      onePxArcAngle: this.onePxArcAngle,
-      filteredSnvData: this.filteredSnvData,
-      lohData: this.lohData,
-      lohInnerRadius: this.lohInnerRadius,
-      cnvData: this.cnvData,
-      cnvInnerRadius: this.cnvInnerRadius,
-      fusionData: this.fusionData,
-      fusionRadius: this.fusionRadius,
-      hasPrioritizedGenes: this.hasPrioritizedGenes,
-      hasWaterfallEligibleChromosome: this.hasWaterfallEligibleChromosome,
-      cnvGainMaxValue: this.cnvGainMaxValue,
-      cnvLossMaxValue: this.cnvLossMaxValue,
-      cappedCnvMaxAbsValue: this.cappedCnvMaxAbsValue,
-      percentilePositive: this.percentilePositive,
-      percentileNegative: this.percentileNegative,
-      cnvMaxPercentileAbs: this.cnvMaxPercentileAbs,
-      lohMaxValue: this.lohMaxValue,
-      lohMinValue: this.lohMinValue,
-      hasMutationFractionData: this.hasMutationFractionData,
-      mutationWaterfallData: this.mutationWaterfallData,
-      mutationWaterfallInnerRadius: this.mutationWaterfallInnerRadius,
-      mutationWaterfallLogRange: this.mutationWaterfallData.length ? { min: this.mutationWaterfallRangeMin, max: this.mutationWaterfallRangeMax } : void 0,
-      invalidDataInfo: {
-        entries: this.invalidEntries,
-        errorMsg: `Entries listed above were skipped due to invalid or unsupported chromosome information.`
-      }
-    };
-    return dataHolder;
-  }
-  addData(dObject, dataArray) {
-    const instance = this.dataObjectMapper.map(dObject);
-    if (instance.isPrioritized) {
-      this.hasPrioritizedGenes = true;
-    }
-    dataArray.push(instance);
-  }
-  filterNonExonicSnvData(data) {
-    if (this.snvFilter(data) && this.passesMutationFractionFilter(data)) {
-      if (this.settings.rings.nonExonicRingEnabled && this.nonExonicFilter(data)) {
-        this.nonExonicSnvData.push(data);
-      }
-    }
-  }
-  filterSnvs(data) {
-    if (this.snvFilter(data)) {
-      this.snvData.push(data);
-      if (this.passesMutationFractionFilter(data) && this.snvRingFilter(data)) {
-        if (this.snvInnerRadius == 0) {
-          this.snvInnerRadius = this.lastInnerRadious - this.settings.rings.snvRingWidth;
-          this.lastInnerRadious = this.snvInnerRadius;
-          this.bpx = Math.floor(this.reference.totalSize / (this.reference.totalChromosomesAngle * this.snvInnerRadius));
-          this.onePxArcAngle = 1 / this.snvInnerRadius;
-        }
-        this.filteredSnvData.push(data);
-        this.labelData.push(data);
-        const currentCount = this.filteredSnvCountByChr.get(data.chr) || 0;
-        this.filteredSnvCountByChr.set(data.chr, currentCount + 1);
-        const arcAngle = this.calculateArcAngle(data);
-        let dataArray = this.snvRingDataMap.get(arcAngle);
-        if (!dataArray) {
-          dataArray = new Array();
-        }
-        dataArray.push(data);
-        this.snvRingDataMap.set(arcAngle, dataArray);
-      }
-    }
-  }
-  passesMutationFractionFilter(data) {
-    if (!this.hasMutationFractionData) return true;
-    const minMutationFraction = this.settings.Disco.minMutationFraction || 0;
-    if (minMutationFraction <= 0) return true;
-    const fraction = getMaxMutationFraction(data.vafs);
-    return fraction != null && fraction >= minMutationFraction;
-  }
-  filterFusion(data) {
-    if (this.fusionFilter(data)) {
-      data.isPrioritized = true;
-      this.fusionData.push(data);
-      this.labelData.push(data);
-    }
-  }
-  filterLohs(data) {
-    if (this.lohFilter(data)) {
-      if (this.lohMaxValue == void 0 || this.lohMaxValue < data.value) {
-        this.lohMaxValue = data.segmean;
-      }
-      if (this.lohMinValue == void 0 || this.lohMinValue > data.value) {
-        this.lohMinValue = data.segmean;
-      }
-      this.lohData.push(data);
-    }
-  }
-  filterCnvs(data) {
-    if (this.cnvFilter(data)) {
-      if (!data.chr || this.reference.chromosomesOrder.indexOf(data.chr) == -1) {
-        return;
-      }
-      if (data.dt == dtcnv) {
-        if (this.cnvGainMaxValue == void 0 || this.cnvGainMaxValue < data.value) {
-          this.cnvGainMaxValue = data.value;
-        }
-        if (this.cnvLossMaxValue == void 0 || this.cnvLossMaxValue > data.value) {
-          this.cnvLossMaxValue = data.value;
-        }
-      }
-      this.cnvData.push(data);
-    }
-  }
-  prepareMutationWaterfallData() {
-    this.mutationWaterfallInnerRadius = this.lastInnerRadious - this.settings.rings.mutationWaterfallRingWidth;
-    this.lastInnerRadious = this.mutationWaterfallInnerRadius;
-    const groupedSnvs = /* @__PURE__ */ new Map();
-    const firstMutationByChr = [];
-    for (const snv of this.filteredSnvData) {
-      const list = groupedSnvs.get(snv.chr) || [];
-      list.push(snv);
-      groupedSnvs.set(snv.chr, list);
-    }
-    for (const [, snvs] of groupedSnvs) {
-      if (snvs.length < 2) continue;
-      snvs.sort((a, b) => a.position - b.position);
-      firstMutationByChr.push({
-        chr: snvs[0].chr,
-        position: snvs[0].position,
-        logDistance: 0
-        // placeholder updated after range computed
-      });
-      for (let i = 1; i < snvs.length; i++) {
-        const prev = snvs[i - 1];
-        const curr = snvs[i];
-        const distance = Math.max(1, Math.abs(curr.position - prev.position));
-        const logDistance = Math.log10(distance);
-        this.mutationWaterfallData.push({
-          chr: curr.chr,
-          position: curr.position,
-          logDistance
-        });
-        if (logDistance < this.mutationWaterfallRangeMin) {
-          this.mutationWaterfallRangeMin = logDistance;
-        }
-        if (logDistance > this.mutationWaterfallRangeMax) {
-          this.mutationWaterfallRangeMax = logDistance;
-        }
-      }
-    }
-    if (!this.mutationWaterfallData.length) {
-      this.mutationWaterfallRangeMin = 0;
-      this.mutationWaterfallRangeMax = 0;
-    }
-    const topLogDistance = this.mutationWaterfallRangeMax;
-    for (const first of firstMutationByChr) {
-      this.mutationWaterfallData.push({
-        ...first,
-        logDistance: topLogDistance
-      });
-    }
-  }
-  calculateArcAngle(data) {
-    const currentChromosome = this.reference.chromosomes[this.reference.chromosomesOrder.findIndex((chromosomeOrder) => data.chr == chromosomeOrder)];
-    const dataAnglePos = Math.floor(data.position / this.bpx);
-    return currentChromosome.startAngle + dataAnglePos * this.onePxArcAngle;
-  }
-  static capMaxValue(value, gainCapped, lossCapped) {
-    if (value && Math.sign(value) == 1) {
-      return value > gainCapped ? gainCapped : value;
-    }
-    if (Math.sign(value) == -1) {
-      return value < lossCapped ? lossCapped : value;
-    }
-    return 0;
-  }
-  static capMinValue(value, capMinValue = 1) {
-    if (Math.sign(value) == 1) {
-      return value > capMinValue ? value : capMinValue;
-    }
-    if (Math.sign(value) == -1) {
-      return value < -1 * capMinValue ? value : -1 * capMinValue;
-    }
-    return 1;
-  }
-};
-
-// plots/disco/legend/Legend.ts
-var Legend = class {
-  constructor(snvTitle, cnvTitle, lohTitle, fusionTitle, cnvPercentile, cnvCutoffmode, snvClassMap, cnvClassMap, cnvRenderingType, fusionLegend, discoInteractions, lohLegend, mutationWaterfallLegend, fusionLegendCounts = { interchromosomal: 0, intrachromosomal: 0 }, cnvCount = 0) {
-    this.snvTitle = snvTitle;
-    this.cnvTitle = cnvTitle;
-    this.lohTitle = lohTitle;
-    this.fusionTitle = fusionTitle;
-    this.cnvPercentile = cnvPercentile;
-    this.cnvCutoffMode = cnvCutoffmode;
-    this.cnvCount = cnvCount;
-    this.snvClassMap = snvClassMap;
-    this.cnvClassMap = cnvClassMap;
-    this.cnvRenderingType = cnvRenderingType;
-    this.lohLegend = lohLegend;
-    this.fusionLegend = fusionLegend;
-    this.fusionLegendCounts = fusionLegendCounts;
-    this.discoInteractions = discoInteractions;
-    this.mutationWaterfallLegend = mutationWaterfallLegend;
-  }
-  legendCount() {
-    const hasItd = this.cnvClassMap.has(4 /* ITD */);
-    return (this.snvClassMap.size > 0 ? 1 : 0) + (this.cnvCount > 0 ? 1 : 0) + (hasItd ? 1 : 0) + (this.lohLegend ? 1 : 0) + (this.fusionLegend ? 1 : 0) + (this.mutationWaterfallLegend ? 1 : 0);
-  }
-};
-
-// plots/disco/fusion/Fusion.ts
-var Fusion = class {
-  constructor(source, target, genes, count, endpts) {
-    this.source = source;
-    this.target = target;
-    this.genes = genes;
-    this.count = count;
-    this.endpts = endpts;
-  }
-};
-
-// plots/disco/fusion/FusionSubgroup.ts
-var FusionSubgroup = class {
-  constructor(startAngle, endAngle, radius, gene, value, genes, positionInChromosome, strand) {
-    this.startAngle = startAngle;
-    this.endAngle = endAngle;
-    this.radius = radius;
-    this.gene = gene;
-    this.value = value;
-    this.genes = genes;
-    this.positionInChromosome = positionInChromosome;
-    this.strand = strand;
-  }
-};
-
-// plots/disco/fusion/FusionMapper.ts
-var FusionMapper = class {
-  constructor(radius, sampleName, reference) {
-    this.radius = radius;
-    this.sampleName = sampleName;
-    this.reference = reference;
-  }
-  map(fusionData) {
-    const fusions = [];
-    fusionData.forEach((data) => {
-      const genes = /* @__PURE__ */ new Set();
-      genes.add(data.geneA);
-      genes.add(data.geneB);
-      const startAngle = this.calculateStartAngle(data.chrA, data.posA);
-      const endAngle = this.calculateEndAngle(data.chrA, data.posA);
-      if (startAngle === null || endAngle === null) return;
-      const source = new FusionSubgroup(
-        startAngle,
-        endAngle,
-        this.radius,
-        data.geneA,
-        data.value,
-        genes,
-        {
-          chromosome: data.chrA,
-          position: data.posA
-        },
-        data.strandA
-      );
-      let target;
-      if (data.chrB && data.posB) {
-        const startAngle2 = this.calculateStartAngle(data.chrB, data.posB);
-        const endAngle2 = this.calculateEndAngle(data.chrB, data.posB);
-        if (startAngle2 === null || endAngle2 === null) return;
-        target = new FusionSubgroup(
-          startAngle2,
-          endAngle2,
-          this.radius,
-          data.geneB,
-          data.value,
-          genes,
-          {
-            chromosome: data.chrB,
-            position: data.posB
-          },
-          data.strandB
-        );
-      }
-      const fusion = new Fusion(source, target, "genes", -1, "Endpoints");
-      fusions.push(fusion);
-    });
-    return fusions;
-  }
-  calculateStartAngle(chr, pos) {
-    const index = this.reference.chromosomesOrder.indexOf(chr);
-    if (index === -1) return null;
-    const chromosome = this.reference.chromosomes[index];
-    return chromosome.startAngle + (chromosome.endAngle - chromosome.startAngle) * (Number(pos) / chromosome.size) - 0.01;
-  }
-  calculateEndAngle(chr, pos) {
-    const index = this.reference.chromosomesOrder.indexOf(chr);
-    if (index === -1) return null;
-    const chromosome = this.reference.chromosomes[index];
-    return 0.01 + chromosome.startAngle + (chromosome.endAngle - chromosome.startAngle) * (Number(pos) / chromosome.size);
-  }
-};
-
-// plots/disco/loh/LohLegend.ts
-var LohLegend = class {
-  constructor(count) {
-    this.count = count;
-  }
-};
-
-// plots/disco/viewmodel/ViewModel.ts
-var ViewModel = class {
-  constructor(settings, rings, legend, fusions, dataHolder, genesetName, snvDataLengthAll) {
-    this.settings = settings;
-    this.rings = rings;
-    this.legend = legend;
-    this.fusions = fusions;
-    this.genesetName = genesetName;
-    const tempHolder = select_default("body").append("div").style("position", "absolute").style("visibility", "hidden");
-    const tempSvg = tempHolder.append("svg");
-    const labels = rings.labelsRing?.elementsToDisplay?.map((l) => l.text) || [];
-    const maxLabelSpace = getMaxLabelWidth(tempSvg, labels);
-    tempHolder.remove();
-    this.width = 2 * (this.settings.horizontalPadding + this.settings.rings.labelLinesInnerRadius + this.settings.rings.labelsToLinesDistance + maxLabelSpace);
-    this.height = 2 * (this.settings.rings.labelLinesInnerRadius + this.settings.rings.labelsToLinesDistance + this.settings.verticalPadding + this.settings.label.fontSize * 2 + maxLabelSpace);
-    this.legendHeight = this.calculateLegendHeight(legend);
-    this.snvDataLength = dataHolder.snvData.length;
-    this.filteredSnvDataLength = dataHolder.filteredSnvData.length;
-    this.snvDataLengthAll = snvDataLengthAll;
-    this.cnvMaxValue = dataHolder.cnvGainMaxValue;
-    this.cnvMinValue = dataHolder.cnvLossMaxValue;
-    this.cappedCnvMaxAbsValue = dataHolder.cappedCnvMaxAbsValue;
-    this.negativePercentile = dataHolder.percentileNegative;
-    this.positivePercentile = dataHolder.percentilePositive;
-    this.invalidDataInfo = dataHolder.invalidDataInfo;
-    this.canShowMutationWaterfallPlot = dataHolder.hasWaterfallEligibleChromosome;
-    this.hasMutationFractionData = dataHolder.hasMutationFractionData;
-  }
-  getElements(ringType) {
-    switch (ringType) {
-      case 0 /* CHROMOSOME */:
-        return this.rings.chromosomesRing ? this.rings.chromosomesRing.elements : [];
-      case 1 /* LABEL */:
-        return this.rings.labelsRing.elementsToDisplay;
-      case 2 /* NONEXONICSNV */:
-        return this.rings.nonExonicArcRing ? this.rings.nonExonicArcRing.elements : [];
-      case 3 /* SNV */:
-        return this.rings.snvArcRing ? this.rings.snvArcRing.elements : [];
-      case 5 /* CNV */:
-        return this.rings.cnvArcRing ? this.rings.cnvArcRing.elements : [];
-      case 6 /* LOH */:
-        return this.rings.lohArcRing ? this.rings.lohArcRing.elements : [];
-      case 4 /* MUTATION_WATERFALL */:
-        return this.rings.mutationWaterfallRing ? this.rings.mutationWaterfallRing.elements : [];
-      default:
-        throw new Error(`ringType ${ringType} not defined`);
-    }
-  }
-  getCollisions(ringType) {
-    if (ringType == 1 /* LABEL */) {
-      return this.rings.labelsRing.collisions;
-    } else {
-      return void 0;
-    }
-  }
-  calculateLegendHeight(legend) {
-    const rawHeight = this.settings.legend.rowHeight;
-    return rawHeight * legend.legendCount();
-  }
-};
-
-// plots/disco/ring/Ring.ts
-var Ring = class {
-  constructor(innerRadius, width, elements) {
-    this.innerRadius = innerRadius;
-    this.outerRadius = innerRadius + width;
-    this.width = width;
-    this.elements = elements;
-  }
-};
-
-// plots/disco/label/MLabel.ts
-var MLabel = class _MLabel {
-  /**
-   * The Singleton's constructor should always be private to prevent direct
-   * construction calls with the `new` operator.
