taxonium-component/dist/Gff3Adapter-BzUNSMTR.js

React component for exploring large phylogenetic trees in the browser

import { I as b } from "./main-D1zX1xg0.js";
import { B as v } from "./index-BnQfM3Nw.js";
import { u as h, a4 as y } from "./JBrowsePanel-uJIA-L6s.js";
import { r as x } from "./rxjs-BnZkaVAs.js";
import { S as T } from "./simpleFeature-Bntv68qr.js";
import { p as D, f as M } from "./featureData-Bm8gwGZK.js";
class E extends v.BaseFeatureDataAdapter {
  constructor() {
    super(...arguments), this.calculatedIntervalTreeMap = {};
  }
  async loadDataP(a) {
    const { statusCallback: t = () => {
    } } = a || {}, r = await h.fetchAndMaybeUnzip(y.openLocation(this.getConf("gffLocation"), this.pluginManager), a), c = [], n = {}, d = new TextDecoder("utf8");
    let i = 0, l = 0;
    for (; i < r.length; ) {
      const s = r.indexOf(10, i), p = s === -1 ? r.subarray(i) : r.subarray(i, s), e = d.decode(p).trim();
      if (e)
        if (e.startsWith("#"))
          c.push(e);
        else {
          if (e.startsWith(">"))
            break;
          {
            const f = e.indexOf("	"), o = e.slice(0, f);
            n[o] || (n[o] = ""), n[o] += `${e}
`;
          }
        }
      l++ % 1e4 === 0 && t(`Loading ${h.getProgressDisplayStr(i, r.length)}`), i = s + 1;
    }
    const u = Object.fromEntries(Object.entries(n).map(([s, p]) => [
      s,
      (e) => {
        if (!this.calculatedIntervalTreeMap[s]) {
          e == null || e("Parsing GFF data");
          const f = new b();
          for (const o of D(p).flat().map((g, m) => new T({
            data: M(g),
            id: `${this.id}-${s}-${m}`
          })))
            f.insert([o.get("start"), o.get("end")], o);
          this.calculatedIntervalTreeMap[s] = f;
        }
        return this.calculatedIntervalTreeMap[s];
      }
    ]));
    return {
      header: c.join(`
`),
      intervalTreeMap: u
    };
  }
  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 x.ObservableCreate(async (r) => {
      var c;
      try {
        const { start: n, end: d, refName: i } = a, { intervalTreeMap: l } = await this.loadData(t);
        for (const u of ((c = l[i]) === null || c === void 0 ? void 0 : c.call(l, t.statusCallback).search([
          n,
          d
        ])) || [])
          r.next(u);
        r.complete();
      } catch (n) {
        r.error(n);
      }
    }, t.stopToken);
  }
}
export {
  E as default
};
//# sourceMappingURL=Gff3Adapter-BzUNSMTR.js.map