taxonium-component/dist/IndexedFastaAdapter-3PsrnaWp.js

React component for exploring large phylogenetic trees in the browser

import { A as b } from "./AbortablePromiseCache-CcuMrnn7.js";
import "./unzip-ASAuJ12U.js";
import { aX as d, a4 as h, u as S, R as F } from "./JBrowsePanel-uJIA-L6s.js";
import { B as I } from "./index-BnQfM3Nw.js";
import { Q as L } from "./QuickLRU-DcNaxluI.js";
import { r as k } from "./rxjs-BnZkaVAs.js";
function x(r, e) {
  return r.offset + r.lineBytes * Math.floor(e / r.lineLength) + e % r.lineLength;
}
async function A(r, e) {
  const s = new TextDecoder("utf8");
  return Object.fromEntries(s.decode(await r.readFile(e)).split(/\r?\n/).map((t) => t.trim()).filter((t) => !!t).map((t) => t.split("	")).map((t) => {
    var n;
    if ((n = t[0]) != null && n.startsWith(">"))
      throw new Error("found > in sequence name, might have supplied FASTA file for the FASTA index");
    return [
      t[0],
      {
        name: t[0],
        length: +t[1],
        start: 0,
        end: +t[1],
        offset: +t[2],
        lineLength: +t[3],
        lineBytes: +t[4]
      }
    ];
  }));
}
class E {
  constructor({ fasta: e, fai: s, path: t, faiPath: n }) {
    if (e)
      this.fasta = e;
    else if (t)
      this.fasta = new d(t);
    else
      throw new Error("Need to pass filehandle for fasta or path to localfile");
    if (s)
      this.fai = s;
    else if (n)
      this.fai = new d(n);
    else if (t)
      this.fai = new d(`${t}.fai`);
    else
      throw new Error("Need to pass filehandle for  or path to localfile");
  }
  async _getIndexes(e) {
    return this.indexes || (this.indexes = A(this.fai, e).catch((s) => {
      throw this.indexes = void 0, s;
    })), this.indexes;
  }
  /**
   * @returns array of string sequence names that are present in the index, in
   * which the array index indicates the sequence ID, and the value is the
   * sequence name
   */
  async getSequenceNames(e) {
    return Object.keys(await this._getIndexes(e));
  }
  /**
   * @returns array of string sequence names that are present in the index, in
   * which the array index indicates the sequence ID, and the value is the
   * sequence name
   */
  async getSequenceSizes(e) {
    const s = {}, t = await this._getIndexes(e);
    for (const n of Object.values(t))
      s[n.name] = n.length;
    return s;
  }
  /**
   * @returns array of string sequence names that are present in the index, in
   * which the array index indicates the sequence ID, and the value is the
   * sequence name
   */
  async getSequenceSize(e, s) {
    var n;
    return (n = (await this._getIndexes(s))[e]) == null ? void 0 : n.length;
  }
  /**
   * @param name
   *
   * @returns true if the file contains the given reference sequence name
   */
  async hasReferenceSequence(e, s) {
    return !!(await this._getIndexes(s))[e];
  }
  /**
   * @param seqName
   * @param min
   * @param max
   */
  async getResiduesByName(e, s, t, n) {
    const a = (await this._getIndexes(n))[e];
    return a ? this._fetchFromIndexEntry(a, s, t, n) : void 0;
  }
  //alias for getResiduesByName
  async getSequence(e, s, t, n) {
    return this.getResiduesByName(e, s, t, n);
  }
  async _fetchFromIndexEntry(e, s = 0, t, n) {
    let a = t;
    if (s < 0)
      throw new TypeError("regionStart cannot be less than 0");
    if ((a === void 0 || a > e.length) && (a = e.length), s >= a)
      return "";
    const i = x(e, s), o = x(e, a) - i;
    return new TextDecoder("utf8").decode(await this.fasta.read(o, i, n)).replace(/\s+/g, "");
  }
}
class O extends I.BaseSequenceAdapter {
  constructor() {
    super(...arguments), this.seqCache = new b({
      cache: new L({ maxSize: 200 }),
      fill: async (e) => {
        const { refName: s, start: t, end: n, fasta: a } = e;
        return a.getSequence(s, t, n);
      }
    });
  }
  async getRefNames(e) {
    const { fasta: s } = await this.setup();
    return s.getSequenceNames();
  }
  async getRegions(e) {
    const { fasta: s } = await this.setup(), t = await s.getSequenceSizes();
    return Object.keys(t).map((n) => ({
      refName: n,
      start: 0,
      end: t[n]
    }));
  }
  async setupPre() {
    const e = this.getConf("fastaLocation"), s = this.getConf("faiLocation");
    return {
      fasta: new E({
        fasta: h.openLocation(e, this.pluginManager),
        fai: h.openLocation(s, this.pluginManager)
      })
    };
  }
  async getHeader() {
    const e = this.getConf("metadataLocation");
    return e.uri === "" || e.uri === "/path/to/fa.metadata.yaml" ? null : h.openLocation(e, this.pluginManager).readFile("utf8");
  }
  async setup() {
    return this.setupP || (this.setupP = this.setupPre().catch((e) => {
      throw this.setupP = void 0, e;
    })), this.setupP;
  }
  getFeatures(e, s) {
    const { statusCallback: t = () => {
    }, stopToken: n } = s || {}, { refName: a, start: i, end: o } = e;
    return k.ObservableCreate(async (f) => {
      await S.updateStatus2("Downloading sequence", t, n, async () => {
        const { fasta: l } = await this.setup(), q = await l.getSequenceSize(a), p = Math.min(q || 0, o), g = [], u = 128e3, m = i - i % u, _ = o + (u - o % u);
        for (let c = m; c < _; c += u) {
          const w = {
            refName: a,
            start: c,
            end: c + u
          };
          F.checkStopToken(n), g.push(await this.seqCache.get(JSON.stringify(w), { ...w, fasta: l }));
        }
        const y = g.filter((c) => !!c).join("").slice(i - m).slice(0, o - i);
        y && f.next(new S.SimpleFeature({
          id: `${a}-${i}-${p}`,
          data: {
            refName: a,
            start: i,
            end: p,
            seq: y
          }
        }));
      }), f.complete();
    });
  }
}
const P = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProperty({
  __proto__: null,
  default: O
}, Symbol.toStringTag, { value: "Module" }));
export {
  E as I,
  O as a,
  P as b
};
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