taxonium-component/dist/BedGraphAdapter-n8izSG8z.js

React component for exploring large phylogenetic trees in the browser

import { I as T } from "./main-D1zX1xg0.js";
import { B as y } from "./index-CpJXUZUB.js";
import { u as m, a1 as F } from "./JBrowsePanel-BNE3gNW1.js";
import { p as w } from "./parseLineByLine-u4wRqQjK.js";
import { r as x } from "./rxjs-L4bS73F7.js";
class $ extends y.BaseFeatureDataAdapter {
  constructor() {
    super(...arguments), this.intervalTrees = {};
  }
  async getNames() {
    const { header: e, columnNames: t } = await this.loadData();
    if (t.length)
      return t;
    const s = e.split(/\n|\r\n|\r/).filter((a) => !!a).at(-1);
    return s != null && s.includes("	") ? s.slice(1).split("	").map((a) => a.trim()) : void 0;
  }
  async loadFeatureIntervalTreeHelper(e) {
    var t;
    const { features: i } = await this.loadData(), s = i[e];
    if (!s)
      return;
    const a = ((t = await this.getNames()) === null || t === void 0 ? void 0 : t.slice(3)) || [], o = new T();
    for (let r = 0; r < s.length; r++) {
      const n = s[r], [d, l, v, ...u] = n.split("	");
      for (let c = 0; c < u.length; c++) {
        const b = `${this.id}-${d}-${r}-${c}`, h = +l, f = +v, p = +u[c], g = a[c] || `col${c}`;
        p && o.insert([h, f], new m.SimpleFeature({
          id: b,
          data: {
            refName: d,
            start: h,
            end: f,
            score: p,
            source: g
          }
        }));
      }
    }
    return o;
  }
  async getRefNames(e = {}) {
    const { features: t } = await this.loadData(e);
    return Object.keys(t);
  }
  async loadDataP(e = {}) {
    const t = this.pluginManager, i = this.getConf("bedGraphLocation"), s = await m.fetchAndMaybeUnzip(F.openLocation(i, t), e), a = {}, o = [];
    w.parseLineByLine(s, (n) => {
      if (n.startsWith("#"))
        o.push(n);
      else {
        const d = n.indexOf("	"), l = n.slice(0, d);
        a[l] || (a[l] = []), a[l].push(n);
      }
      return !0;
    }, e.statusCallback);
    const r = this.getConf("columnNames");
    return {
      header: o.join(`
`),
      features: a,
      columnNames: r
    };
  }
  async loadFeatureIntervalTree(e) {
    return this.intervalTrees[e] || (this.intervalTrees[e] = this.loadFeatureIntervalTreeHelper(e).catch((t) => {
      throw this.intervalTrees[e] = void 0, t;
    })), this.intervalTrees[e];
  }
  async loadData(e = {}) {
    return this.bedFeatures || (this.bedFeatures = this.loadDataP(e).catch((t) => {
      throw this.bedFeatures = void 0, t;
    })), this.bedFeatures;
  }
  getFeatures(e, t = {}) {
    return x.ObservableCreate(async (i) => {
      const { start: s, end: a, refName: o } = e, r = await this.loadFeatureIntervalTree(o);
      for (const n of (r == null ? void 0 : r.search([s, a])) || [])
        i.next(n);
      i.complete();
    });
  }
}
export {
  $ as default
};
//# sourceMappingURL=BedGraphAdapter-n8izSG8z.js.map