taxonium-component/dist/BedAdapter-CKtgo-RC.js

React component for exploring large phylogenetic trees in the browser

import { I as v } from "./main-D1zX1xg0.js";
import { B as b, f as T } from "./util-DIF6WZFN.js";
import { B as w } from "./index-CpJXUZUB.js";
import { u as m, a1 as y } from "./JBrowsePanel-BNE3gNW1.js";
import { p as C } from "./parseLineByLine-u4wRqQjK.js";
import { r as F } from "./rxjs-L4bS73F7.js";
class x extends w.BaseFeatureDataAdapter {
  constructor() {
    super(...arguments), this.intervalTrees = {};
  }
  async loadDataP(e) {
    const t = this.getConf("bedLocation"), o = await m.fetchAndMaybeUnzip(y.openLocation(t, this.pluginManager), e), s = [], a = {};
    C.parseLineByLine(o, (r) => {
      if (r.startsWith("#"))
        s.push(r);
      else {
        const g = r.indexOf("	"), p = r.slice(0, g);
        a[p] || (a[p] = []), a[p].push(r);
      }
      return !0;
    }, e == null ? void 0 : e.statusCallback);
    const l = s.join(`
`), i = this.getConf("autoSql"), n = new b({ autoSql: i }), u = this.getConf("columnNames"), d = this.getConf("scoreColumn"), c = this.getConf("colRef"), f = this.getConf("colStart"), h = this.getConf("colEnd");
    return {
      header: l,
      features: a,
      parser: n,
      columnNames: u,
      scoreColumn: d,
      colRef: c,
      colStart: f,
      colEnd: h
    };
  }
  async loadData(e = {}) {
    return this.bedFeatures || (this.bedFeatures = this.loadDataP(e).catch((t) => {
      throw this.bedFeatures = void 0, t;
    })), this.bedFeatures;
  }
  async getRefNames(e = {}) {
    const { features: t } = await this.loadData(e);
    return Object.keys(t);
  }
  async getHeader(e = {}) {
    const { header: t } = await this.loadData(e);
    return t;
  }
  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) {
    const { colRef: t, colStart: o, colEnd: s, features: a, parser: l, scoreColumn: i } = await this.loadData(), n = a[e];
    if (!n)
      return;
    const u = await this.getNames(), d = new v();
    for (let c = 0; c < n.length; c++) {
      const f = n[c], h = `${this.id}-${e}-${c}`, r = new m.SimpleFeature(T({
        line: f,
        colRef: t,
        colStart: o,
        colEnd: s,
        scoreColumn: i,
        parser: l,
        uniqueId: h,
        names: u
      }));
      d.insert([r.get("start"), r.get("end")], r);
    }
    return d;
  }
  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];
  }
  getFeatures(e, t = {}) {
    return F.ObservableCreate(async (o) => {
      const { start: s, end: a, refName: l } = e, i = await this.loadFeatureIntervalTree(l), n = i == null ? void 0 : i.search([s, a]);
      if (n)
        for (const u of n)
          o.next(u);
      o.complete();
    }, t.stopToken);
  }
}
x.capabilities = ["getFeatures", "getRefNames"];
export {
  x as default
};
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