taxonium-component/dist/BedpeAdapter-DkDBWo2P.js

React component for exploring large phylogenetic trees in the browser

import { I as D } from "./main-D1zX1xg0.js";
import { B as x } from "./index-BnQfM3Nw.js";
import { u as g, a4 as A } from "./JBrowsePanel-uJIA-L6s.js";
import { r as $ } from "./rxjs-BnZkaVAs.js";
const j = /* @__PURE__ */ new Set(["DUP", "TRA", "INV", "CNV", "DEL"]);
function v(u, e, s, n) {
  const t = u.split("	"), a = t[s ? 3 : 0], l = +t[s ? 4 : 1], o = +t[s ? 5 : 2], i = t[s ? 0 : 3], f = +t[s ? 1 : 4], c = +t[s ? 2 : 5], h = t[6], r = +t[7], d = T(t[8]), b = T(t[9]), p = t.slice(10), w = n ? Object.fromEntries(n.slice(10).map((y, F) => [y, p[F]])) : {}, m = j.has(p[0]) ? `<${p[0]}>` : void 0;
  return new g.SimpleFeature({
    ...w,
    start: l,
    end: o,
    type: "paired_feature",
    refName: a,
    strand: d,
    name: h,
    score: r,
    uniqueId: e,
    mate: {
      refName: i,
      start: f,
      end: c,
      strand: b
    },
    ...m ? { ALT: [m] } : {}
  });
}
function T(u) {
  return u === "+" ? 1 : u === "-" ? -1 : u === "." ? 0 : void 0;
}
class E extends x.BaseFeatureDataAdapter {
  constructor() {
    super(...arguments), this.intervalTrees = {};
  }
  async loadDataP(e) {
    const n = (await g.fetchAndMaybeUnzipText(A.openLocation(this.getConf("bedpeLocation"), this.pluginManager), e)).split(/\n|\r\n|\r/).filter((c) => !!c), t = [];
    let a = 0;
    for (; a < n.length && n[a].startsWith("#"); a++)
      t.push(n[a]);
    const l = t.join(`
`), o = {}, i = {};
    for (; a < n.length; a++) {
      const c = n[a], h = c.split("	"), r = h[0], d = h[3];
      o[r] || (o[r] = []), i[d] || (i[d] = []), o[r].push(c), i[d].push(c);
    }
    const f = this.getConf("columnNames");
    return {
      header: l,
      feats1: o,
      feats2: i,
      columnNames: f
    };
  }
  async loadData(e = {}) {
    return this.bedpeFeatures || (this.bedpeFeatures = this.loadDataP(e).catch((s) => {
      throw this.bedpeFeatures = void 0, s;
    })), this.bedpeFeatures;
  }
  async getRefNames(e = {}) {
    const { feats1: s, feats2: n } = await this.loadData(e);
    return [.../* @__PURE__ */ new Set([...Object.keys(s), ...Object.keys(n)])];
  }
  async getHeader(e = {}) {
    const { header: s } = await this.loadData(e);
    return s;
  }
  async getNames() {
    const { header: e, columnNames: s } = await this.loadData();
    if (s.length)
      return s;
    const t = e.split(/\n|\r\n|\r/).filter((a) => !!a).at(-1);
    return t != null && t.includes("	") ? t.slice(1).split("	").map((a) => a.trim()) : void 0;
  }
  async loadFeatureTreeP(e) {
    var s, n, t, a;
    const { feats1: l, feats2: o } = await this.loadData(), i = await this.getNames(), f = new D(), c = (n = (s = l[e]) === null || s === void 0 ? void 0 : s.map((r, d) => v(r, `${this.id}-${e}-${d}-r1`, !1, i))) !== null && n !== void 0 ? n : [], h = (a = (t = o[e]) === null || t === void 0 ? void 0 : t.map((r, d) => v(r, `${this.id}-${e}-${d}-r2`, !0, i))) !== null && a !== void 0 ? a : [];
    for (const r of [...c, ...h])
      f.insert([r.get("start"), r.get("end")], r);
    return f;
  }
  async loadFeatureTree(e) {
    return this.intervalTrees[e] || (this.intervalTrees[e] = this.loadFeatureTreeP(e).catch((s) => {
      throw this.intervalTrees[e] = void 0, s;
    })), this.intervalTrees[e];
  }
  getFeatures(e, s = {}) {
    return $.ObservableCreate(async (n) => {
      const { start: t, end: a, refName: l } = e, o = await this.loadFeatureTree(l);
      for (const i of (o == null ? void 0 : o.search([t, a])) || [])
        n.next(i);
      n.complete();
    }, s.stopToken);
  }
}
E.capabilities = ["getFeatures", "getRefNames"];
export {
  E as default
};
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