-   */
-  constructor() {
-    const mlabel = {};
-    for (const key in mclass) {
-      mlabel[mclass[key].label] = mclass[key];
-      mlabel[key] = mclass[key];
-    }
-    this.mlabel = mlabel;
-  }
-  /**
-   * The static method that controls the access to the singleton instance.
-   *
-   * This implementation let you subclass the Singleton class while keeping
-   * just one instance of each subclass around.
-   */
-  static getInstance() {
-    if (!_MLabel.instance) {
-      _MLabel.instance = new _MLabel();
-    }
-    return _MLabel.instance;
-  }
-};
-
-// plots/disco/snv/SnvLegendElement.ts
-var SnvLegendElement = class {
-  constructor(snvType, color, count) {
-    this.snvType = snvType;
-    this.color = color;
-    this.count = count;
-  }
-};
-
-// plots/disco/snv/SnvArcsMapper.ts
-var SnvArcsMapper = class {
-  constructor(svnInnerRadius, svnWidth, sampleName, reference) {
-    this.snvClassMap = /* @__PURE__ */ new Map();
-    this.svnInnerRadius = svnInnerRadius;
-    this.svnWidth = svnWidth;
-    this.sampleName = sampleName;
-    this.reference = reference;
-    this.bpx = Math.floor(this.reference.totalSize / (this.reference.totalChromosomesAngle * svnInnerRadius));
-    this.onePxArcAngle = 1 / svnInnerRadius;
-  }
-  map(exonicSnvDataMap) {
-    const snvArray = [];
-    for (const angle of exonicSnvDataMap.keys()) {
-      const array = exonicSnvDataMap.get(angle);
-      if (array) {
-        const arraySize = array.length;
-        for (let i = 0; i < array.length; i++) {
-          const data = array[i];
-          const snvLegendElement = this.snvClassMap.get(data.mClass);
-          if (snvLegendElement) {
-            this.snvClassMap.set(data.mClass, this.createSnvLegend(data.mClass, ++snvLegendElement.count));
-          } else {
-            this.snvClassMap.set(data.mClass, this.createSnvLegend(data.mClass, 1));
-          }
-          const startAngle = angle;
-          const endAngle = angle + this.onePxArcAngle;
-          const mLabel = MLabel.getInstance().mlabel ? MLabel.getInstance().mlabel[data.mClass] : void 0;
-          const arc = {
-            startAngle,
-            endAngle,
-            innerRadius: this.svnInnerRadius + i * this.svnWidth / arraySize,
-            outerRadius: this.svnInnerRadius + (i + 1) * this.svnWidth / arraySize,
-            color: mLabel.color,
-            text: data.gene,
-            dataClass: mLabel.label,
-            mname: data.mname,
-            chr: data.chr,
-            pos: data.position,
-            vafs: data.vafs,
-            sampleName: [data.sampleName]
-          };
-          snvArray.push(arc);
-        }
-      }
-    }
-    return snvArray;
-  }
-  createSnvLegend(dataClass, count) {
-    const mClass = MLabel.getInstance().mlabel[dataClass];
-    return new SnvLegendElement(mClass.label, mClass.color, count);
-  }
-};
-
-// plots/disco/cnv/CnvLegend.ts
-var CnvLegend = class {
-  constructor(text, cnvType, color, value) {
-    this.text = text;
-    this.cnvType = cnvType;
-    this.color = color;
-    this.value = value;
-  }
-};
-
-// plots/disco/cnv/CnvColorProvider.ts
-var CnvColorProvider = class {
-  static getColor(value, settings, cnvMaxPercentileAbs = 0) {
-    const cnv = settings.cnv;
-    const gainCapped = settings.Disco.cnvRenderingType == "heatmap" /* heatmap */ ? settings.Disco.cnvCapping : cnvMaxPercentileAbs;
-    const lossCapped = settings.Disco.cnvRenderingType == "heatmap" /* heatmap */ ? -1 * settings.Disco.cnvCapping : -1 * cnvMaxPercentileAbs;
-    if (value < lossCapped) {
-      return cnv.cappedLossColor;
-    } else if (value >= lossCapped && value <= 0) {
-      return cnv.lossColor;
-    } else if (value > 0 && value <= gainCapped) {
-      return cnv.ampColor;
-    } else {
-      return cnv.cappedAmpColor;
-    }
-  }
-};
-
-// plots/disco/cnv/CnvArcsMapper.ts
-var CnvArcsMapper = class {
-  constructor(cnvInnerRadius, cnvWidth, settings, sampleName, reference, cnvMaxValue = 0, cnvMinValue = 0, cnvMaxAbsValue = 0, cnvAbsPercentile = 0, cnvUnit = "", cnvRenderingType) {
-    this.cnvClassMap = /* @__PURE__ */ new Map();
-    this.cnvInnerRadius = cnvInnerRadius;
-    this.cnvWidth = cnvWidth;
-    this.settings = settings;
-    this.sampleName = sampleName;
-    this.reference = reference;
-    this.cnvMaxValue = cnvMaxValue;
-    this.cnvMinValue = cnvMinValue;
-    this.cnvMaxAbsValue = cnvMaxAbsValue;
-    this.cnvAbsPercentile = cnvAbsPercentile;
-    this.cnvUnit = cnvUnit;
-    this.cnvRenderingType = cnvRenderingType;
-    this.gainCapped = Math.min(cnvAbsPercentile, this.settings.Disco.cnvCapping);
-    this.lossCapped = -1 * Math.min(cnvAbsPercentile, this.settings.Disco.cnvCapping);
-    this.lossOnly = cnvMaxValue <= 0;
-    this.gainOnly = cnvMinValue >= 0;
-    this.onePxArcAngle = 1 / this.cnvInnerRadius;
-    const gain = new CnvLegend(
-      "Max",
-      cnvMaxValue > 0 ? 1 /* Gain */ : 0 /* Loss */,
-      this.getColor(cnvMaxValue),
-      cnvMaxValue
-    );
-    const loss = new CnvLegend(
-      "Min",
-      cnvMinValue > 0 ? 1 /* Gain */ : 0 /* Loss */,
-      this.getColor(cnvMinValue),
-      cnvMinValue
-    );
-    const cap = new CnvLegend(
-      "Capping",
-      0 /* Loss */,
-      this.getColor(cnvMinValue > 0 ? cnvMinValue : cnvMaxValue),
-      this.settings.Disco.cnvCapping
-    );
-    this.cnvClassMap.set(1 /* Gain */, gain);
-    this.cnvClassMap.set(0 /* Loss */, loss);
-    this.cnvClassMap.set(2 /* Cap */, cap);
-  }
-  map(arcData) {
-    const arcs = [];
-    let itdCount = 0;
-    arcData.forEach((data) => {
-      let startAngle = this.calculateStartAngle(data);
-      let endAngle = this.calculateEndAngle(data);
-      if (startAngle === null || endAngle === null) return;
-      if (endAngle - startAngle < this.onePxArcAngle) {
-        const restAngle = this.onePxArcAngle - (endAngle - startAngle);
-        startAngle = startAngle - restAngle / 2;
-        endAngle = endAngle + restAngle / 2;
-      }
-      const isItd = data.dt == dtitd;
-      if (isItd) itdCount++;
-      const color = isItd ? mclass[mclassitd].color : this.getColor(data.value);
-      const innerRadius = isItd ? this.cnvInnerRadius : this.calculateInnerRadius(data);
-      const outerRadius = isItd ? this.cnvInnerRadius + this.cnvWidth : this.calculateOuterRadius(data);
-      const arc = {
-        startAngle,
-        endAngle,
-        innerRadius,
-        outerRadius,
-        color,
-        dt: data.dt,
-        dataClass: data.mClass,
-        text: data.gene,
-        chr: data.chr,
-        start: data.start,
-        stop: data.stop,
-        value: data.value,
-        unit: this.cnvUnit,
-        sampleName: [this.sampleName]
-      };
-      arcs.push(arc);
-    });
-    if (itdCount) {
-      this.cnvClassMap.set(4 /* ITD */, new CnvLegend("ITD", 4 /* ITD */, mclass[mclassitd].color, itdCount));
-    }
-    return arcs;
-  }
-  calculateStartAngle(data) {
-    const index = this.reference.chromosomesOrder.indexOf(data.chr);
-    if (index == -1) return null;
-    const chromosome = this.reference.chromosomes[index];
-    return chromosome.startAngle + (chromosome.endAngle - chromosome.startAngle) * (Number(data.start) / chromosome.size);
-  }
-  calculateEndAngle(data) {
-    const index = this.reference.chromosomesOrder.indexOf(data.chr);
-    const chromosome = this.reference.chromosomes[index];
-    return chromosome.startAngle + (chromosome.endAngle - chromosome.startAngle) * (Number(data.stop) / chromosome.size);
-  }
-  getColor(value) {
-    return CnvColorProvider.getColor(value, this.settings, this.cnvAbsPercentile);
-  }
-  calculateInnerRadius(data) {
-    if (this.cnvRenderingType == "heatmap" /* heatmap */) {
-      return this.cnvInnerRadius;
-    }
-    if (this.gainOnly) {
-      return this.cnvInnerRadius;
-    }
-    if (this.lossOnly) {
-      const outerRadius = this.cnvInnerRadius + this.cnvWidth;
-      return outerRadius + DataMapper.capMinValue(
-        this.cnvWidth * DataMapper.capMaxValue(data.value, this.gainCapped, this.lossCapped) / this.cnvAbsPercentile
-      );
-    }
-    const centerRadius = this.cnvInnerRadius + this.cnvWidth / 2;
-    if (Math.sign(data.value) == 1) {
-      return centerRadius;
-    }
-    if (Math.sign(data.value) == -1) {
-      return centerRadius + DataMapper.capMinValue(
-        DataMapper.capMaxValue(data.value, this.gainCapped, this.lossCapped) / this.cnvAbsPercentile * (this.cnvWidth / 2)
-      );
-    }
-    return 1;
-  }
-  calculateOuterRadius(data) {
-    const maxOuterRadius = this.cnvInnerRadius + this.cnvWidth;
-    if (this.cnvRenderingType == "heatmap" /* heatmap */) {
-      return maxOuterRadius;
-    }
-    if (this.gainOnly) {
-      return this.cnvInnerRadius + DataMapper.capMinValue(
-        this.cnvWidth * DataMapper.capMaxValue(data.value, this.gainCapped, this.lossCapped) / this.cnvAbsPercentile
-      );
-    }
-    if (this.lossOnly) {
-      return maxOuterRadius;
-    }
-    const centerRadius = this.cnvInnerRadius + this.cnvWidth / 2;
-    if (Math.sign(data.value) == 1) {
-      return centerRadius + DataMapper.capMinValue(
-        DataMapper.capMaxValue(data.value, this.gainCapped, this.lossCapped) / this.cnvMaxAbsValue * (this.cnvWidth / 2)
-      );
-    }
-    if (Math.sign(data.value) == -1) {
-      return centerRadius;
-    }
-    return 1;
-  }
-};
-
-// plots/disco/label/Line.ts
-var Line = class {
-  constructor(points, color) {
-    this.points = new Array();
-    this.points = points;
-    this.color = color;
-  }
-};
-
-// plots/disco/label/LabelFactory.ts
-var LabelFactory = class {
-  static createLabel(startAngle, endAngle, innerRadius, outerRadius, value, gene, color, dataClass, chr, position, isPrioritized = false, labelsToLinesGap, mutationTooltip, fusionTooltip) {
-    const angle = (startAngle + endAngle) / 2;
-    const ccAngle = angle - Math.PI / 2;
-    const transform = `rotate(${angle * 180 / Math.PI - 90}) translate(${outerRadius})${angle > Math.PI ? "rotate(180)" : ""}`;
-    const textAnchor = angle > Math.PI ? "end" : "";
-    const r0 = innerRadius;
-    const r1 = outerRadius - labelsToLinesGap;
-    const points = [];
-    const point0 = {
-      x: r0 * Math.cos(ccAngle),
-      y: r0 * Math.sin(ccAngle)
-    };
-    const point1 = {
-      x: r1 * Math.cos(ccAngle),
-      y: r1 * Math.sin(ccAngle)
-    };
-    points.push(point0);
-    points.push(point1);
-    const line = new Line(points, color);
-    const label = {
-      startAngle,
-      endAngle,
-      innerRadius,
-      outerRadius,
-      angle,
-      value,
-      text: gene,
-      color,
-      transform,
-      textAnchor,
-      ccAngle,
-      line,
-      isPrioritized,
-      start: position,
-      stop: position,
-      chr,
-      mutationsTooltip: mutationTooltip ? [mutationTooltip] : void 0,
-      fusionTooltip: fusionTooltip ? [fusionTooltip] : void 0
-    };
-    return label;
-  }
-  static createMovedLabel(element, overlap) {
-    const startAngle = element.startAngle + overlap;
-    const endAngle = element.endAngle + overlap;
-    const angle = (startAngle + endAngle) / 2;
-    const ccAngle = angle - Math.PI / 2;
-    const r0 = element.innerRadius;
-    const r1 = element.outerRadius - 2;
-    const dr = (r1 - r0) / 3;
-    const cos0 = Math.cos(element.ccAngle);
-    const sin0 = Math.sin(element.ccAngle);
-    const cos1 = Math.cos(element.ccAngle + overlap);
-    const sin1 = Math.sin(element.ccAngle + overlap);
-    const points = [];
-    const point0 = {
-      x: r0 * cos0,
-      y: r0 * sin0
-    };
-    const point1 = {
-      x: (r0 + dr) * cos0,
-      y: (r0 + dr) * sin0
-    };
-    const point2 = {
-      x: (r0 + 2 * dr) * cos1,
-      y: (r0 + 2 * dr) * sin1
-    };
-    const point3 = {
-      x: (r0 + 3 * dr) * cos1,
-      y: (r0 + 3 * dr) * sin1
-    };
-    points.push(point0);
-    points.push(point1);
-    points.push(point2);
-    points.push(point3);
-    const line = new Line(points, element.color);
