@genome-spy/core 0.64.0 → 0.66.1

package/dist/bundle/index-ByuE8dvu.js

@@ -0,0 +1,332 @@
+var v = Object.defineProperty;
+var F = (n, e, t) => e in n ? v(n, e, { enumerable: !0, configurable: !0, writable: !0, value: t }) : n[e] = t;
+var f = (n, e, t) => F(n, typeof e != "symbol" ? e + "" : e, t);
+const y = /%([0-9A-Fa-f]{2})/g, R = /^\s*##\s*(\S+)\s*(.*)/, g = /\r?\n$/, b = /\s+/, C = /\D/g;
+function p(n) {
+  return n.includes("%") ? n.replaceAll(y, (e, t) => String.fromCharCode(parseInt(t, 16))) : n;
+}
+function k(n) {
+  if (!n.length || n === ".")
+    return {};
+  const e = {};
+  let t = n;
+  t.endsWith(`
+`) && (t = t.slice(0, t.endsWith(`\r
+`) ? -2 : -1));
+  for (const r of t.split(";")) {
+    const s = r.indexOf("=");
+    if (s === -1)
+      continue;
+    const c = r.slice(s + 1);
+    if (!c.length)
+      continue;
+    const i = r.slice(0, s).trim();
+    let o = e[i];
+    o || (o = [], e[i] = o);
+    for (const l of c.split(","))
+      o.push(p(l.trim()));
+  }
+  return e;
+}
+function I(n) {
+  if (!n.length || n === ".")
+    return {};
+  const e = {};
+  let t = n;
+  t.endsWith(`
+`) && (t = t.slice(0, t.endsWith(`\r
+`) ? -2 : -1));
+  for (const r of t.split(";")) {
+    const s = r.indexOf("=");
+    if (s === -1)
+      continue;
+    const c = r.slice(s + 1);
+    if (!c.length)
+      continue;
+    const i = r.slice(0, s).trim();
+    let o = e[i];
+    o || (o = [], e[i] = o);
+    for (const l of c.split(","))
+      o.push(l.trim());
+  }
+  return e;
+}
+function L(n) {
+  return _(n.split("	"));
+}
+function a(n) {
+  return n === "." || n === "" || n === void 0 ? null : n;
+}
+function _(n) {
+  const e = a(n[0]), t = a(n[1]), r = a(n[2]), s = a(n[3]), c = a(n[4]), i = a(n[5]), o = a(n[6]), l = a(n[7]), u = a(n[8]);
+  return {
+    seq_id: e ? p(e) : null,
+    source: t ? p(t) : null,
+    type: r ? p(r) : null,
+    start: s === null ? null : parseInt(s, 10),
+    end: c === null ? null : parseInt(c, 10),
+    score: i === null ? null : parseFloat(i),
+    strand: o,
+    phase: l,
+    attributes: u === null ? null : k(u)
+  };
+}
+function D(n) {
+  const e = a(n[0]), t = a(n[1]), r = a(n[2]), s = a(n[3]), c = a(n[4]), i = a(n[5]), o = a(n[6]), l = a(n[7]), u = a(n[8]);
+  return {
+    seq_id: e,
+    source: t,
+    type: r,
+    start: s === null ? null : parseInt(s, 10),
+    end: c === null ? null : parseInt(c, 10),
+    score: i === null ? null : parseFloat(i),
+    strand: o,
+    phase: l,
+    attributes: u === null ? null : I(u)
+  };
+}
+function A(n) {
+  var c, i;
+  const e = R.exec(n);
+  if (!e)
+    return null;
+  const [, t] = e;
+  let [, , r] = e;
+  const s = { directive: t };
+  if (r.length && (r = r.replace(g, ""), s.value = r), t === "sequence-region") {
+    const o = r.split(b, 3);
+    return {
+      ...s,
+      seq_id: o[0],
+      start: (c = o[1]) == null ? void 0 : c.replaceAll(C, ""),
+      end: (i = o[2]) == null ? void 0 : i.replaceAll(C, "")
+    };
+  } else if (t === "genome-build") {
+    const [o, l] = r.split(b, 2);
+    return {
+      ...s,
+      source: o,
+      buildName: l
+    };
+  }
+  return s;
+}
+const x = /^\s*[^#\s>]/, w = /^\s*(#+)(.*)/, S = /^\s*$/, E = /^\s*>/, P = /\r?\n?$/g;
+class m {
+  constructor(e) {
+    f(this, "featureCallback");
+    f(this, "endCallback");
+    f(this, "commentCallback");
+    f(this, "errorCallback");
+    f(this, "disableDerivesFromReferences");
+    f(this, "directiveCallback");
+    f(this, "bufferSize");
+    f(this, "eof", !1);
+    f(this, "lineNumber", 0);
+    // features that we have to keep on hand for now because they
+    // might be referenced by something else
