taxonium-component/dist/Gff3Adapter-Cm8K4l2t.js

React component for exploring large phylogenetic trees in the browser

import { I as h } from "./main-D1zX1xg0.js";
import { B as m } from "./index-CpJXUZUB.js";
import { u as g, a1 as v } from "./JBrowsePanel-BNE3gNW1.js";
import { r as y } from "./rxjs-L4bS73F7.js";
import { S as M } from "./simpleFeature-DimH8SQV.js";
import { p as x, f as T } from "./featureData-Bm8gwGZK.js";
import { p as F } from "./parseLineByLine-u4wRqQjK.js";
function b(l, a = () => {
}) {
  const t = [], r = {};
  return F.parseLineByLine(l, (e) => {
    if (e.startsWith("#"))
      t.push(e);
    else {
      if (e.startsWith(">"))
        return !1;
      {
        const s = e.indexOf("	"), n = e.slice(0, s);
        r[n] || (r[n] = ""), r[n] += `${e}
`;
      }
    }
    return !0;
  }, a), {
    header: t.join(`
`),
    featureMap: r
  };
}
class O extends m.BaseFeatureDataAdapter {
  constructor() {
    super(...arguments), this.calculatedIntervalTreeMap = {};
  }
  async loadDataP(a) {
    const { statusCallback: t = () => {
    } } = a || {}, r = await g.fetchAndMaybeUnzip(v.openLocation(this.getConf("gffLocation"), this.pluginManager), a), { header: e, featureMap: s } = b(r, t), n = Object.fromEntries(Object.entries(s).map(([o, c]) => [
      o,
      (i) => {
        if (!this.calculatedIntervalTreeMap[o]) {
          i == null || i("Parsing GFF data");
          const u = new h();
          for (const f of x(c).flat().map((p, d) => new M({
            data: T(p),
            id: `${this.id}-${o}-${d}`
          })))
            u.insert([f.get("start"), f.get("end")], f);
          this.calculatedIntervalTreeMap[o] = u;
        }
        return this.calculatedIntervalTreeMap[o];
      }
    ]));
    return {
      header: e,
      intervalTreeMap: n
    };
  }
  async loadData(a) {
    return this.gffFeatures || (this.gffFeatures = this.loadDataP(a).catch((t) => {
      throw this.gffFeatures = void 0, t;
    })), this.gffFeatures;
  }
  async getRefNames(a = {}) {
    const { intervalTreeMap: t } = await this.loadData(a);
    return Object.keys(t);
  }
  async getHeader(a = {}) {
    const { header: t } = await this.loadData(a);
    return t;
  }
  getFeatures(a, t = {}) {
    return y.ObservableCreate(async (r) => {
      var e;
      try {
        const { start: s, end: n, refName: o } = a, { intervalTreeMap: c } = await this.loadData(t);
        for (const i of ((e = c[o]) === null || e === void 0 ? void 0 : e.call(c, t.statusCallback).search([
          s,
          n
        ])) || [])
          r.next(i);
        r.complete();
      } catch (s) {
        r.error(s);
      }
    }, t.stopToken);
  }
}
export {
  O as default
};
//# sourceMappingURL=Gff3Adapter-Cm8K4l2t.js.map