taxonium-component/dist/BedTabixAdapter-BBaLvhwe.js

React component for exploring large phylogenetic trees in the browser

import { B as C, f as b } from "./util-X8nqr6IJ.js";
import { T as x } from "./tabixIndexedFile-B-0sKywF.js";
import "./unzip-ASAuJ12U.js";
import { B as w } from "./index-BnQfM3Nw.js";
import { a4 as c, u as d, R as u } from "./JBrowsePanel-uJIA-L6s.js";
import { r as S } from "./rxjs-BnZkaVAs.js";
class N extends w.BaseFeatureDataAdapter {
  constructor(e, a, t) {
    super(e, a, t);
    const s = this.getConf("bedGzLocation"), n = this.getConf(["index", "indexType"]), r = this.getConf(["index", "location"]), o = this.getConf("autoSql"), i = this.pluginManager;
    this.bed = new x({
      filehandle: c.openLocation(s, i),
      csiFilehandle: n === "CSI" ? c.openLocation(r, i) : void 0,
      tbiFilehandle: n !== "CSI" ? c.openLocation(r, i) : void 0,
      chunkCacheSize: 50 * 2 ** 20
    }), this.columnNames = this.getConf("columnNames"), this.scoreColumn = this.getConf("scoreColumn"), this.parser = new C({ autoSql: o });
  }
  async getRefNames(e = {}) {
    return this.bed.getReferenceSequenceNames(e);
  }
  async getHeader(e) {
    return this.bed.getHeader(e);
  }
  async getMetadataPre2(e) {
    return this.setupP || (this.setupP = this.getMetadataPre().catch((a) => {
      throw this.setupP = void 0, a;
    })), this.setupP;
  }
  async getMetadataPre() {
    return { meta: await this.bed.getMetadata() };
  }
  async getMetadata(e) {
    const { statusCallback: a = () => {
    } } = e || {};
    return d.updateStatus("Downloading index", a, () => this.getMetadataPre2(e));
  }
  async getNames() {
    if (this.columnNames.length)
      return this.columnNames;
    const t = (await this.getHeader()).split(/\n|\r\n|\r/).filter((s) => !!s).at(-1);
    return t != null && t.includes("	") ? t.slice(1).split("	").map((s) => s.trim()) : void 0;
  }
  getFeatures(e, a) {
    const { stopToken: t, statusCallback: s = () => {
    } } = a || {};
    return S.ObservableCreate(async (n) => {
      const { meta: r } = await this.getMetadata(), { columnNumbers: o } = r, i = o.ref - 1, p = o.start - 1, m = o.end - 1, h = await this.getNames();
      let l = performance.now();
      u.checkStopToken(t), await d.updateStatus("Downloading features", s, () => this.bed.getLines(e.refName, e.start, e.end, {
        lineCallback: (f, g) => {
          performance.now() - l > 200 && (u.checkStopToken(t), l = performance.now()), n.next(new d.SimpleFeature(b({
            line: f,
            colRef: i,
            colStart: p,
            colEnd: m,
            scoreColumn: this.scoreColumn,
            parser: this.parser,
            uniqueId: `${this.id}-${g}`,
            names: h
          })));
        },
        stopToken: t
      })), n.complete();
    }, t);
  }
}
N.capabilities = ["getFeatures", "getRefNames"];
export {
  N as default
};
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