+    f(this, "_underConstructionTopLevel", []);
+    // index of the above by ID
+    f(this, "_underConstructionById", {});
+    f(this, "_completedReferences", {});
+    // features that reference something we have not seen yet
+    // structured as:
+    // {  'some_id' : {
+    //     'Parent' : [ orphans that have a Parent attr referencing it ],
+    //     'Derives_from' : [ orphans that have a Derives_from attr referencing it ],
+    //    }
+    // }
+    f(this, "_underConstructionOrphans", {});
+    const t = () => {
+    };
+    this.featureCallback = e.featureCallback || t, this.endCallback = e.endCallback || t, this.commentCallback = e.commentCallback || t, this.errorCallback = e.errorCallback || t, this.directiveCallback = e.directiveCallback || t, this.disableDerivesFromReferences = e.disableDerivesFromReferences || !1, this.bufferSize = e.bufferSize === void 0 ? 1 / 0 : e.bufferSize;
+  }
+  addLine(e) {
+    if (this.eof)
+      return;
+    if (this.lineNumber += 1, x.test(e)) {
+      this._bufferLine(e);
+      return;
+    }
+    const t = w.exec(e);
+    if (t) {
+      const [, r] = t;
+      let [, , s] = t;
+      if (r.length === 3)
+        this._emitAllUnderConstructionFeatures();
+      else if (r.length === 2) {
+        const c = A(e);
+        c && (c.directive === "FASTA" ? (this._emitAllUnderConstructionFeatures(), this.eof = !0) : this._emitItem(c));
+      } else
+        this._emitItem({ comment: s.trimStart() });
+    } else if (!S.test(e)) if (E.test(e))
+      this._emitAllUnderConstructionFeatures(), this.eof = !0;
+    else {
+      const r = e.replaceAll(P, "");
+      throw new Error(`GFF3 parse error.  Cannot parse '${r}'.`);
+    }
+  }
+  addParsedFeatureLine(e) {
+    this.eof || (this.lineNumber += 1, this._bufferParsedLine(e));
+  }
+  finish() {
+    this._emitAllUnderConstructionFeatures(), 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 t = (r) => {
+      var s, c;
+      r && Array.isArray(r) && ((c = (s = r[0].attributes) == null ? void 0 : s.ID) != null && c[0]) && (r[0].attributes.ID.forEach((o) => {
+        delete this._underConstructionById[o], delete this._completedReferences[o];
+      }), r.forEach((o) => {
+        o.child_features && o.child_features.forEach((l) => {
+          t(l);
+        }), o.derived_features && o.derived_features.forEach((l) => {
+          t(l);
+        });
+      }));
+    };
+    for (; this._underConstructionTopLevel.length + e > this.bufferSize; ) {
+      const r = this._underConstructionTopLevel.shift();
+      r && (this._emitItem(r), t(r));
+    }
+  }
+  /**
+   * return all under-construction features, called when we know
+   * there will be no additional data to attach to them
+   */
+  _emitAllUnderConstructionFeatures() {
+    this._underConstructionTopLevel.forEach(this._emitItem.bind(this)), this._underConstructionTopLevel = [], this._underConstructionById = {}, this._completedReferences = {};
+    const e = Object.keys(this._underConstructionOrphans);
+    if (e.length)
+      throw new Error(`some features reference other features that do not exist in the file (or in the same '###' scope). ${e.join(",")}`);
+  }
+  _bufferLine(e) {
+    this._bufferParsedLine(L(e));
+  }
+  _bufferParsedLine(e) {
+    var o, l, u;
+    const t = e;
+    t.child_features = [], t.derived_features = [];
+    const r = ((o = t.attributes) == null ? void 0 : o.ID) || [], s = ((l = t.attributes) == null ? void 0 : l.Parent) || [], c = this.disableDerivesFromReferences ? [] : ((u = t.attributes) == null ? void 0 : u.Derives_from) || [];
+    if (!r.length && !s.length && !c.length) {
+      this._emitItem([t]);
+      return;
+    }
+    let i;
+    r.forEach((d) => {