-    const transform = "rotate(" + (angle * 180 / Math.PI - 90) + ")translate(" + element.outerRadius + ")" + (angle > Math.PI ? "rotate(180)" : "");
-    const textAnchor = angle > Math.PI ? "end" : "";
-    const color = element.mutationsTooltip ? element.mutationsTooltip[0].color : element.fusionTooltip ? element.fusionTooltip[0].color : void 0;
-    const label = {
-      startAngle,
-      endAngle,
-      innerRadius: element.innerRadius,
-      outerRadius: element.outerRadius,
-      angle,
-      value: element.value,
-      text: element.text,
-      transform,
-      textAnchor,
-      ccAngle,
-      color,
-      line,
-      isPrioritized: element.isPrioritized,
-      start: element.start,
-      stop: element.stop,
-      chr: element.chr,
-      mutationsTooltip: element.mutationsTooltip,
-      fusionTooltip: element.fusionTooltip,
-      cnvTooltip: element.cnvTooltip
-    };
-    return label;
-  }
-};
-
-// plots/disco/label/LabelsMapper.ts
-var LabelsMapper = class {
-  constructor(settings, sampleName, reference, cnvMaxPercentileAbs = 0) {
-    this.labelMap = /* @__PURE__ */ new Map();
-    this.settings = settings;
-    this.sampleName = sampleName;
-    this.reference = reference;
-    this.cnvMaxPercentileAbs = cnvMaxPercentileAbs;
-  }
-  map(data, cnvData = []) {
-    const innerRadius = this.settings.rings.labelLinesInnerRadius;
-    const outerRadius = innerRadius + this.settings.rings.labelsToLinesDistance;
-    data.forEach((data2) => {
-      if (data2.dt == dtsnvindel) {
-        const startAngle = this.calculateStartAngle(data2.chr, data2.position);
-        const endAngle = this.calculateEndAngle(data2.chr, data2.position);
-        if (startAngle === null || endAngle === null) return;
-        const mLabel = MLabel.getInstance().mlabel ? MLabel.getInstance().mlabel[data2.mClass] : void 0;
-        this.addLabelOrMutation(
-          data2,
-          data2.gene,
-          data2.mname,
-          startAngle,
-          endAngle,
-          innerRadius,
-          outerRadius,
-          mLabel.color,
-          mLabel.label
-        );
-      }
-      if (data2.dt == dtfusionrna) {
-        const color = FusionColorProvider.getColor(data2.chrA, data2.chrB);
-        if (data2.geneA) {
-          const startAngleSource = this.calculateStartAngle(data2.chrA, data2.posA);
-          const endAngleSource = this.calculateEndAngle(data2.chrA, data2.posA);
-          if (startAngleSource === null || endAngleSource === null) return;
-          this.addLabelOrFusion(
-            data2,
-            data2.geneA,
-            data2.posA,
-            data2.chrA,
-            startAngleSource,
-            endAngleSource,
-            innerRadius,
-            outerRadius,
-            color
-          );
-        }
-        if (data2.geneB && data2.geneA != data2.geneB) {
-          const startAngleTarget = this.calculateStartAngle(data2.chrB, data2.posB);
-          const endAngleTarget = this.calculateEndAngle(data2.chrB, data2.posB);
-          if (startAngleTarget == null || endAngleTarget == null) return;
-          this.addLabelOrFusion(
-            data2,
-            data2.geneB,
-            data2.posB,
-            data2.chrB,
-            startAngleTarget,
-            endAngleTarget,
-            innerRadius,
-            outerRadius,
-            color
-          );
-        }
-      }
-    });
-    const labelsArray = Array.from(this.labelMap.values());
-    labelsArray.forEach((label) => {
-      cnvData.forEach((cnv) => {
-        if ((cnv.dt == dtcnv || cnv.dt == dtitd) && label.chr == cnv.chr && label.stop >= cnv.start && cnv.stop >= label.start) {
-          const mutation = {
-            dt: cnv.dt,
-            value: cnv.value,
-            color: cnv.dt == dtitd ? mclass[mclassitd].color : CnvColorProvider.getColor(cnv.value, this.settings, this.cnvMaxPercentileAbs),
-            chr: cnv.chr,
-            start: cnv.start,
-            stop: cnv.stop
-          };
-          if (label.cnvTooltip) {
-            label.cnvTooltip.push(mutation);
-          } else {
-            label.cnvTooltip = [];
-            label.cnvTooltip.push(mutation);
-          }
-        }
-      });
-    });
-    return Array.from(this.labelMap.values());
-  }
-  addLabelOrMutation(data, gene, mname, startAngle, endAngle, innerRadius, outerRadius, color, dataClass) {
-    const label = this.labelMap.get(gene);
-    const mutation = {
-      mname,
-      color,
-      dataClass,
-      chr: data.chr,
-      position: data.position,
-      vafs: data.vafs
-    };
-    if (!label) {
-      this.labelMap.set(
-        gene,
-        LabelFactory.createLabel(
-          startAngle,
-          endAngle,
-          innerRadius,
-          outerRadius,
-          data.value,
-          gene,
-          color,
-          dataClass,
-          data.chr,
-          data.position,
-          data.isPrioritized,
-          this.settings.rings.labelsToLinesGap,
-          mutation
-        )
-      );
-    } else {
-      if (label.mutationsTooltip) {
-        label.start = Math.min(label.start, data.position);
-        label.stop = Math.max(label.stop, data.position);
-        label.mutationsTooltip.push(mutation);
-      } else {
-        label.mutationsTooltip = [];
-        label.start = Math.min(label.start, data.position);
-        label.stop = Math.max(label.stop, data.position);
-        label.mutationsTooltip.push(mutation);
-      }
-    }
-  }
-  addLabelOrFusion(data, gene, position, chr, startAngle, endAngle, innerRadius, outerRadius, color) {
-    const label = this.labelMap.get(gene);
-    const fusionTooltip = {
-      color,
-      chrA: data.chrA,
-      chrB: data.chrB,
-      posA: data.posA,
-      posB: data.posB,
-      geneA: data.geneA,
-      geneB: data.geneB,
-      strandA: data.strandA,
-      strandB: data.strandB
-    };
-    if (!label) {
-      this.labelMap.set(
-        gene,
-        LabelFactory.createLabel(
-          startAngle,
-          endAngle,
-          innerRadius,
-          outerRadius,
-          data.value,
-          gene,
-          color,
-          "Fusion transcript",
-          chr,
-          position,
-          data.isPrioritized,
-          this.settings.rings.labelsToLinesGap,
-          void 0,
-          fusionTooltip
-        )
-      );
-    } else {
-      if (label.fusionTooltip) {
-        label.start = Math.min(label.start, position);
-        label.stop = Math.max(label.stop, position);
-        label.fusionTooltip.push(fusionTooltip);
-      } else {
-        label.fusionTooltip = [];
-        label.start = Math.min(label.start, position);
-        label.stop = Math.max(label.stop, position);
-        label.fusionTooltip.push(fusionTooltip);
-      }
-    }
-  }
-  calculateStartAngle(chr, position) {
-    const index = this.reference.chromosomesOrder.findIndex((element) => element == chr);
-    if (index === -1) return null;
-    const chromosome = this.reference.chromosomes[index];
-    return chromosome.startAngle + (chromosome.endAngle - chromosome.startAngle) * (Number(position) / chromosome.size);
-  }
-  calculateEndAngle(chr, position) {
-    const index = this.reference.chromosomesOrder.findIndex((element) => element == chr);
-    if (index === -1) return null;
-    const chromosome = this.reference.chromosomes[index];
-    return chromosome.startAngle + (chromosome.endAngle - chromosome.startAngle) * (Number(position) / chromosome.size);
-  }
-};
-
-// plots/disco/label/Labels.ts
-var Labels = class extends Ring {
-  constructor(settings, elements, hasPrioritizedGenes) {
-    super(
-      settings.rings.labelLinesInnerRadius,
-      settings.rings.labelsToLinesDistance,
-      elements.sort((a, b) => {
-        return a.startAngle < b.startAngle ? -1 : a.startAngle > b.startAngle ? 1 : 0;
-      })
-    );
-    this.elementsToDisplay = [];
-    this.settings = settings;
-    this.hasPrioritizedGenes = hasPrioritizedGenes;
-    const circumference = 2 * Math.PI * (settings.rings.labelLinesInnerRadius + settings.rings.labelsToLinesDistance);
-    this.overlapAngle = this.settings.label.overlapAngleFactor * this.settings.label.fontSize / circumference;
-    this.calculateCollisions();
-  }
-  calculateCollisions() {
-    this.collisions = [];
-    let hasPrioritizedGenesList = [];
-    hasPrioritizedGenesList = this.elements.filter((label) => label.isPrioritized);
-    if (this.settings.label.prioritizeGeneLabelsByGeneSets) {
-      this.elementsToDisplay = this.getLabelsWithPrioritizedGenes(hasPrioritizedGenesList);
-    } else if (this.hasPrioritizedGenes) {
-      const prioritizedGenesList = this.elements.filter((label) => label.isPrioritized);
-      const filteredPrioritizedGenesList = this.getLabelsWithPrioritizedGenes(prioritizedGenesList);
-      const withoutPrioritizedGenesList = this.elements.filter((label) => !label.isPrioritized);
-      const combinedAndSortedList = [...withoutPrioritizedGenesList, ...filteredPrioritizedGenesList].sort(
-        (a, b) => a.startAngle - b.startAngle
-      );
-      this.elementsToDisplay = this.getAllLabels(combinedAndSortedList);
-    } else {
-      this.elementsToDisplay = this.getLabelsWithPrioritizedGenes(this.elements);
-    }
-  }
-  getLabelsWithPrioritizedGenes(elemenets) {
-    const filteredList = [];
-    let prev = { endAngle: 0 };
-    elemenets.forEach((element, index) => {
-      if (index == 0) {
-        filteredList.push(element);
-        prev = element;
-      } else {
-        const overlap = prev.endAngle - element.startAngle + this.overlapAngle;
-        if (overlap > 0 && overlap < this.settings.label.maxDeltaAngle) {
-          const labelCopy = LabelFactory.createMovedLabel(element, overlap);
-          filteredList?.push(labelCopy);
-          prev = labelCopy;
-        }
-        if (overlap <= 0) {
-          filteredList.push(element);
-          prev = element;
-        }
-      }
-    });
-    return filteredList;
-  }
-  getAllLabels(elemenets) {
-    const filteredList = [];
-    let prev = { endAngle: 0 };
-    const elemenetsLength = elemenets.length;
-    let lastCancerGeneLabelIndex = -1;
-    for (let index = 0; index < elemenets.length; index++) {
-      const element = elemenets[index];
-      if (element.isPrioritized) {
-        filteredList.push(element);
-        lastCancerGeneLabelIndex = index;
-        prev = element;
-        continue;
-      }
-      if (index == 0) {
-        if (elemenetsLength > 1) {
-          if (this.isElementOverlappingNextCancerGene(elemenets, lastCancerGeneLabelIndex, element, 0)) {
-            continue;
-          }
-          filteredList.push(element);
-          prev = element;
-        }
-        continue;
-      }
-      const prevOverlap = prev.endAngle - element.startAngle + this.overlapAngle;
-      if (prevOverlap > 0 && prevOverlap < this.settings.label.maxDeltaAngle) {
-        if (index == length - 1) {
-          filteredList.push(element);
-          continue;
-        }
-        if (this.isElementOverlappingNextCancerGene(elemenets, lastCancerGeneLabelIndex, element, prevOverlap)) {
-          continue;
-        }
-        const labelCopy = LabelFactory.createMovedLabel(element, prevOverlap);
-        this.collisions?.push(labelCopy);
-        filteredList.push(element);
-        prev = labelCopy;
-      }
-      if (prevOverlap <= 0) {
-        if (this.isElementOverlappingNextCancerGene(elemenets, lastCancerGeneLabelIndex, element, 0)) {
-          continue;
-        }
-        filteredList.push(element);
-        prev = element;
-      }
-    }
-    return filteredList;
-  }
-  isElementOverlappingNextCancerGene(elemenets, lastCancerGeneLabelIndex, element, prevOverlap) {
-    const nextLabelWithCancerGene = this.getNextLabelWithCancerGene(elemenets, lastCancerGeneLabelIndex);
-    if (nextLabelWithCancerGene) {
-      const nextOverlap = element.endAngle + prevOverlap - nextLabelWithCancerGene.startAngle + this.overlapAngle;
