taxonium-component/dist/BgzipFastaAdapter-CewYltRn.js

React component for exploring large phylogenetic trees in the browser

import { aX as m, a4 as h } from "./JBrowsePanel-uJIA-L6s.js";
import { u as x, c as _ } from "./unzip-ASAuJ12U.js";
import { I as b, a as y } from "./IndexedFastaAdapter-3PsrnaWp.js";
const g = 65536, B = g * g;
function u(i, e = 0) {
  const t = i[e] | i[e + 1] << 8 | i[e + 2] << 16 | i[e + 3] << 24;
  return ((i[e + 4] | i[e + 5] << 8 | i[e + 6] << 16 | i[e + 7] << 24) >>> 0) * B + (t >>> 0);
}
const d = 1;
function p(i, e, t) {
  const s = e[d], n = t ? t[d] : 1 / 0;
  return s <= i && n > i ? 0 : s < i ? -1 : 1;
}
class I {
  constructor({ filehandle: e, path: t }) {
    if (e)
      this.filehandle = e;
    else if (t)
      this.filehandle = new m(t);
    else
      throw new TypeError("either filehandle or path must be defined");
  }
  _getIndex() {
    return this.index || (this.index = this._readIndex().catch((e) => {
      throw this.index = void 0, e;
    })), this.index;
  }
  async _readIndex() {
    const e = await this.filehandle.read(8, 0), t = u(e);
    if (!t)
      return [[0, 0]];
    const s = new Array(t + 1);
    s[0] = [0, 0];
    const n = 8 * 2 * t;
    if (n > Number.MAX_SAFE_INTEGER)
      throw new TypeError("integer overflow");
    const o = await this.filehandle.read(n, 8);
    for (let r = 0; r < t; r += 1) {
      const c = u(o, r * 16), a = u(o, r * 16 + 8);
      s[r + 1] = [c, a];
    }
    return s;
  }
  async getLastBlock() {
    return (await this._getIndex()).at(-1);
  }
  async getRelevantBlocksForRead(e, t) {
    const s = t + e;
    if (e === 0)
      return [];
    const n = await this._getIndex(), o = [];
    let r = 0, c = n.length - 1, a = Math.floor(n.length / 2), l = p(t, n[a], n[a + 1]);
    for (; l !== 0; )
      l > 0 ? c = a - 1 : l < 0 && (r = a + 1), a = Math.ceil((c - r) / 2) + r, l = p(t, n[a], n[a + 1]);
    o.push(n[a]);
    let f = a + 1;
    for (; f < n.length && (o.push(n[f]), !(n[f][d] >= s)); f += 1)
      ;
    return o[o.length - 1][d] < s && o.push([]), o;
  }
}
class w {
  constructor({ filehandle: e, path: t, gziFilehandle: s, gziPath: n }) {
    if (e)
      this.filehandle = e;
    else if (t)
      this.filehandle = new m(t);
    else
      throw new TypeError("either filehandle or path must be defined");
    if (!s && !n && !t)
      throw new TypeError("either gziFilehandle or gziPath must be defined");
    this.gzi = new I({
      filehandle: s,
      path: !s && !n && t ? n : `${t}.gzi`
    });
  }
  async _readAndUncompressBlock(e, t) {
    let s = t;
    s || (s = (await this.filehandle.stat()).size);
    const n = s - e, o = await this.filehandle.read(n, e);
    return x(o);
  }
  async read(e, t) {
    const s = await this.gzi.getRelevantBlocksForRead(e, t), n = [];
    for (let o = 0; o < s.length - 1; o += 1) {
      const r = await this._readAndUncompressBlock(s[o][0], s[o + 1][0]), [, c] = s[o], a = c >= t ? 0 : t - c, l = Math.min(t + e, c + r.length) - c;
      a >= 0 && a < r.length && n.push(r.subarray(a, l));
    }
    return _(n);
  }
}
class L extends b {
  constructor({ fasta: e, path: t, fai: s, faiPath: n, gzi: o, gziPath: r }) {
    super({ fasta: e, path: t, fai: s, faiPath: n }), e && o ? this.fasta = new w({
      filehandle: e,
      gziFilehandle: o
    }) : t && r && (this.fasta = new w({
      path: t,
      gziPath: r
    }));
  }
}
class F extends y {
  async setupPre() {
    const e = this.getConf("fastaLocation"), t = this.getConf("faiLocation"), s = this.getConf("gziLocation"), n = {
      fasta: h.openLocation(e, this.pluginManager),
      fai: h.openLocation(t, this.pluginManager),
      gzi: h.openLocation(s, this.pluginManager)
    };
    return { fasta: new L(n) };
  }
}
export {
  F as default
};
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