taxonium-component/dist/SequenceSearchAdapter-CaFz3leo.js

React component for exploring large phylogenetic trees in the browser

import { B as v } from "./index-BnQfM3Nw.js";
import { a2 as F, a3 as E, u as r } from "./JBrowsePanel-uJIA-L6s.js";
import { r as $ } from "./rxjs-BnZkaVAs.js";
class B extends v.BaseFeatureDataAdapter {
  async configure() {
    var e;
    const o = await ((e = this.getSubAdapter) === null || e === void 0 ? void 0 : e.call(this, this.getConf("sequenceAdapter")));
    if (!o)
      throw new Error("Error getting subadapter");
    return o.dataAdapter;
  }
  async getRefNames() {
    return (await this.configure()).getRefNames();
  }
  getFeatures(e, o) {
    return $.ObservableCreate(async (c) => {
      var d;
      const g = await this.configure(), h = 1e4, n = e.end + h, i = Math.max(0, e.start - h);
      if (n < 0 || i > n) {
        c.complete();
        return;
      }
      const l = g.getFeatures({
        ...e,
        start: i,
        end: n
      }, o), m = ((d = (await F(l.pipe(E())))[0]) === null || d === void 0 ? void 0 : d.get("seq")) || "", p = this.getConf("search"), x = this.getConf("searchForward"), w = this.getConf("searchReverse"), A = this.getConf("caseInsensitive"), u = new RegExp(p, `g${A ? "i" : ""}`);
      if (p) {
        if (x) {
          const f = m.matchAll(u);
          for (const t of f) {
            const a = i + t.index, s = i + t.index + t[0].length;
            r.doesIntersect2(a, s, e.start, e.end) && c.next(new r.SimpleFeature({
              uniqueId: `${this.id}-${a}-${t[0]}-pos`,
              refName: e.refName,
              start: a,
              end: s,
              name: t[0],
              strand: 1
            }));
          }
        }
        if (w) {
          const f = r.revcom(m).matchAll(u);
          for (const t of f) {
            const a = n - t.index, s = n - t.index - t[0].length;
            r.doesIntersect2(s, a, e.start, e.end) && c.next(new r.SimpleFeature({
              uniqueId: `${this.id}-${s}-${t[0]}-neg`,
              refName: e.refName,
              start: s,
              end: a,
              name: t[0],
              strand: -1
            }));
          }
        }
      }
      c.complete();
    });
  }
}
export {
  B as default
};
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