taxonium-component/dist/Gff3TabixAdapter-RPdaIXNV.js

React component for exploring large phylogenetic trees in the browser

import { T as H } from "./tabixIndexedFile-WXUhSlHL.js";
import "./unzip-NIBF0hze.js";
import { B as S } from "./index-CpJXUZUB.js";
import { aI as F, a1 as g, u as h } from "./JBrowsePanel-BNE3gNW1.js";
import { r as T } from "./rxjs-L4bS73F7.js";
import { S as C } from "./simpleFeature-DimH8SQV.js";
import { p as L, f as N } from "./featureData-Bm8gwGZK.js";
var E = F();
class G extends S.BaseFeatureDataAdapter {
  async configurePre(e) {
    const t = this.getConf("gffGzLocation"), s = this.getConf(["index", "indexType"]), n = this.getConf(["index", "location"]), f = this.getConf("dontRedispatch"), c = new H({
      filehandle: g.openLocation(t, this.pluginManager),
      csiFilehandle: s === "CSI" ? g.openLocation(n, this.pluginManager) : void 0,
      tbiFilehandle: s !== "CSI" ? g.openLocation(n, this.pluginManager) : void 0,
      chunkCacheSize: 50 * 2 ** 20,
      renameRefSeqs: (d) => d
    });
    return {
      gff: c,
      dontRedispatch: f,
      header: await c.getHeader()
    };
  }
  async configurePre2() {
    return this.configured || (this.configured = this.configurePre().catch((e) => {
      throw this.configured = void 0, e;
    })), this.configured;
  }
  async configure(e) {
    const { statusCallback: t = () => {
    } } = e || {};
    return h.updateStatus("Downloading index", t, () => this.configurePre2());
  }
  async getRefNames(e = {}) {
    const { gff: t } = await this.configure(e);
    return t.getReferenceSequenceNames(e);
  }
  async getHeader(e = {}) {
    const { gff: t } = await this.configure(e);
    return t.getHeader();
  }
  getFeatures(e, t = {}) {
    return T.ObservableCreate(async (s) => {
      const { gff: n } = await this.configure(t), f = await n.getMetadata();
      await this.getFeaturesHelper(e, t, f, s, !0);
    }, t.stopToken);
  }
  async getFeaturesHelper(e, t, s, n, f, c = e) {
    var d, u;
    const { statusCallback: p = () => {
    } } = t;
    try {
      const o = [], { dontRedispatch: m, gff: x } = await this.configure(t);
      if (await h.updateStatus("Downloading features", p, () => x.getLines(e.refName, e.start, e.end, (a, i) => {
        o.push(this.parseLine(s.columnNumbers, a, i));
      })), f && o.length) {
        let a = Number.POSITIVE_INFINITY, i = Number.NEGATIVE_INFINITY;
        for (const r of o) {
          const I = r.fields[2];
          if (!m.includes(I)) {
            const l = r.start - 1;
            l < a && (a = l), r.end > i && (i = r.end);
          }
        }
        if (i > e.end || a < e.start) {
          await this.getFeaturesHelper({ ...e, start: a, end: i }, t, s, n, !1, e);
          return;
        }
      }
      const w = o.map((a) => (a.fields[8] && a.fields[8] !== "." ? a.fields[8].includes("_lineHash") || (a.fields[8] += `;_lineHash=${a.lineHash}`) : a.fields[8] = `_lineHash=${a.lineHash}`, a.fields.join("	"))).join(`
`);
      for (const a of L(w))
        for (const i of a) {
          const r = new C({
            data: N(i),
            id: `${this.id}-offset-${(u = (d = i.attributes) === null || d === void 0 ? void 0 : d._lineHash) === null || u === void 0 ? void 0 : u[0]}`
          });
          E.doesIntersect2(r.get("start"), r.get("end"), c.start, c.end) && n.next(r);
        }
      n.complete();
    } catch (o) {
      n.error(o);
    }
  }
  parseLine(e, t, s) {
    const n = t.split("	");
    return {
      start: +n[e.start - 1],
      end: +n[e.end - 1],
      lineHash: s,
      fields: n
    };
  }
}
export {
  G as default
};
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