taxonium-component/dist/UnindexedFastaAdapter-Ep1DTjtt.js

React component for exploring large phylogenetic trees in the browser

import { a4 as p, s as u, u as f } from "./JBrowsePanel-uJIA-L6s.js";
import { B as d } from "./index-BnQfM3Nw.js";
import { r as l } from "./rxjs-BnZkaVAs.js";
function h(i) {
  return new Map(i.split(">").filter((t) => /\S/.test(t)).map((t) => {
    const [e, ...a] = t.split(`
`), [s, ...n] = e.split(" "), r = a.join("").replace(/\s/g, "");
    return [
      s,
      {
        description: n.join(" "),
        sequence: r
      }
    ];
  }));
}
class w extends d.BaseSequenceAdapter {
  async getRefNames(t) {
    const { fasta: e } = await this.setup(t);
    return [...e.keys()];
  }
  async getRegions(t) {
    const { fasta: e } = await this.setup(t);
    return [...e.entries()].map(([a, s]) => ({
      refName: a,
      start: 0,
      end: s.sequence.length
    }));
  }
  async setupPre(t) {
    const e = this.getConf("fastaLocation"), a = h(await p.openLocation(e, this.pluginManager).readFile("utf8"));
    return {
      fasta: new Map([...a.entries()].map(([s, n]) => [
        u.readConfObject(this.config, "rewriteRefNames", { refName: s }) || s,
        n
      ]))
    };
  }
  async getHeader() {
    const t = this.getConf("metadataLocation");
    return t.uri === "" || t.uri === "/path/to/fa.metadata.yaml" ? null : p.openLocation(t, this.pluginManager).readFile("utf8");
  }
  async setup(t) {
    return this.setupP || (this.setupP = this.setupPre(t).catch((e) => {
      throw this.setupP = void 0, e;
    })), this.setupP;
  }
  getFeatures(t, e) {
    const { refName: a, start: s, end: n } = t;
    return l.ObservableCreate(async (r) => {
      const { fasta: c } = await this.setup(e), o = c.get(a);
      o && r.next(new f.SimpleFeature({
        id: `${a}-${s}-${n}`,
        data: {
          refName: a,
          start: s,
          end: n,
          seq: o.sequence.slice(s, n)
        }
      })), r.complete();
    });
  }
}
export {
  w as default
};
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