taxonium-component/dist/makeImageData-D0Rxqm57.js

React component for exploring large phylogenetic trees in the browser

import { O as D, u as p, ak as N, al as W } from "./JBrowsePanel-BNE3gNW1.js";
import { d as z, f as u, g as K, a as Q } from "./drawPhased-CAb_z73L.js";
async function Z(d, P) {
  const { scrollTop: I, minorAlleleFrequencyFilter: O, sources: x, rowHeight: g, features: R, regions: q, bpPerPx: v, renderingMode: H, stopToken: h, lengthCutoffFilter: B, referenceDrawingMode: C } = P, G = q[0], { statusCallback: S = () => {
  } } = P;
  D.checkStopToken(h);
  const T = await p.updateStatus("Calculating stats", S, () => N({
    stopToken: h,
    features: R.values(),
    minorAlleleFrequencyFilter: O,
    lengthCutoffFilter: B
  }));
  D.checkStopToken(h);
  const k = new W();
  return await p.updateStatus("Drawing variants", S, () => {
    p.forEachWithStopTokenCheck(T, h, ({ mostFrequentAlt: t, feature: n }) => {
      const [w, J] = p.featureSpanPx(n, G, v), L = n.get("end") - n.get("start"), c = Math.max(Math.round(J - w), 2), F = n.get("genotypes");
      let s = -I;
      const b = x.length;
      if (H === "phased")
        for (let a = 0; a < b; a++) {
          const { name: l, HP: f } = x[a], e = F[l], o = Math.floor(w), i = Math.max(g, 1);
          if (e)
            if (e.includes("|")) {
              const m = e.split("|");
              z(m, d, o, s, c, i, f, void 0, C === "draw") && k.insert({
                minX: o,
                maxX: o + c,
                minY: s,
                maxY: s + i,
                genotype: e,
                name: l,
                featureId: n.id()
              });
            } else
              d.fillStyle = "black", d.fillRect(o - u, s - u, c + u, i + u);
          s += g;
        }
      else {
        const a = {};
        for (let l = 0; l < b; l++) {
          const { name: f } = x[l], e = F[f], o = Math.floor(w), i = Math.max(g, 1);
          if (e) {
            let r = a[e];
            if (r === void 0) {
              let m = 0, A = 0, E = 0, X = 0;
              const Y = e.split(/[/|]/), j = Y.length;
              for (let y = 0; y < j; y++) {
                const M = Y[y];
                M === t ? m++ : M === "0" ? X++ : M === "." ? A++ : E++;
              }
              r = K(X, m, E, A, j, C === "draw"), a[e] = r;
            }
            r && (Q(r, d, o, s, c, i, n.get("type"), n.get("strand"), L > 5 ? 0.75 : 1), k.insert({
              minX: o,
              maxX: o + c,
              minY: s,
              maxY: s + i,
              genotype: e,
              name: f,
              featureId: n.id()
            }));
          }
          s += g;
        }
      }
    });
  }), {
    rbush: k.toJSON(),
    featureGenotypeMap: Object.fromEntries(T.map(({ feature: t }) => [
      t.id(),
      {
        alt: t.get("ALT"),
        ref: t.get("REF"),
        name: t.get("name"),
        description: t.get("description"),
        length: t.get("end") - t.get("start")
      }
    ]))
  };
}
export {
  Z as makeImageData
};
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