-      if (nextOverlap > 0) {
-        return true;
-      }
-    }
-    return false;
-  }
-  getNextLabelWithCancerGene(elemenets, lastCancerGeneLabelIndex) {
-    return elemenets.find((label, index) => label.isPrioritized && index > lastCancerGeneLabelIndex);
-  }
-};
-
-// plots/disco/snv/NonExonicSnvArcsMapper.ts
-var NonExonicSnvArcsMapper = class {
-  constructor(nonExonicInnerRadius, nonExonicWidht, sampleName, reference) {
-    this.nonExonicInnerRadius = nonExonicInnerRadius;
-    this.nonExonicWidht = nonExonicWidht;
-    this.sampleName = sampleName;
-    this.reference = reference;
-    this.onePxArcAngle = 1 / nonExonicInnerRadius;
-  }
-  map(arcData) {
-    const innerRadius = this.nonExonicInnerRadius;
-    const outerRadius = innerRadius + this.nonExonicWidht;
-    const arcs = [];
-    arcData.forEach((data) => {
-      const mLabel = MLabel.getInstance().mlabel ? MLabel.getInstance().mlabel[data.mClass] : void 0;
-      const startAngle = this.calculateStartAngle(data);
-      const endAngle = this.calculateEndAngle(data);
-      if (startAngle === null || endAngle === null) return;
-      const arc = {
-        startAngle,
-        endAngle,
-        innerRadius,
-        outerRadius,
-        color: mLabel.color,
-        text: data.gene,
-        dataClass: mLabel.label,
-        mname: data.mname,
-        chr: data.chr,
-        pos: data.position,
-        vafs: data.vafs,
-        sampleName: [data.sampleName]
-      };
-      arcs.push(arc);
-    });
-    return arcs;
-  }
-  calculateStartAngle(data) {
-    const index = this.reference.chromosomesOrder.indexOf(data.chr);
-    if (index === -1) return null;
-    const chromosome = this.reference.chromosomes[index];
-    return chromosome.startAngle + (chromosome.endAngle - chromosome.startAngle) * (Number(data.position) / chromosome.size) - this.onePxArcAngle;
-  }
-  calculateEndAngle(data) {
-    const index = this.reference.chromosomesOrder.indexOf(data.chr);
-    const chromosome = this.reference.chromosomes[index];
-    return this.onePxArcAngle + chromosome.startAngle + (chromosome.endAngle - chromosome.startAngle) * (Number(data.position) / chromosome.size);
-  }
-};
-
-// plots/disco/loh/GradientColorProvider.ts
-var GradientColorProvider = class {
-  static provide(value) {
-    const clampedValue = Math.min(Math.max(value, 0), 1);
-    const colorValue = Math.round(clampedValue * 255);
-    return `rgb(${colorValue}, ${colorValue}, ${colorValue})`;
-  }
-};
-
-// plots/disco/loh/LohArcMapper.ts
-var LohArcMapper = class {
-  constructor(lohInnerRadius, lohWidth, sampleName, reference) {
-    this.lohInnerRadius = lohInnerRadius;
-    this.lohWidth = lohWidth;
-    this.sampleName = sampleName;
-    this.reference = reference;
-  }
-  map(arcData) {
-    const arcs = [];
-    arcData.forEach((data) => {
-      const startAngle = this.calculateStartAngle(data);
-      const endAngle = this.calculateEndAngle(data);
-      if (startAngle === null || endAngle === null) return;
-      const innerRadius = this.lohInnerRadius;
-      const outerRadius = innerRadius + this.lohWidth;
-      const color = GradientColorProvider.provide(data.segmean);
-      const arc = {
-        startAngle,
-        endAngle,
-        innerRadius,
-        outerRadius,
-        color,
-        text: data.gene,
-        chr: data.chr,
-        start: data.start,
-        stop: data.stop,
-        value: data.segmean
-      };
-      arcs.push(arc);
-    });
-    return arcs;
-  }
-  calculateStartAngle(data) {
-    const index = this.reference.chromosomesOrder.indexOf(data.chr);
-    if (index === -1) return null;
-    const chromosome = this.reference.chromosomes[index];
-    return chromosome.startAngle + (chromosome.endAngle - chromosome.startAngle) * (Number(data.start) / chromosome.size);
-  }
-  calculateEndAngle(data) {
-    const index = this.reference.chromosomesOrder.indexOf(data.chr);
-    const chromosome = this.reference.chromosomes[index];
-    return chromosome.startAngle + (chromosome.endAngle - chromosome.startAngle) * (Number(data.stop) / chromosome.size);
-  }
-};
-
-// plots/disco/ring/Rings.ts
-var Rings = class {
-  constructor(labelsRing, chromosomesRing, nonExonicArcRing, snvArcRing, cnvArcRing, lohArcRing, mutationWaterfallRing) {
-    this.labelsRing = labelsRing;
-    this.chromosomesRing = chromosomesRing;
-    this.nonExonicArcRing = nonExonicArcRing;
-    this.snvArcRing = snvArcRing;
-    this.cnvArcRing = cnvArcRing;
-    this.lohArcRing = lohArcRing;
-    this.mutationWaterfallRing = mutationWaterfallRing;
-  }
-};
-
-// plots/disco/waterfall/MutationWaterfallMapper.ts
-var MutationWaterfallMapper = class {
-  constructor(innerRadius, ringWidth, reference, logRange, color = "#4d4d4d") {
-    this.innerRadius = innerRadius;
-    this.ringWidth = ringWidth;
-    this.reference = reference;
-    this.logRange = logRange;
-    this.color = color;
-  }
-  map(data = []) {
-    if (!data.length) return [];
-    const min = this.logRange?.min ?? 0;
-    const max = this.logRange?.max ?? min + 1;
-    const span = max - min || 1;
-    const points = [];
-    for (const datum of data) {
-      const chrIndex = this.reference.chromosomesOrder.indexOf(datum.chr);
-      if (chrIndex === -1) continue;
-      const chromosome = this.reference.chromosomes[chrIndex];
-      const chrAngleSpan = chromosome.endAngle - chromosome.startAngle;
-      const relPos = chromosome.size > 0 ? datum.position / chromosome.size : 0;
-      const angle = chromosome.startAngle + chrAngleSpan * relPos;
-      const normalized = Math.max(0, Math.min(1, (datum.logDistance - min) / span));
-      const radius = this.innerRadius + this.ringWidth * normalized;
-      points.push({
-        startAngle: angle,
-        endAngle: angle,
-        innerRadius: radius,
-        outerRadius: radius,
-        text: chromosome.text,
-        color: this.color,
-        chr: datum.chr,
-        position: datum.position,
-        logDistance: datum.logDistance,
-        ringInnerRadius: this.innerRadius,
-        ringWidth: this.ringWidth,
-        rangeMin: min,
-        rangeMax: max
-      });
-    }
-    return points;
-  }
-};
-
-// plots/disco/viewmodel/ViewModelProvider.ts
-var ViewModelProvider = class {
-  constructor(settings, dataMapper, reference, sampleName, genesetName, discoInteractions) {
-    this.nonExonicArcRing = void 0;
-    this.settings = settings;
-    this.dataMapper = dataMapper;
-    this.reference = reference;
-    this.sampleName = sampleName;
-    this.genesetName = genesetName;
-    this.discoInteractions = discoInteractions;
-  }
-  map(data) {
-    const dataHolder = this.dataMapper.map(data);
-    let labelsRing;
-    if (this.settings.Disco.showGeneNames) {
-      const labelsMapper = new LabelsMapper(
-        this.settings,
-        this.sampleName,
-        this.reference,
-        dataHolder.cnvMaxPercentileAbs
-      );
-      const labelsData = labelsMapper.map(dataHolder.labelData, dataHolder.cnvData);
-      labelsRing = new Labels(this.settings, labelsData, dataHolder.hasPrioritizedGenes);
-    } else {
-      labelsRing = new Labels(this.settings, [], false);
-    }
-    const chromosomesRing = new Ring(
-      this.settings.rings.chromosomeInnerRadius,
-      this.settings.rings.chromosomeWidth,
-      this.reference.chromosomes
-    );
-    const nonExonicSnvArcsMapper = new NonExonicSnvArcsMapper(
-      dataHolder.nonExonicInnerRadius,
-      this.settings.rings.nonExonicRingWidth,
-      this.sampleName,
-      this.reference
-    );
-    const nonExonicData = nonExonicSnvArcsMapper.map(dataHolder.nonExonicSnvData);
-    if (nonExonicData.length > 0) {
-      this.nonExonicArcRing = new Ring(
-        dataHolder.nonExonicInnerRadius,
-        this.settings.rings.nonExonicRingWidth,
-        nonExonicData
-      );
-    }
-    this.snvArcsMapper = new SnvArcsMapper(
-      dataHolder.snvInnerRadius,
-      this.settings.rings.snvRingWidth,
-      this.sampleName,
-      this.reference
-    );
-    const snvData = this.snvArcsMapper.map(dataHolder.snvRingDataMap);
-    if (snvData.length > 0) {
-      this.snvArcRing = new Ring(dataHolder.snvInnerRadius, this.settings.rings.snvRingWidth, snvData);
-    }
-    const lohMapper = new LohArcMapper(
-      dataHolder.lohInnerRadius,
-      this.settings.rings.lohRingWidth,
-      this.sampleName,
-      this.reference
-    );
-    const lohData = lohMapper.map(dataHolder.lohData);
-    if (lohData.length > 0) {
-      this.lohArcRing = new Ring(dataHolder.lohInnerRadius, this.settings.rings.lohRingWidth, lohData);
-    }
-    this.cnvArcsMapper = new CnvArcsMapper(
-      dataHolder.cnvInnerRadius,
-      this.settings.rings.cnvRingWidth,
-      this.settings,
-      this.sampleName,
-      this.reference,
-      dataHolder.percentilePositive,
-      dataHolder.percentileNegative,
-      dataHolder.cappedCnvMaxAbsValue,
-      dataHolder.cnvMaxPercentileAbs,
-      this.settings.cnv.unit,
-      this.settings.Disco.cnvRenderingType
-    );
-    const cnvData = this.cnvArcsMapper.map(dataHolder.cnvData);
-    if (cnvData.length > 0) {
-      this.cnvArcRing = new Ring(dataHolder.cnvInnerRadius, this.settings.rings.cnvRingWidth, cnvData);
-    }
-    if (this.settings.Disco.mutationWaterfallPlot && dataHolder.mutationWaterfallData?.length && dataHolder.mutationWaterfallInnerRadius !== void 0 && //Added this check to prevent TypeScript error "mutationWaterfallInnerRadius might be undefined"
-    (dataHolder.mutationWaterfallInnerRadius ?? 0) > 0 && dataHolder.mutationWaterfallLogRange) {
-      const mutationWaterfallMapper = new MutationWaterfallMapper(
-        dataHolder.mutationWaterfallInnerRadius,
-        this.settings.rings.mutationWaterfallRingWidth,
-        this.reference,
-        dataHolder.mutationWaterfallLogRange,
-        this.settings.Disco.mutationWaterfallColor || "#4d4d4d"
-      );
-      const waterfallData = mutationWaterfallMapper.map(dataHolder.mutationWaterfallData);
-      if (waterfallData.length > 0) {
-        this.mutationWaterfallRing = new Ring(
-          dataHolder.mutationWaterfallInnerRadius,
-          this.settings.rings.mutationWaterfallRingWidth,
-          waterfallData
-        );
-      }
-    }
-    const fusionMapper = new FusionMapper(dataHolder.fusionRadius, this.sampleName, this.reference);
-    const fusions = fusionMapper.map(dataHolder.fusionData);
-    let lohLegend;
-    if (this.settings.legend.lohLegendEnabled && dataHolder.lohData.length) {
-      lohLegend = new LohLegend(dataHolder.lohData.length);
-    }
-    const fusionLegendCounts = fusions.reduce(
-      (counts, fusion) => {
-        if (fusion.target && fusion.source.positionInChromosome.chromosome == fusion.target.positionInChromosome.chromosome)
-          counts.intrachromosomal++;
-        else counts.interchromosomal++;
-        return counts;
-      },
-      { interchromosomal: 0, intrachromosomal: 0 }
-    );
-    const legend = new Legend(
-      this.settings.legend.snvTitle,
-      this.settings.legend.cnvTitle,
-      this.settings.legend.lohTitle,
-      this.settings.legend.fusionTitle,
-      this.settings.Disco.cnvPercentile,
-      this.settings.Disco.cnvCutoffMode,
-      this.snvArcsMapper ? this.snvArcsMapper.snvClassMap : /* @__PURE__ */ new Map(),
-      this.cnvArcsMapper ? this.cnvArcsMapper.cnvClassMap : /* @__PURE__ */ new Map(),
-      this.settings.Disco.cnvRenderingType,
-      fusions.length > 0,
-      this.discoInteractions,
-      lohLegend,
-      this.settings.Disco.mutationWaterfallPlot && this.mutationWaterfallRing ? {
-        color: this.settings.Disco.mutationWaterfallColor || "#4d4d4d",
-        onColorChange: this.discoInteractions.onMutationWaterfallColorChange
-      } : void 0,
-      fusionLegendCounts,
-      dataHolder.cnvData.filter((event) => event.dt == dtcnv).length
-    );
-    const rings = new Rings(
-      labelsRing,
-      chromosomesRing,
-      this.nonExonicArcRing,
-      this.snvArcRing,
