taxonium-component/dist/featureData-Bm8gwGZK.js

React component for exploring large phylogenetic trees in the browser

function m(c) {
  return c.replaceAll(/%([0-9A-Fa-f]{2})/g, (e, r) => String.fromCharCode(parseInt(r, 16)));
}
function y(c) {
  if (!c.length || c === ".")
    return {};
  const e = {};
  return c.replace(/\r?\n$/, "").split(";").forEach((r) => {
    var t;
    const i = r.split("=", 2);
    if (!(!((t = i[1]) === null || t === void 0) && t.length))
      return;
    i[0] = i[0].trim();
    let n = e[i[0].trim()];
    n || (n = [], e[i[0]] = n), n.push(...i[1].split(",").map((a) => a.trim()).map(m));
  }), e;
}
function F(c) {
  const e = c.split("	").map((t) => t === "." || t === "" ? null : t);
  return {
    seq_id: e[0] && m(e[0]),
    source: e[1] && m(e[1]),
    type: e[2] && m(e[2]),
    start: e[3] === null ? null : parseInt(e[3], 10),
    end: e[4] === null ? null : parseInt(e[4], 10),
    score: e[5] === null ? null : parseFloat(e[5]),
    strand: e[6],
    phase: e[7],
    attributes: e[8] === null ? null : y(e[8])
  };
}
function D(c) {
  var e, r;
  const t = /^\s*##\s*(\S+)\s*(.*)/.exec(c);
  if (!t)
    return null;
  const [, i] = t;
  let [, , n] = t;
  const a = { directive: i };
  if (n.length && (n = n.replace(/\r?\n$/, ""), a.value = n), i === "sequence-region") {
    const s = n.split(/\s+/, 3);
    return {
      ...a,
      seq_id: s[0],
      start: (e = s[1]) === null || e === void 0 ? void 0 : e.replaceAll(/\D/g, ""),
      end: (r = s[2]) === null || r === void 0 ? void 0 : r.replaceAll(/\D/g, "")
    };
  } else if (i === "genome-build") {
    const [s, o] = n.split(/\s+/, 2);
    return {
      ...a,
      source: s,
      buildName: o
    };
  }
  return a;
}
const C = {
  Parent: "child_features",
  Derives_from: "derived_features"
};
class A {
  constructor(e) {
    this.seqCallback = e, this.currentSequence = void 0;
  }
  addLine(e) {
    const r = /^>\s*(\S+)\s*(.*)/.exec(e);
    r ? (this._flush(), this.currentSequence = { id: r[1], sequence: "" }, r[2] && (this.currentSequence.description = r[2].trim())) : this.currentSequence && /\S/.test(e) && (this.currentSequence.sequence += e.replaceAll(/\s/g, ""));
  }
  _flush() {
    this.currentSequence && this.seqCallback(this.currentSequence);
  }
  finish() {
    this._flush();
  }
}
class S {
  constructor(e) {
    this.fastaParser = void 0, this.eof = !1, this.lineNumber = 0, this._underConstructionTopLevel = [], this._underConstructionById = {}, this._completedReferences = {}, this._underConstructionOrphans = {};
    const r = () => {
    };
    this.featureCallback = e.featureCallback || r, this.endCallback = e.endCallback || r, this.commentCallback = e.commentCallback || r, this.errorCallback = e.errorCallback || r, this.directiveCallback = e.directiveCallback || r, this.sequenceCallback = e.sequenceCallback || r, this.disableDerivesFromReferences = e.disableDerivesFromReferences || !1, this.bufferSize = e.bufferSize === void 0 ? 1e3 : e.bufferSize;
  }
  addLine(e) {
    if (this.fastaParser) {
      this.fastaParser.addLine(e);
      return;
    }
    if (this.eof)
      return;
    if (this.lineNumber += 1, /^\s*[^#\s>]/.test(e)) {
      this._bufferLine(e);
      return;
    }
    const r = /^\s*(#+)(.*)/.exec(e);
    if (r) {
      const [, t] = r;
      let [, , i] = r;
      if (t.length === 3)
        this._emitAllUnderConstructionFeatures();
      else if (t.length === 2) {
        const n = D(e);
        n && (n.directive === "FASTA" ? (this._emitAllUnderConstructionFeatures(), this.eof = !0, this.fastaParser = new A(this.sequenceCallback)) : this._emitItem(n));
      } else
        i = i.replace(/\s*/, ""), this._emitItem({ comment: i });
    } else if (!/^\s*$/.test(e)) if (/^\s*>/.test(e))
      this._emitAllUnderConstructionFeatures(), this.eof = !0, this.fastaParser = new A(this.sequenceCallback), this.fastaParser.addLine(e);
    else {
      const t = e.replaceAll(/\r?\n?$/g, "");
      throw new Error(`GFF3 parse error.  Cannot parse '${t}'.`);
    }
  }
  finish() {
    this._emitAllUnderConstructionFeatures(), this.fastaParser && this.fastaParser.finish(), this.endCallback();
  }
  _emitItem(e) {
    Array.isArray(e) ? this.featureCallback(e) : "directive" in e ? this.directiveCallback(e) : "comment" in e && this.commentCallback(e);
  }
  _enforceBufferSizeLimit(e = 0) {
    const r = (t) => {
      var i, n;
      t && Array.isArray(t) && (!((n = (i = t[0].attributes) === null || i === void 0 ? void 0 : i.ID) === null || n === void 0) && n[0]) && (t[0].attributes.ID.forEach((s) => {
        delete this._underConstructionById[s], delete this._completedReferences[s];
      }), t.forEach((s) => {