+      const h = this._underConstructionById[d];
+      h ? (h[h.length - 1].type !== t.type && this._parseError(`multi-line feature "${d}" has inconsistent types: "${t.type}", "${h[h.length - 1].type}"`), h.push(t), i = h) : (i = [t], this._enforceBufferSizeLimit(1), !s.length && !c.length && this._underConstructionTopLevel.push(i), this._underConstructionById[d] = i, this._resolveReferencesTo(i, d));
+    }), this._resolveReferencesFrom(
+      // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+      i || [t],
+      { Parent: s, Derives_from: c },
+      r
+    );
+  }
+  _resolveReferencesTo(e, t) {
+    const r = this._underConstructionOrphans[t];
+    if (r) {
+      for (const s of e)
+        s.child_features.push(...r.Parent), s.derived_features.push(...r.Derives_from);
+      delete this._underConstructionOrphans[t];
+    }
+  }
+  _parseError(e) {
+    this.eof = !0, this.errorCallback(`${this.lineNumber}: ${e}`);
+  }
+  _resolveReferencesFrom(e, t, r) {
+    for (const s of t.Parent) {
+      const c = this._underConstructionById[s];
+      if (c) {
+        let i = !1;
+        for (const o of r) {
+          const l = `Parent,${s}`, u = this._completedReferences[o] || (this._completedReferences[o] = {});
+          u[l] && (i = !0), u[l] = !0;
+        }
+        if (!i)
+          for (const o of c)
+            o.child_features.push(e);
+      } else {
+        let i = this._underConstructionOrphans[s];
+        i || (i = { Parent: [], Derives_from: [] }, this._underConstructionOrphans[s] = i), i.Parent.push(e);
+      }
+    }
+    for (const s of t.Derives_from) {
+      const c = this._underConstructionById[s];
+      if (c) {
+        let i = !1;
+        for (const o of r) {
+          const l = `Derives_from,${s}`, u = this._completedReferences[o] || (this._completedReferences[o] = {});
+          u[l] && (i = !0), u[l] = !0;
+        }
+        if (!i)
+          for (const o of c)
+            o.derived_features.push(e);
+      } else {
+        let i = this._underConstructionOrphans[s];
+        i || (i = { Parent: [], Derives_from: [] }, this._underConstructionOrphans[s] = i), i.Derives_from.push(e);
+      }
+    }
+  }
+}
+function $(n) {
+  const e = [], t = new m({
+    featureCallback: (r) => e.push(r),
+    disableDerivesFromReferences: !0,
+    errorCallback: (r) => {
+      throw new Error(r);
+    }
+  });
+  for (const r of n.split(/\r?\n/))
+    t.addLine(r);
+  return t.finish(), e;
+}
+function B(n) {
+  const e = [], t = new m({
+    featureCallback: (r) => e.push(r),
+    disableDerivesFromReferences: !0,
+    errorCallback: (r) => {
+      throw new Error(r);
+    }
+  });
+  for (const r of n)
+    t.addLine(r);
+  return t.finish(), e;
+}
+function T(n) {
+  const e = [], t = new m({
+    featureCallback: (r) => e.push(r),
+    disableDerivesFromReferences: !0,
+    errorCallback: (r) => {
+      throw new Error(r);
+    }
+  });
+  for (const r of n) {
+    const s = _(r.fields);
+    r.lineHash !== void 0 && (s.attributes || (s.attributes = {}), s.attributes._lineHash = [String(r.lineHash)]), t.addParsedFeatureLine(s);
+  }
+  return t.finish(), e;
+}
+function q(n, e) {
+  const t = [], r = new m({
+    featureCallback: (c) => t.push(c),
+    disableDerivesFromReferences: !0,
+    errorCallback: (c) => {
+      throw new Error(c);
+    }
+  }), s = e ? _ : D;
+  for (const c of n) {
+    const i = s(c.fields);
+    c.lineHash !== void 0 && (i.attributes || (i.attributes = {}), i.attributes._lineHash = [String(c.lineHash)]), r.addParsedFeatureLine(i);
+  }
+  return r.finish(), t;
+}
+export {
+  B as parseArraySync,
+  T as parseRecordsSync,
+  q as parseRecordsSyncFast,
+  $ as parseStringSync
+};