-      this.cnvArcRing,
-      this.lohArcRing,
-      this.mutationWaterfallRing
-    );
-    return new ViewModel(
-      this.settings,
-      rings,
-      legend,
-      fusions,
-      dataHolder,
-      this.genesetName,
-      data.filter((i) => i.dt == dtsnvindel).length
-    );
-  }
-};
-
-// plots/disco/viewmodel/ViewModelMapper.ts
-var ViewModelMapper = class _ViewModelMapper {
-  static {
-    this.snvClassLayer = {
-      M: "exonic",
-      E: "exonic",
-      F: "exonic",
-      N: "exonic",
-      S: "exonic",
-      D: "exonic",
-      I: "exonic",
-      P: "exonic",
-      L: "exonic",
-      Utr3: "exonic",
-      Utr5: "exonic",
-      ProteinAltering: "exonic",
-      mnv: "non-exonic",
-      ITD: "non-exonic",
-      insertion: "non-exonic",
-      deletion: "non-exonic",
-      Intron: "non-exonic",
-      X: "non-exonic",
-      noncoding: "non-exonic"
-    };
-  }
-  constructor(settings, discoInteractions) {
-    this.settings = JSON.parse(JSON.stringify(settings));
-    this.discoInteractions = discoInteractions;
-  }
-  applyRadius() {
-    const radius = this.settings.Disco.radius;
-    if (!radius) return;
-    const scale = radius / this.settings.rings.labelLinesInnerRadius;
-    this.settings.rings.labelLinesInnerRadius *= scale;
-    this.settings.rings.labelsToLinesDistance *= scale;
-    this.settings.rings.chromosomeInnerRadius *= scale;
-  }
-  static computeDynamicRadius(data) {
-    let ringCount = 0;
-    if (data.some((d) => d.dt == dtsnvindel)) ringCount++;
-    if (data.some((d) => d.dt == dtcnv || d.dt == dtitd)) ringCount++;
-    if (data.some((d) => d.dt == dtloh)) ringCount++;
-    if (ringCount <= 1) return 200;
-    if (ringCount == 2) return 250;
-    return 300;
-  }
-  map(opts) {
-    const chrSizes = opts.args.genome.majorchr;
-    const chromosomesOverride = {};
-    for (const chr of Object.keys(chrSizes)) {
-      if (!this.settings.Disco.hiddenChromosomes.includes(chr)) {
-        chromosomesOverride[chr] = chrSizes[chr];
-      }
-    }
-    const sampleName = opts.args.sampleName;
-    const genome = opts.args.genome;
-    const prioritizedGenes = genome?.geneset?.[0] ? genome.geneset[0].lst : [];
-    const genesetName = genome?.geneset?.[0] ? genome.geneset[0].name : "";
-    const data = opts.args.data;
-    if (this.settings.Disco.autoRadius) {
-      this.settings.Disco.radius = _ViewModelMapper.computeDynamicRadius(data);
-    }
-    this.applyRadius();
-    const reference = new Reference(this.settings, chrSizes, chromosomesOverride);
-    const dataMapper = new DataMapper(this.settings, reference, sampleName, prioritizedGenes);
-    return new ViewModelProvider(
-      this.settings,
-      dataMapper,
-      reference,
-      sampleName,
-      genesetName,
-      this.discoInteractions
-    ).map(data);
-  }
-};
-
-// plots/disco/legend/LegendJSONMapper.ts
-var LegendJSONMapper = class {
-  constructor(cappedCnvMaxAbsValue) {
-    this.cappedCnvMaxAbsValue = cappedCnvMaxAbsValue;
-  }
-  map(legend) {
-    const legendJSON = [];
-    let order = 0;
-    if (legend.snvClassMap) {
-      this.mapSnv(legend, legendJSON, order++);
-    }
-    if (legend.cnvCount > 0 && legend.cnvRenderingType == "heatmap" /* heatmap */) {
-      this.mapCnvHeatmap(legend, legendJSON, order++);
-    } else if (legend.cnvCount > 0 && legend.cnvRenderingType == "bar" /* bar */) {
-      if (legend.cnvClassMap) {
-        this.mapCnvBar(legend, legendJSON, order++);
-      }
-    }
-    if (legend.cnvClassMap.has(4 /* ITD */)) {
-      this.mapItd(legend, legendJSON, order++);
-    }
-    if (legend.lohLegend) {
-      this.mapLoh(legend, legendJSON, order++);
-    }
-    if (legend.fusionLegend) {
-      this.mapFusion(legend, legendJSON, order++);
-    }
-    if (legend.mutationWaterfallLegend) {
-      this.mapMutationWaterfall(legend, legendJSON, order++);
-    }
-    return legendJSON;
-  }
-  mapSnv(legend, legendJSON, order) {
-    const snvItems = [];
-    let snvOrder = 0;
-    for (const [snvKey, snvLegendElement] of legend.snvClassMap) {
-      snvItems.push({
-        termid: legend.snvTitle,
-        key: snvKey,
-        text: `${snvLegendElement.snvType} (${snvLegendElement.count})`,
-        color: snvLegendElement.color,
-        order: snvOrder++
-      });
-    }
-    legendJSON.push({
-      name: legend.snvTitle,
-      order,
-      items: snvItems
-    });
-  }
-  mapCnvBar(legend, legendJSON, order) {
-    if (!legend.cnvClassMap) return;
-    const gain = legend.cnvClassMap.get(1 /* Gain */);
-    const loss = legend.cnvClassMap.get(0 /* Loss */);
-    const cap = legend.cnvClassMap.get(2 /* Cap */);
-    if (gain && loss && cap) {
-      let cnvOrder = 0;
-      const cnvItems = [];
-      if (gain.value > 0) {
-        cnvItems.push({
-          termid: legend.cnvTitle,
-          key: 1 /* Gain */,
-          text: `Max: ${gain.value}`,
-          color: gain.color,
-          order: cnvOrder++
-        });
-      }
-      if (loss.value < 0) {
-        cnvItems.push({
-          termid: legend.cnvTitle,
-          key: 0 /* Loss */,
-          text: `Min: ${loss.value}`,
-          color: loss.color,
-          order: cnvOrder++
-        });
-      }
-      cnvItems.push({
-        termid: legend.cnvTitle,
-        key: 2 /* Cap */,
-        text: `Capping: ${cap.value}`,
-        color: cap.color,
-        order: cnvOrder++
-        // ,
-        // onClickCallback: this.onClickCallback
-      });
-      legendJSON.push({
-        name: legend.cnvTitle,
-        id: "sjpp-disco-cnv-legend",
-        order,
-        items: cnvItems
-      });
-    }
-  }
-  mapCnvHeatmap(legend, legendJSON, order) {
-    if (!legend.cnvClassMap) return;
-    const gain = legend.cnvClassMap.get(1 /* Gain */);
-    const loss = legend.cnvClassMap.get(0 /* Loss */);
-    const cap = legend.cnvClassMap.get(2 /* Cap */);
-    if (gain && loss && cap) {
-      let cnvOrder = 0;
-      const cnvItems = [];
-      const base = {
-        termid: legend.cnvTitle,
-        width: 100,
-        order: cnvOrder++,
-        isLegendItem: true,
-        dt: 4
-      };
-      if (gain.value > 0 && loss.value < 0) {
-        const maxValue = Math.max(Math.abs(loss.value), gain.value);
-        const domain = [-maxValue, 0, maxValue];
-        cnvItems.push(
-          Object.assign(
-            {
-              key: 3 /* LossGain */,
-              domain,
-              scale: linear([-1, 0, 1], [loss.color, "white", gain.color]),
-              labels: { left: "Loss", right: "Gain" },
-              numericInputs: {
-                cutoffMode: legend.cnvCutoffMode,
-                defaultPercentile: legend.cnvPercentile,
-                callback: (obj) => legend.discoInteractions.colorScaleNumericInputsCallback(obj)
-              }
-            },
-            base
-          )
-        );
-      } else {
-        if (gain.value > 0) {
-          cnvItems.push(
-            Object.assign(
-              {
-                key: 1 /* Gain */,
-                text: "Copy number gain",
-                domain: [0, gain.value],
-                scale: linear([0, 1], ["white", gain.color])
-              },
-              base
-            )
-          );
-        }
-        if (loss.value < 0) {
-          cnvItems.push(
-            Object.assign(
-              {
-                key: 0 /* Loss */,
-                text: "Copy number loss",
-                domain: [loss.value, 0],
-                scale: linear([0, 1], [loss.color, "white"])
-              },
-              base
-            )
-          );
-        }
-      }
-      legendJSON.push({
-        name: legend.cnvTitle,
-        order,
-        id: "sjpp-disco-cnv-legend",
-        items: cnvItems
-      });
-    }
-  }
-  mapItd(legend, legendJSON, order) {
-    const itd = legend.cnvClassMap.get(4 /* ITD */);
-    if (!itd) return;
-    legendJSON.push({
-      name: "ITD",
-      order,
-      items: [
-        {
-          termid: "ITD",
-          key: 4 /* ITD */,
-          text: `ITD (${itd.value})`,
-          color: itd.color,
-          order: 0
-        }
-      ]
-    });
-  }
-  mapLoh(legend, legendJSON, order) {
-    if (!legend.lohLegend) return;
-    legendJSON.push({
-      name: legend.lohTitle,
-      order,
-      items: [
-        {
-          termid: legend.lohTitle,
-          key: "count",
-          text: `LOH (${legend.lohLegend.count})`,
-          skipIcon: true,
-          order: 0
-        }
-      ]
-    });
-  }
-  mapFusion(legend, legendJSON, order) {
-    const fusionItems = [];
-    fusionItems.push({
-      termid: legend.fusionTitle,
-      key: "#6A3D9A" /* Interchromosomal */,
-      text: `Interchromosomal (${legend.fusionLegendCounts.interchromosomal})`,
-      color: "#6A3D9A" /* Interchromosomal */.valueOf(),
-      order: 0
-    });
-    fusionItems.push({
-      termid: legend.fusionTitle,
-      key: "#1B9E77" /* Intrachromosomal */,
-      text: `Intrachromosomal (${legend.fusionLegendCounts.intrachromosomal})`,
-      color: "#1B9E77" /* Intrachromosomal */.valueOf(),
-      order: 1
-    });
-    legendJSON.push({
-      name: legend.fusionTitle,
-      order,
-      items: fusionItems
-    });
-  }
-  mapMutationWaterfall(legend, legendJSON, order) {
-    if (!legend.mutationWaterfallLegend) return;
-    const waterfallItems = [];
-    waterfallItems.push({
-      termid: "Mutation Waterfall Plot",
-      key: "mutation-waterfall-color",
-      text: "Dot color",
-      color: legend.mutationWaterfallLegend.color,
-      order: 0,
-      colorPicker: true,
-      inputWidth: 28,
-      width: 0,
-      onColorChange: legend.mutationWaterfallLegend.onColorChange
-    });
-    waterfallItems.push({
-      termid: "Mutation Waterfall Plot",
-      key: "mutation-waterfall-axis",
-      text: "Axis: log10 intermutation distance",
-      order: 1,
-      skipIcon: true,
-      width: 0
-    });
-    legendJSON.push({
-      name: "Mutation Waterfall Plot",
-      order,
-      items: waterfallItems
-    });
-  }
-};
-
-// plots/disco/cnv/renderCnvSourceLegend.ts
-function parseSetLabel(set, index) {
-  let text = set.name || `Set ${index + 1}`;
-  let href;
-  let target = "_blank";
-  if (set.nameHtml) {
-    const parser = new DOMParser();
-    const doc = parser.parseFromString(set.nameHtml, "text/html");
-    const anchor = doc.querySelector("a");
-    if (anchor) {
-      href = anchor.getAttribute("href") || void 0;
-      target = anchor.getAttribute("target") || "_blank";
-      text = anchor.textContent?.trim() || text;
-    } else {
-      text = doc.body.textContent?.trim() || text;
-    }
-  }
-  return { text, href, target };
-}
-function renderCnvSourceLegend(legendG, datasets, fontSize, onChange) {
-  if (!legendG || legendG.empty()) throw new Error("legendG is required");
-  if (!datasets || datasets.length === 0) throw new Error("at least one dataset is required");
-  legendG.select("g.sjpp-cnv-source").remove();
-  const gBBox = legendG.node().getBBox();
-  const cnvSrcWrapper = legendG.append("g").attr("class", "sjpp-cnv-source").attr("transform", `translate(${gBBox.width},${gBBox.y + fontSize})`);
-  const btnPaddingX = Math.round(fontSize * 0.8);
-  const btnHgt = Math.round(fontSize * 1.8);
-  const btnWrapper = cnvSrcWrapper.append("g").attr("transform", `translate(${fontSize},${-btnHgt / 2})`).style("cursor", "pointer").on("click", function(event) {
-    event.stopPropagation();
-    showCnvMenu(this);
-  });
-  const btnText = btnWrapper.append("text").attr("x", 0).attr("y", btnHgt / 2).attr("font-size", fontSize).attr("text-anchor", "start").attr("dominant-baseline", "middle").text("Select source \u25B2".toUpperCase());
-  const textW = btnText.node() ? Math.ceil(btnText.node().getBBox().width) : 0;
-  const btnWdt = textW + btnPaddingX * 2;
-  btnWrapper.insert("rect", ":first-child").attr("width", btnWdt).attr("height", btnHgt).attr("rx", 10).attr("ry", 10).style("fill", "#f2f2f2");
-  btnText.attr("x", btnWdt / 2).attr("text-anchor", "middle");