        s.child_features && s.child_features.forEach((o) => r(o)), s.derived_features && s.derived_features.forEach((o) => r(o));
      }));
    };
    for (; this._underConstructionTopLevel.length + e > this.bufferSize; ) {
      const t = this._underConstructionTopLevel.shift();
      t && (this._emitItem(t), r(t));
    }
  }
  /**
   * return all under-construction features, called when we know
   * there will be no additional data to attach to them
   */
  _emitAllUnderConstructionFeatures() {
    if (this._underConstructionTopLevel.forEach(this._emitItem.bind(this)), this._underConstructionTopLevel = [], this._underConstructionById = {}, this._completedReferences = {}, Array.from(Object.values(this._underConstructionOrphans)).length)
      throw new Error(`some features reference other features that do not exist in the file (or in the same '###' scope). ${Object.keys(this._underConstructionOrphans).join(",")}`);
  }
  // do the right thing with a newly-parsed feature line
  _bufferLine(e) {
    var r, t, i;
    const a = {
      ...F(e),
      child_features: [],
      derived_features: []
    }, s = ((r = a.attributes) === null || r === void 0 ? void 0 : r.ID) || [], o = ((t = a.attributes) === null || t === void 0 ? void 0 : t.Parent) || [], h = this.disableDerivesFromReferences ? [] : ((i = a.attributes) === null || i === void 0 ? void 0 : i.Derives_from) || [];
    if (!s.length && !o.length && !h.length) {
      this._emitItem([a]);
      return;
    }
    let l;
    s.forEach((f) => {
      const u = this._underConstructionById[f];
      u ? (u[u.length - 1].type !== a.type && this._parseError(`multi-line feature "${f}" has inconsistent types: "${a.type}", "${u[u.length - 1].type}"`), u.push(a), l = u) : (l = [a], this._enforceBufferSizeLimit(1), !o.length && !h.length && this._underConstructionTopLevel.push(l), this._underConstructionById[f] = l, this._resolveReferencesTo(l, f));
    }), this._resolveReferencesFrom(l || [a], { Parent: o, Derives_from: h }, s);
  }
  _resolveReferencesTo(e, r) {
    const t = this._underConstructionOrphans[r];
    t && (e.forEach((i) => {
      i.child_features.push(...t.Parent);
    }), e.forEach((i) => {
      i.derived_features.push(...t.Derives_from);
    }), delete this._underConstructionOrphans[r]);
  }
  _parseError(e) {
    this.eof = !0, this.errorCallback(`${this.lineNumber}: ${e}`);
  }
  _resolveReferencesFrom(e, r, t) {
    function i(n, a, s) {
      let o = n[a];
      o || (o = {}, n[a] = o);
      const h = o[s] || !1;
      return o[s] = !0, h;
    }
    r.Parent.forEach((n) => {
      const a = this._underConstructionById[n];
      if (a) {
        const s = C.Parent;
        t.filter((o) => i(this._completedReferences, o, `Parent,${n}`)).length || a.forEach((o) => {
          o[s].push(e);
        });
      } else {
        let s = this._underConstructionOrphans[n];
        s || (s = {
          Parent: [],
          Derives_from: []
        }, this._underConstructionOrphans[n] = s), s.Parent.push(e);
      }
    }), r.Derives_from.forEach((n) => {
      const a = this._underConstructionById[n];
      if (a) {
        const s = C.Derives_from;
        t.filter((o) => i(this._completedReferences, o, `Derives_from,${n}`)).length || a.forEach((o) => {
          o[s].push(e);
        });
      } else {
        let s = this._underConstructionOrphans[n];
        s || (s = {
          Parent: [],
          Derives_from: []
        }, this._underConstructionOrphans[n] = s), s.Derives_from.push(e);
      }
    });
  }
}
function L(c) {
  const e = [], r = new S({
    featureCallback: (t) => e.push(t),
    disableDerivesFromReferences: !0,
    errorCallback: (t) => {
      throw t;
    }
  });
  for (const t of c.split(/\r?\n/))
    r.addLine(t);
  return r.finish(), e;
}
function q(c) {
  const { end: e, start: r, child_features: t, derived_features: i, attributes: n, type: a, source: s, phase: o, seq_id: h, score: l, strand: f } = c;
  let u;
  f === "+" ? u = 1 : f === "-" ? u = -1 : f === "." && (u = 0);
  const k = /* @__PURE__ */ new Set([
    "start",
    "end",
    "seq_id",
    "score",
    "type",
    "source",
    "phase",
    "strand"
  ]), v = n || {}, b = {};
  for (const d of Object.keys(v)) {
    let _ = d.toLowerCase();
    if (k.has(_) && (_ += "2"), v[d] && d !== "_lineHash") {
      let p = v[d];
      Array.isArray(p) && p.length === 1 && ([p] = p), b[_] = p;
    }
  }
  return {
    ...b,
    start: r - 1,
    end: e,
    strand: u,
    type: a,
    source: s,
    refName: h,
    derived_features: i,
    phase: o === null ? void 0 : Number(o),
    score: l === null ? void 0 : l,
    subfeatures: t.flatMap((d) => d.map((_) => q(_)))
  };
}
export {
  q as f,
  L as p
};
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