-  const cnvMenu = new Menu({
-    onHide: () => {
-      btnText.text("Select source \u25B2".toUpperCase());
-    }
-  });
-  function showCnvMenu(dom) {
-    btnText.text("Select source \u25BC".toUpperCase());
-    cnvMenu.clear().showunder(dom);
-    cnvMenu.d.append("div").text("Choose data source for CNV:").style("margin", "5px 5px 0 5px");
-    const tableHolder = cnvMenu.d.append("div").style("padding", "5px");
-    const { columns, rows } = buildTableData(datasets);
-    const [, activeIndex] = getActiveDataset(datasets);
-    renderTable({
-      columns,
-      rows,
-      div: tableHolder,
-      singleMode: true,
-      maxWidth: "70vw",
-      maxHeight: "60vh",
-      selectedRows: [activeIndex],
-      header: { allowSort: false },
-      noButtonCallback: (rowIndex, node) => {
-        const inputIndex = Number(node?.value);
-        const selectedIndex = Number.isNaN(inputIndex) ? rowIndex : inputIndex;
-        if (!Number.isNaN(selectedIndex)) onChange(selectedIndex);
-        cnvMenu.hide();
-      }
-    });
-  }
-}
-function getActiveDataset(datasets) {
-  let currentIndex = datasets.findIndex((d) => d.inuse);
-  if (currentIndex == -1) currentIndex = 0;
-  return [datasets[currentIndex], currentIndex];
-}
-function buildTableData(datasets) {
-  const attrKeys = [];
-  for (const set of datasets) {
-    if (!set.attrs) continue;
-    for (const key of Object.keys(set.attrs)) {
-      if (!attrKeys.includes(key)) attrKeys.push(key);
-    }
-  }
-  const columns = [{ label: "Source" }];
-  for (const key of attrKeys) columns.push({ label: key });
-  const rows = datasets.map((set, index) => {
-    const sourceInfo = parseSetLabel(set, index);
-    const cells = [];
-    if (set.nameHtml) cells.push({ html: set.nameHtml });
-    else if (sourceInfo.href) cells.push({ value: sourceInfo.text, url: sourceInfo.href });
-    else cells.push({ value: sourceInfo.text });
-    for (const key of attrKeys) {
-      const value = set.attrs?.[key];
-      cells.push({ value: value ?? "" });
-    }
-    return cells;
-  });
-  return { columns, rows };
-}
-
-// plots/disco/legend/LegendRenderer.ts
-var LegendRenderer = class {
-  constructor(cappedCnvMaxAbsValue = 0, fontSize) {
-    this.fontSize = fontSize;
-    this.legendJSONMapper = new LegendJSONMapper(cappedCnvMaxAbsValue);
-  }
-  render(holder, legend, xOffset, svgw, svgh, viewModel, onCnvSourceSelect) {
-    const svgLegendRenderer = svgLegend({
-      holder: holder.append("g").attr("data-testid", "sjpp_disco_plot_legend"),
-      rectFillFxn: (d2) => d2.color,
-      iconStroke: "#aaa"
-    });
-    const data = this.legendJSONMapper.map(legend);
-    const legendTitles = data.map((d2) => d2.name.trim());
-    const maxLabelWidth = getMaxLabelWidth(holder, legendTitles);
-    const d = {
-      xOffset: maxLabelWidth + xOffset
-    };
-    svgLegendRenderer(data, {
-      settings: Object.assign(
-        {},
-        {
-          svgw,
-          svgh,
-          dimensions: d,
-          fontsize: this.fontSize
-        }
-      )
-    });
-    const altCnv = viewModel.appState.args.alternativeDataByDt?.[dtcnv];
-    if (altCnv && altCnv.length > 0) {
-      const legendG = holder.select('g[data-testid="sjpp_disco_plot_legend"]');
-      const cnvLegendG = legendG.select("#sjpp-disco-cnv-legend");
-      if (!legendG.empty()) {
-        const add2G = cnvLegendG.empty() ? legendG : cnvLegendG;
-        renderCnvSourceLegend(add2G, altCnv, this.fontSize, onCnvSourceSelect);
-      }
-    }
-  }
-};
-
-// plots/disco/chromosome/ChromosomesRenderer.ts
-var ChromosomesRenderer = class {
-  constructor(padAngle, innerRadius, outerRadius, fontSize) {
-    this.padAngle = padAngle;
-    this.innerRadius = innerRadius;
-    this.outerRadius = outerRadius;
-    this.fontSize = fontSize;
-  }
-  render(holder, elements) {
-    const pie = pie_default().padAngle(this.padAngle).value((d) => d.size).sort(null);
-    const arcData = pie(elements);
-    const arc = arc_default().innerRadius(this.innerRadius).outerRadius(this.outerRadius);
-    const arcs = holder.append("g").attr("data-testid", "sjpp_chromosomes_arc_group");
-    const menu = MenuProvider.create();
-    arcs.selectAll("path").data(arcData).enter().append("path").attr("d", arc).attr("fill", "black").on("mousemove", (event, d) => {
-      const [x, y] = pointer_default(event, arcs.node());
-      let angle = Math.atan2(y, x) + Math.PI / 2;
-      if (angle < 0) angle += 2 * Math.PI;
-      const frac = Math.max(0, Math.min(1, (angle - d.data.startAngle) / (d.data.endAngle - d.data.startAngle)));
-      const pos = Math.round(frac * d.data.size);
-      menu.d.html(`<span style="font-size:.8em">chr${d.data.text}</span> ${bplen(pos)}`).style("padding", "5px");
-      menu.show(event.x, event.y);
-    }).on("mouseenter", (event) => {
-      select_default(event.currentTarget).attr("stroke", "orange").attr("stroke-width", 1);
-    }).on("mouseleave", (event) => {
-      select_default(event.currentTarget).attr("stroke", null).attr("stroke-width", null);
-      menu.hide();
-    });
-    arcs.selectAll("text").data(arcData).enter().append("text").attr("transform", (d) => {
-      return `translate(${arc.centroid(d)}) rotate(${d.data.angle * 180 / Math.PI - 90})${d.data.angle > Math.PI ? "rotate(180)" : ""}`;
-    }).attr("dy", "0.35em").attr("text-anchor", "middle").text((d) => d.data.text).style("fill", "white").style("font-size", `${this.fontSize}px`).style("padding", "500px").style("pointer-events", "none").style("padding", "500px");
-  }
-};
-
-// plots/disco/label/LabelsRenderer.ts
-var LabelsRenderer = class {
-  constructor(animationDuration, fontSize, geneClickListener, genomeName, intervalEvents = [], geneLookup = async (gene, genome) => await dofetch3("genelookup", { body: { deep: 1, input: gene, genome } })) {
-    this.geneCoordinatesCache = /* @__PURE__ */ new Map();
-    this.hoverRequestId = 0;
-    this.animationDuration = animationDuration;
-    this.fontSize = fontSize;
-    this.geneClickListener = geneClickListener;
-    this.genomeName = genomeName;
-    this.intervalEvents = intervalEvents;
-    this.geneLookup = geneLookup;
-  }
-  render(holder, elements, collisions) {
-    const labelsG = holder.append("g");
-    const lineFunction = line_default().x((point) => point.x).y((point) => point.y);
-    const menu = MenuProvider.create();
-    labelsG.selectAll(".group").data(elements).enter().append("g").attr("class", "group").each((label, i, nodes) => {
-      const g = select_default(nodes[i]);
-      g.append("text").attr("class", "chord-text").attr("data-testid", "sjpp-disco-genelabel").attr("dy", ".35em").attr("transform", label.transform).style("text-anchor", label.textAnchor).style("font-size", `${this.fontSize}px`).style("fill", label.color).style("cursor", "pointer").text(label.text).on("click", () => {
-        if (label.mutationsTooltip) {
-          this.geneClickListener(
-            label.text,
-            label.mutationsTooltip.map((value) => value.mname)
-          );
-        }
-      }).on("mouseover", async (mouseEvent) => {
-        const requestId = ++this.hoverRequestId;
-        this.renderTooltip(menu, label);
-        menu.show(mouseEvent.x, mouseEvent.y);
-        const coordinates = await this.getGeneCoordinates(label);
-        if (requestId != this.hoverRequestId || !coordinates) return;
-        const overlappingEvents = this.intervalEvents.filter(
-          (event) => this.sameChromosome(event.chr, coordinates.chr) && coordinates.stop >= event.start && event.stop >= coordinates.start
-        );
-        this.renderTooltip(menu, label, overlappingEvents);
-      }).on("mouseout", () => {
-        this.hoverRequestId++;
-        menu.clear();
-        menu.hide();
-      });
-      g.append("path").attr("class", "chord-tick").datum(label.line.points).style("stroke", label.color).style("fill", "none").attr("d", lineFunction);
-    });
-    labelsG.selectAll(".group").each((label, i, nodes) => {
-      const collision = collisions ? collisions.find((l) => l.text === label.text) : void 0;
-      if (collision) {
-        const g = select_default(nodes[i]);
-        g.selectAll(".chord-text").datum(collision).transition().duration(this.animationDuration).attr("transform", collision.transform).style("text-anchor", collision.textAnchor);
-        g.selectAll(".chord-tick").datum(collision.line.points).transition().duration(this.animationDuration).style("fill", "none").attr("d", lineFunction);
-      }
-    });
-  }
-  renderTooltip(menu, label, intervalEvents = label.cnvTooltip) {
-    menu.clear();
-    const table = table2col({ holder: menu.d });
-    this.createTooltip(table, label, intervalEvents);
-  }
-  async getGeneCoordinates(label) {
-    if (!this.genomeName || !this.intervalEvents.length) return;
-    const cacheKey = `${this.genomeName}:${label.text}:${label.chr}`;
-    let lookup = this.geneCoordinatesCache.get(cacheKey);
-    if (!lookup) {
-      lookup = this.lookupGeneCoordinates(label);
-      this.geneCoordinatesCache.set(cacheKey, lookup);
-    }
-    return await lookup;
-  }
-  async lookupGeneCoordinates(label) {
-    try {
-      const response = await this.geneLookup(label.text, this.genomeName);
-      if (response?.error || !Array.isArray(response?.gmlst)) return;
-      const models = response.gmlst.filter(
-        (model) => this.sameChromosome(model.chr, label.chr) && Number.isFinite(model.start) && Number.isFinite(model.stop)
-      );
-      if (!models.length) return;
-      return {
-        chr: models[0].chr,
-        start: Math.min(...models.map((model) => model.start)),
-        stop: Math.max(...models.map((model) => model.stop))
-      };
-    } catch {
-      return;
-    }
-  }
-  sameChromosome(a, b) {
-    return a?.replace(/^chr/i, "").toLowerCase() == b?.replace(/^chr/i, "").toLowerCase();
-  }
-  createTooltip(table, label, intervalEvents = label.cnvTooltip) {
-    if (label.mutationsTooltip) {
-      const [td1, td2] = table.addRow();
-      td1.text("Gene");
-      td2.append("span").style("margin-left", "5px").text(label.text);
-      label.mutationsTooltip.forEach((mutation) => {
-        {
-          const [td12, td22] = table.addRow();
-          td12.text("Mutation");
-          td22.append("span").style("margin-left", "5px").text(mutation.mname).append("span").style("margin-left", "5px").style("color", mutation.color).text(`${mutation.dataClass}`).append("span").style("margin-left", "5px").style("color", "black").style("font-size", "0.8em").text(` ${mutation.chr}:${mutation.position}`);
-          if (hasAnyValidVafEntry(mutation.vafs)) {
-            appendVafBars(td22, mutation.vafs);
-          }
-        }
-      });
-    }
-    if (label.fusionTooltip) {
-      const [td1, td2] = table.addRow();
-      td1.text("Data type");
-      td2.append("span").text("Fusion transcript");
-      label.fusionTooltip.forEach((fusionTooltip) => {
-        const [td12, td22] = table.addRow();
-        td12.text("Position");
-        td22.append("span").text(
-          ` ${fusionTooltip.geneA ? fusionTooltip.geneA : "?"} ${fusionTooltip.chrA}:${fusionTooltip.posA}
-						${fusionTooltip.strandA == "+" ? "forward" : "reverse"} > ${fusionTooltip.geneB ? fusionTooltip.geneB : "?"} ${fusionTooltip.chrB}:${fusionTooltip.posB} ${fusionTooltip.strandB == "+" ? "forward" : "reverse"} `
-        );
-      });
-    }
-    if (intervalEvents) {
-      intervalEvents.forEach((cnv) => {
-        const [td1, td2] = table.addRow();
-        td1.text(cnv.dt == dtitd ? "ITD" : cnv.dt == dtloh ? "LOH" : "CNV");
-        td2.append("span").style("margin-left", "5px").style("background-color", cnv.color).html("&nbsp;&nbsp;");
-        if (cnv.dt != dtitd && cnv.dt != dtloh) td2.append("span").style("margin-left", "7.5px").text(cnv.value);
-        td2.append("span").style("margin-left", "7.5px").style("font-size", "0.8em").text(`${cnv.chr}:${cnv.start}-${cnv.stop}`);
-      });
-    }
-  }
-};
-
-// plots/disco/defaults.ts
-function discoDefaults(overrides = {}, app) {
-  const hiddenChromosomes = [];
-  if (app?.vocabApi?.termdbConfig?.queries?.singleSampleMutation?.discoPlot?.skipChrM) {
-    hiddenChromosomes.push("chrM");
-  }
-  const defaults = {
-    downloadImgName: "disco.plot",
-    Disco: {
-      centerText: null,
-      cnvCapping: 5,
-      isOpen: false,
-      prioritizeGeneLabelsByGeneSets: false,
-      showPrioritizeGeneLabelsByGeneSets: false,
-      showGeneNames: true,
-      mutationWaterfallPlot: false,
-      mutationWaterfallColor: "#4d4d4d",
-      minMutationFraction: 0,
-      cnvRenderingType: "heatmap" /* heatmap */,
-      cnvPercentile: 90,
-      // 90th percentile for removing outliers
-      cnvCutoffMode: "percentile",
-      autoRadius: true,
-      radius: 300,
-      fusionOpacity: 1,
-      hiddenChromosomes
-    },
-    rings: {
-      nonExonicRingWidth: 20,
-      snvRingWidth: 20,
-      lohRingWidth: 20,
-      cnvRingWidth: 30,
-      mutationWaterfallRingWidth: 35,
-      snvRingFilters: ["exonic"],
-      chromosomeInnerRadius: 190,
-      chromosomeWidth: 20,
-      labelLinesInnerRadius: 210,
-      labelsToLinesDistance: 30,
-      labelsToLinesGap: 2,
-      nonExonicRingEnabled: true,
-      nonExonicFilterValues: ["non-exonic"]
-    },
-    verticalPadding: 0,
-    horizontalPadding: 50,
-    layerScaler: 1,
-    padAngle: 2e-3,
-    //0.01, //0.04,
-    label: {
-      fontSize: 12,
-      maxDeltaAngle: 0.05,
-      animationDuration: 1e3,
-      overlapAngleFactor: 5
-      // 5 is set by testing, because label height is not known before rendering
-    },
-    cnv: {
-      capping: 5,
-      percentile: 80,
-      ampColor: "#D6683C",
-      lossColor: "#67a9cf",
-      cappedAmpColor: "#8B0000",
-      cappedLossColor: "#00008B",
-      unit: "Unit"
-    },
-    snv: {
-      maxMutationCount: 1e4
-    },
-    legend: {
-      snvTitle: "Mutations",
-      cnvTitle: "CNV",
-      lohTitle: "LOH",
-      fusionTitle: "SV",
-      // Structural Variants (color by co-location)
-      lohLegendEnabled: true,
-      fontSize: 12,
-      rowHeight: 48
-    },
-    menu: {
-      padding: 5
-    }
-  };
-  if (overrides?.Disco?.radius != null && (overrides.Disco.radius > 1e3 || overrides.Disco.radius < 200)) {
-    console.log(`${overrides?.Disco?.radius} is greater or lower than the min and max for the radius`);
-  }
-  return copyMerge(defaults, overrides);
-}
-
-// plots/disco/snv/NonExonicSnvRenderer.ts
-var NonExonicSnvRenderer = class {
-  constructor(geneClickListener) {
-    this.geneClickListener = geneClickListener;
-  }
-  render(holder, elements) {
-    const arcGenerator = arc_default();
-    const arcs = holder.append("g");
-    const menu = MenuProvider.create();
-    arcs.selectAll("path").data(elements).enter().append("path").attr("d", (d) => arcGenerator(d)).attr("fill", (d) => d.color).on("mouseover", (mouseEvent, arc) => {
-      const table = table2col({ holder: menu.d });
-      const snv = structuredClone(arc);
-      snv.dt = dtsnvindel;
-      snv.class = arc.dataClass;
-      snv.gene = snv.text;
-      {
-        const [td1, td2] = table.addRow();
-        td1.text("Consequence");
-        td2.append("span").text(snv.mname);
-        td2.append("span").style("margin-left", "5px").style("color", snv.color).style("font-size", ".8em").text(snv.dataClass);
-      }
-      {
-        const [td1, td2] = table.addRow();
-        td1.text(snv.ref && snv.alt ? "Mutation" : "Position");
-        td2.append("span").text(`${snv.chr}:${snv.pos + 1} ${snv.ref && snv.alt ? snv.ref + ">" + snv.alt : ""}`);
-      }
-      if (snv.gene) {
-        const [td1, td2] = table.addRow();
-        td1.text("Gene");
-        td2.text(snv.gene);
-      }
-      if (snv.occurrence > 1) {
-        const [td1, td2] = table.addRow();
-        td1.text("Occurrence");
-        td2.text(snv.occurrence);
-      }
-      if (hasAnyValidVafEntry(arc.vafs)) {
-        const [td1, td2] = table.addRow();
-        td1.text("Read count");
-        appendVafBars(td2, arc.vafs);
-      }
-      menu.show(mouseEvent.x, mouseEvent.y);
-    }).on("mouseout", () => {
-      menu.clear();
-      menu.hide();
-    }).on("click", (mouseEvent, arc) => {
-      this.geneClickListener(arc.text, [arc.mname]);
-    });
-  }
-};
-
-// plots/disco/snv/SnvRenderer.ts
-var SnvRenderer = class {
-  constructor(svnWidth, geneClickListener) {
-    this.svnWidth = svnWidth;
-    this.geneClickListener = geneClickListener;
-  }
-  render(holder, elements) {
-    if (elements.length > 0) {
-      const svnInnerRadius = elements[0].innerRadius;
-      const fullArcRenderer = new FullArcRenderer(svnInnerRadius, this.svnWidth, "#6464641A");
-      fullArcRenderer.render(holder);
-    }
-    const arcGenerator = arc_default();
-    const arcs = holder.append("g");
-    const menu = MenuProvider.create();
-    arcs.selectAll("path").data(elements).enter().append("path").attr("d", (d) => arcGenerator(d)).attr("fill", (d) => d.color).on("mouseover", (mouseEvent, arc) => {
-      const table = table2col({ holder: menu.d });
-      const snv = structuredClone(arc);
-      snv.dt = dtsnvindel;
-      snv.class = arc.dataClass;
-      snv.gene = snv.text;
-      {
-        const [td1, td2] = table.addRow();
-        td1.text("Consequence");
-        td2.append("span").text(snv.mname);
-        td2.append("span").style("margin-left", "5px").style("color", snv.color).style("font-size", ".8em").text(snv.dataClass);
-      }
-      {
-        const [td1, td2] = table.addRow();
-        td1.text(snv.ref && snv.alt ? "Mutation" : "Position");
-        td2.append("span").text(`${snv.chr}:${snv.pos + 1} ${snv.ref && snv.alt ? snv.ref + ">" + snv.alt : ""}`);
-      }
-      if (snv.gene) {
-        const [td1, td2] = table.addRow();
-        td1.text("Gene");
-        td2.text(snv.gene);
-      }
-      if (snv.occurrence > 1) {
-        const [td1, td2] = table.addRow();
-        td1.text("Occurrence");
-        td2.text(snv.occurrence);
-      }
-      if (hasAnyValidVafEntry(arc.vafs)) {
-        const [td1, td2] = table.addRow();
-        td1.text("Read count");
-        appendVafBars(td2, arc.vafs);
-      }
-      menu.show(mouseEvent.x, mouseEvent.y);
-    }).on("mouseout", () => {
-      menu.clear();
-      menu.hide();
-    }).on("click", (mouseEvent, arc) => {
-      this.geneClickListener(arc.text, [arc.mname]);
-    });
-  }
-};
-
-// plots/disco/loh/LohRenderer.ts
-var LohRenderer = class {
-  render(holder, elements) {
-    const arcGenerator = arc_default();
-    const arcs = holder.append("g");
-    const menu = MenuProvider.create();
-    arcs.selectAll("path").data(elements).enter().append("path").attr("d", (d) => arcGenerator(d)).attr("fill", (d) => d.color).on("mouseover", (mouseEvent, arc) => {
-      const table = table2col({ holder: menu.d });
-      const loh = structuredClone(arc);
-      loh.dt = dtloh;
-      loh.gene = loh.text;
-      {
-        const [td12, td22] = table.addRow();
-        td12.text("Data type");
-        td22.append("span").style("margin-left", "5px").text("Loss of Heterozygosity");
-      }
-      const [td1, td2] = table.addRow();
-      td1.text("Position");
-      td2.append("span").text(`${arc.chr}:${arc.start}-${arc.stop}`);
-      menu.show(mouseEvent.x, mouseEvent.y);
-    }).on("mouseout", () => {
-      menu.clear();
-      menu.hide();
-    });
-  }
-};
-
-// plots/disco/cnv/CnvBarRenderer.ts
-var CnvBarRenderer = class {
-  render(holder, elements) {
-    const arcGenerator = arc_default();
-    const arcs = holder.append("g");
-    const hoverOverlay = holder.append("g").attr("class", "hover-overlay").style("pointer-events", "none");
-    const menu = MenuProvider.create();
-    arcs.selectAll("path").data(elements).enter().append("path").attr("d", (d) => arcGenerator(d)).attr("fill", (d) => d.color).on("mouseover", (mouseEvent, arc) => {
-      hoverOverlay.selectAll("*").remove();
-      hoverOverlay.append("path").datum(arc).attr("d", arcGenerator(arc)).attr("fill", "none").attr("stroke", "black").attr("stroke-width", 1);
-      const cnv = structuredClone(arc);
-      cnv.dt = arc.dt;
-      cnv.samples = [{ sample_id: arc.sampleName }];
-      cnv.gene = cnv.text;
-      const table = table2col({ holder: menu.d });
-      if (arc.dt == dtcnv) {
-        const [c1, c2] = table.addRow();
-        c1.text("CNV");
-        c2.html(`<span style="background:${cnv.color}">&nbsp;&nbsp;</span> ${cnv.value}`);
-      }
-      if (arc.dt == dtitd) {
-        const [c1, c2] = table.addRow();
-        c1.text("ITD");
-        c2.html(`<span style="background:${cnv.color}">&nbsp;&nbsp;</span>`);
-      }
-      {
-        const [c1, c2] = table.addRow();
-        c1.text("Position");
-        c2.text(cnv.chr + ":" + cnv.start + "-" + cnv.stop);
-      }
-      if (arc.dt == dtcnv) {
-        const [c1, c2] = table.addRow();
-        c1.text("Unit");
-        c2.text(cnv.value);
-      }
-      menu.show(mouseEvent.x, mouseEvent.y);
-    }).on("mouseout", () => {
-      hoverOverlay.selectAll("*").remove();
-      menu.clear();
-      menu.hide();
-    });
-  }
-};
-
-// plots/disco/cnv/CnvHeatmapRenderer.ts
-var CnvHeatmapRenderer = class {
-  constructor(positivePercentile = 0, negativePercentile = 0) {
-    this.positivePercentile = positivePercentile;
-    this.negativePercentile = negativePercentile;
-  }
-  render(holder, elements) {
-    const arcGenerator = arc_default();
-    const arcs = holder.append("g");
-    const hoverOverlay = holder.append("g").attr("class", "hover-overlay").style("pointer-events", "none");
-    const menu = MenuProvider.create();
-    arcs.selectAll("path").data(elements).enter().append("path").attr("d", (d) => arcGenerator(d)).attr("fill", (d) => this.getColor(d.color, d.value, d.dt)).on("mouseenter", (mouseEvent, arc) => {
-      hoverOverlay.append("path").datum(arc).attr("d", arcGenerator(arc)).attr("fill", "none").attr("stroke", "black").attr("stroke-width", 1);
-      const table = table2col({ holder: menu.d });
-      const cnv = structuredClone(arc);
-      cnv.dt = arc.dt;
-      cnv.samples = [{ sample_id: arc.sampleName }];
-      cnv.gene = cnv.text;
-      if (arc.dt == dtcnv) {
-        const [c1, c2] = table.addRow();
-        c1.text("CNV");
-        c2.html(
-          `<span style="background:${this.getColor(
-            cnv.color,
-            cnv.value,
-            cnv.dt
-          )}; border:solid lightgrey 0.1px;">&nbsp;&nbsp;</span> ${cnv.value}`
-        );
-      }
-      if (arc.dt == dtitd) {
-        const [c1, c2] = table.addRow();
-        c1.text("ITD");
-        c2.html(`<span style="background:${cnv.color}; border:solid lightgrey 0.1px;">&nbsp;&nbsp;</span>`);
-      }
-      {
-        const [c1, c2] = table.addRow();
-        c1.text("Position");
-        c2.text(cnv.chr + ":" + cnv.start + "-" + cnv.stop);
-      }
-      menu.show(mouseEvent.x, mouseEvent.y);
-    }).on("mouseleave", () => {
-      hoverOverlay.selectAll("*").remove();
-      menu.clear();
-      menu.hide();
-    });
-  }
-  // Computes fill color using linear scale between -P80, 0, and +P80
-  getColor(color, value, dt = dtcnv) {
-    if (dt == dtitd) return color;
-    const maxValue = Math.max(this.positivePercentile, Math.abs(this.negativePercentile));
-    return linear(
-      [-maxValue, 0, maxValue],
-      [color, "white", color]
-      // transitions to white in the middle
-    ).clamp(true)(value);
-  }
-};
-
-// plots/disco/waterfall/MutationWaterfallRenderer.ts
-var MutationWaterfallRenderer = class {
-  constructor(dotRadius = 1.5) {
-    this.dotRadius = dotRadius;
-  }
-  render(holder, elements) {
-    if (!elements.length) return;
-    const ringGroup = holder.append("g").attr("data-testid", "sjpp_mutation_waterfall_ring");
-    const menu = MenuProvider.create();
-    ringGroup.append("g").selectAll("circle").data(elements).enter().append("circle").attr("cx", (d) => Math.cos(d.startAngle - Math.PI / 2) * d.innerRadius).attr("cy", (d) => Math.sin(d.startAngle - Math.PI / 2) * d.innerRadius).attr("r", this.dotRadius).attr("fill", (d) => d.color).attr("opacity", 0.9).on("mouseover", (event, d) => {
-      const distance = Math.round(Math.pow(10, d.logDistance));
-      menu.clear();
-      const table = table2col({ holder: menu.d });
-      {
-        const [td1, td2] = table.addRow();
-        td1.text("Intermutation distance");
-        td2.text(`${bplen(distance)}`);
-      }
-      menu.show(event.x, event.y);
-    }).on("mouseout", () => {
-      menu.clear();
-      menu.hide();
-    });
-    this.renderAxis(ringGroup, elements[0]);
-  }
-  renderAxis(holder, referencePoint) {
-    const { ringInnerRadius, ringWidth, rangeMin, rangeMax } = referencePoint;
-    const axisGroup = holder.append("g").attr("class", "sjpp-waterfall-axis");
-    const topRadius = ringInnerRadius + ringWidth;
-    axisGroup.append("line").attr("x1", 0).attr("y1", -topRadius).attr("x2", 0).attr("y2", -ringInnerRadius).attr("stroke", "#6e6e6e").attr("stroke-width", 1);
-    const span = rangeMax - rangeMin || 1;
-    const tickValues = rangeMax === rangeMin ? [rangeMin] : ticks(rangeMin, rangeMax, 4);
-    tickValues.forEach((value) => {
-      const ratio = (value - rangeMin) / span;
-      const radius = ringInnerRadius + ringWidth * ratio;
-      const y = -radius;
-      axisGroup.append("line").attr("x1", -4).attr("x2", 4).attr("y1", y).attr("y2", y).attr("stroke", "#6e6e6e");
-      const exponent = Math.round(value * 10) / 10;
-      const formatted = Number.isInteger(exponent) ? `${exponent}` : exponent.toFixed(1);
-      axisGroup.append("text").attr("x", 6).attr("y", y + 3).style("font-size", "10px").style("fill", "#4d4d4d").text(`10^${formatted} bp`);
-    });
-  }
-};
-
-// plots/disco/Disco.ts
-var Disco = class _Disco extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.recreateViewModel = false;
-    this.onCnvSourceSelect = (index) => {
-      const state = this.app.getState();
-      const args = state.args;
-      const alt = args.alternativeDataByDt?.[dtcnv];
-      if (!alt) return;
-      const altClone = structuredClone(args.alternativeDataByDt);
-      altClone[dtcnv].forEach((d, i) => d.inuse = i === index);
-      const selected = altClone[dtcnv][index];
-      selected.mlst.forEach((d) => d.position = d.pos);
-      const baseData = args.data.filter((d) => d.dt != dtcnv && d.dt != dtloh);
-      const newData = baseData.concat(selected.mlst);
-      this.app.dispatch({
-        type: "app_refresh",
-        state: { args: { ...args, data: newData, alternativeDataByDt: altClone } }
-      });
-    };
-    this.type = _Disco.type;
-    this.dom.errdiv = opts.holder.append("div").attr("class", "sja_errorbar").style("display", "none");
-    this.isOpen = false;
-    this.discoInteractions = new DiscoInteractions(this);
-  }
-  static {
-    this.type = "Disco";
-  }
-  async init() {
-    const state = this.app.getState();
-    const settings = state.plots.find((p) => p.id === this.id).settings;
-    this.stateViewModelMapper = new ViewModelMapper(settings, this.discoInteractions);
-    this.viewModel = this.stateViewModelMapper.map(state);
-    const holder = this.opts.holder;
-    const controlsHolder = holder.append("div").style("display", "inline-block").style("vertical-align", "top");
-    const mainDiv = holder.append("div").style("display", "inline-block");
-    const topbar = controlsHolder.append("div");
-    const config_div = controlsHolder.append("div");
-    const configInputsOptions = this.getConfigInputsOptions(this.viewModel);
-    this.features = await multiInit({
-      topbar: topBarInit({
-        app: this.app,
-        id: this.id,
-        // TODO change the way svg is selected
-        downloadHandler: () => this.discoInteractions.downloadClickListener(holder.select('svg[id="sjpp_disco_plot"]').node()),
-        callback: () => this.toggleVisibility(this.isOpen),
-        isOpen: () => this.isOpen,
-        holder: topbar
-      }),
-      config: configUiInit({
-        app: this.app,
-        id: this.id,
-        holder: config_div,
-        isOpen: () => this.isOpen,
-        inputs: configInputsOptions
-      })
-    });
-    this.errorDiv = mainDiv.append("div").attr("data-testid", "sjpp-disco-errorDiv");
-    this.svgDiv = mainDiv.append("div").attr("data-testid", "sjpp-disco-svgDiv");
-  }
-  getConfigInputsOptions(viewModel) {
-    const configInputsOptions = [];
-    if (viewModel.settings.Disco.showPrioritizeGeneLabelsByGeneSets) {
-      const filterMutationsGenesCheckbox = [
-        {
-          boxLabel: viewModel.genesetName,
-          label: `Filter mutations`,
-          type: "checkbox",
-          chartType: "Disco",
-          settingsKey: "prioritizeGeneLabelsByGeneSets",
-          title: `Only show mutations for ${viewModel.genesetName} genes`
-        }
-      ];
-      configInputsOptions.push(...filterMutationsGenesCheckbox);
-    }
-    if (viewModel.cnvMaxValue !== 0 || viewModel.cnvMinValue !== 0) {
-      const cnvConfigInputOptions = [
-        {
-          boxLabel: "",
-          label: "CNV rendering type",
-          type: "radio",
-          chartType: "Disco",
-          settingsKey: "cnvRenderingType",
-          title: "CNV rendering type",
-          options: [
-            { label: "Heatmap", value: "heatmap" /* heatmap */ },
-            { label: "Bar", value: "bar" /* bar */ }
-          ]
-        }
-      ];
-      configInputsOptions.push(...cnvConfigInputOptions);
-    }
-    if (viewModel.hasMutationFractionData) {
-      configInputsOptions.push({
-        boxLabel: "",
-        label: "Minimum mutation fraction",
-        type: "number",
-        chartType: "Disco",
-        settingsKey: "minMutationFraction",
-        title: "Only show SNV/indel mutations with at least one DNA/RNA mutation fraction at or above this value.",
-        step: 0.01,
-        min: 0,
-        max: 1,
-        debounceInterval: 500
-      });
-    }
-    configInputsOptions.push({
-      boxLabel: "",
-      label: "Show gene names",
-      type: "checkbox",
-      chartType: "Disco",
-      settingsKey: "showGeneNames",
-      title: "Show gene name labels on the outside of the plot"
-    });
-    const genomeChr = this.app.opts.state.args.genome.majorchr;
-    const chromosomeConfigOption = {
-      label: "Chromosomes",
-      title: "Chromosomes shown in the plot",
-      type: "multiCheckbox",
-      chartType: "Disco",
-      settingsKey: "hiddenChromosomes",
-      style: {
-        colNum: 4
-      },
-      options: Object.keys(genomeChr).map((c) => ({ label: c, value: c })),
-      processInput: (values = []) => {
-        const reverse = Object.keys(genomeChr).filter((c) => !values.includes(c));
-        return reverse;
-      }
-    };
-    configInputsOptions.push(chromosomeConfigOption);
-    configInputsOptions.push({
-      boxLabel: "",
-      label: "Auto radius",
-      type: "checkbox",
-      chartType: "Disco",
-      settingsKey: "autoRadius",
-      title: "Automatically set the radius based on the number of data rings"
-    });
-    const dimensionOptions = [
-      {
-        label: "Radius",
-        title: "Set the radius of the entire plot, between 200 and 1000 pixels.",
-        type: "number",
-        chartType: "Disco",
-        settingsKey: "radius",
-        debounceInterval: 500,
-        step: 25,
-        min: 200,
-        max: 1e3,
-        getDisplayStyle: (plot) => plot.settings.Disco.autoRadius ? "none" : "table-row"
-      },
-      {
-        label: "Fusion opacity",
-        title: "Adjust opacity of fusion arcs, between 0 and 1",
-        type: "number",
-        chartType: "Disco",
-        settingsKey: "fusionOpacity",
-        step: 0.01,
-        min: 0,
-        max: 1,
-        debounceInterval: 500
-      }
-    ];
-    configInputsOptions.push(...dimensionOptions);
-    if (viewModel.canShowMutationWaterfallPlot && viewModel.snvDataLength > 0) {
-      configInputsOptions.push({
-        boxLabel: "",
-        label: "Mutation Waterfall Plot",
-        type: "checkbox",
-        chartType: "Disco",
-        settingsKey: "mutationWaterfallPlot",
-        title: "Render log10 intermutation distance ring for SNV/indel data"
-      });
-    }
-    return configInputsOptions;
-  }
-  async main() {
-    const settings = this.state.settings;
-    this.isOpen = settings.Disco.isOpen;
-    if (this.recreateViewModel) {
-      this.stateViewModelMapper = new ViewModelMapper(settings, this.discoInteractions);
-      this.viewModel = this.stateViewModelMapper.map(this.app.getState());
-    }
-    this.recreateViewModel = true;
-    if (this.viewModel) {
-      this.svgDiv.selectAll("*").remove();
-      const appState = this.app.getState();
-      this.viewModel.svgDiv = this.svgDiv;
-      this.viewModel.appState = appState;
-      for (const name in this.features) {
-        this.features[name].update({ state: this.state, appState });
-      }
-      const legendRenderer = new LegendRenderer(this.viewModel.cappedCnvMaxAbsValue, settings.label.fontSize);
-      const discoRenderer = new DiscoRenderer(
-        this.getRingRenderers(this.viewModel.settings, this.viewModel, this.discoInteractions.geneClickListener),
-        legendRenderer,
-        this.app.opts.state.args.genome
-      );
-      discoRenderer.render(this.svgDiv, this.viewModel, this.onCnvSourceSelect);
-      if (this.viewModel.invalidDataInfo?.entries?.length) {
-        InvalidDataUI.render(this.errorDiv, this.viewModel.invalidDataInfo);
-      }
-    }
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) return config;
-    return { ...config, mlst: appState.args.data };
-  }
-  getRingRenderers(settings, viewModel, geneClickListener) {
-    const chromosomesRenderer = new ChromosomesRenderer(
-      settings.padAngle,
-      settings.rings.chromosomeInnerRadius,
-      settings.rings.chromosomeInnerRadius + settings.rings.chromosomeWidth,
-      settings.label.fontSize
-    );
-    const labelsRenderer = new LabelsRenderer(
-      settings.label.animationDuration,
-      settings.label.fontSize,
-      geneClickListener,
-      this.app.opts.state.args.genome.name,
-      [
-        ...viewModel.rings.cnvArcRing?.elements || [],
-        ...(viewModel.rings.lohArcRing?.elements || []).map((event) => ({ ...event, dt: dtloh }))
-      ]
-    );
-    const nonExonicSnvRenderer = new NonExonicSnvRenderer(geneClickListener);
-    const snvRenderer = new SnvRenderer(settings.rings.snvRingWidth, geneClickListener);
-    const cnvRenderer = settings.Disco.cnvRenderingType === "heatmap" /* heatmap */ ? new CnvHeatmapRenderer(viewModel.positivePercentile, viewModel.negativePercentile) : new CnvBarRenderer();
-    const lohRenderer = new LohRenderer();
-    const mutationWaterfallRenderer = new MutationWaterfallRenderer();
-    const renderersMap = /* @__PURE__ */ new Map();
-    renderersMap.set(0 /* CHROMOSOME */, chromosomesRenderer);
-    renderersMap.set(1 /* LABEL */, labelsRenderer);
-    renderersMap.set(2 /* NONEXONICSNV */, nonExonicSnvRenderer);
-    renderersMap.set(3 /* SNV */, snvRenderer);
-    renderersMap.set(4 /* MUTATION_WATERFALL */, mutationWaterfallRenderer);
-    renderersMap.set(5 /* CNV */, cnvRenderer);
-    renderersMap.set(6 /* LOH */, lohRenderer);
-    return renderersMap;
-  }
-  toggleVisibility(isOpen) {
-    this.app.dispatch({
-      type: "plot_edit",
-      id: this.opts.id,
-      config: {
-        settings: {
-          Disco: { isOpen: !isOpen }
-        }
-      }
-    });
-  }
-};
-var discoInit = getCompInit(Disco);
-var componentInit = discoInit;
-async function getPlotConfig(opts, app) {
-  return {
-    chartType: "Disco",
-    subfolder: "disco",
-    extension: "ts",
-    settings: discoDefaults(opts.overrides, app)
-  };
-}
-export {
-  componentInit,
-  Disco as default,
-  discoInit,
-  getPlotConfig
-};
-//# sourceMappingURL=Disco-ME53U25C.js.map