@genome-spy/core 0.77.0 → 0.79.0

package/dist/bundle/{browser-KWU9rWZT.js → browser-CETrb2cm.js}

@@ -1,17 +1,37 @@
-import { t as e } from "./chunk-DmhlhrBa.js";
+import { t as e } from "./rolldown-runtime-Dy4uBu1J.js";
 //#region ../../node_modules/generic-filehandle2/esm/util.js
 async function t(e) {
 	return e.bytes ? e.bytes() : new Uint8Array(await e.arrayBuffer());
 }
+var n = 50;
+async function r(e, r) {
+	let i = e.headers.get("content-length"), a = i ? parseInt(i, 10) : void 0, o = e.body;
+	if (!o || a === void 0) {
+		let n = await t(e);
+		return r(n.byteLength, a ?? n.byteLength), n;
+	}
+	let s = o.getReader(), c = new Uint8Array(a), l = 0, u = 0;
+	r(0, a);
+	for (let e = await s.read(); !e.done; e = await s.read()) {
+		if (l + e.value.byteLength > c.length) {
+			let t = new Uint8Array(Math.max(l + e.value.byteLength, c.length * 2));
+			t.set(c.subarray(0, l)), c = t;
+		}
+		c.set(e.value, l), l += e.value.byteLength;
+		let t = Date.now();
+		t - u >= n && (u = t, r(l, a));
+	}
+	return r(l, a), l === c.length ? c : c.subarray(0, l);
+}
 //#endregion
 //#region ../../node_modules/generic-filehandle2/esm/blobFile.js
-var n = class {
+var i = class {
 	blob;
 	constructor(e) {
 		this.blob = e;
 	}
 	async read(e, n = 0) {
-		return e === 0 ? new Uint8Array() : t(this.blob.slice(n, n + e));
+		return e === 0 ? /* @__PURE__ */ new Uint8Array() : t(this.blob.slice(n, n + e));
 	}
 	async readFile(e) {
 		let n = typeof e == "string" ? e : e?.encoding;
@@ -28,10 +48,10 @@ var n = class {
 };
 //#endregion
 //#region ../../node_modules/generic-filehandle2/esm/remoteFile.js
-function r(e) {
+function a(e) {
 	return (typeof e == "object" && e && "message" in e && typeof e.message == "string" ? e.message : `${e}`).replace(/\.$/, "");
 }
-var i = class {
+var o = class {
 	url;
 	_stat;
 	fetchImplementation;
@@ -56,44 +76,44 @@ var i = class {
 		};
 	}
 	async fetch(e, t) {
-		let n = (t) => Error(`${r(t)} fetching ${e}`, { cause: t }), i;
+		let n = (t) => Error(`${a(t)} fetching ${e}`, { cause: t }), r;
 		try {
-			i = await this.fetchImplementation(e, t);
-		} catch (r) {
-			if (`${r}`.includes("Failed to fetch")) {
+			r = await this.fetchImplementation(e, t);
+		} catch (i) {
+			if (`${i}`.includes("Failed to fetch")) {
 				console.warn(`generic-filehandle: refetching ${e} to attempt to work around chrome CORS header caching bug`);
 				try {
-					i = await this.fetchImplementation(e, {
+					r = await this.fetchImplementation(e, {
 						...t,
 						cache: "reload"
 					});
 				} catch (e) {
 					throw n(e);
 				}
-			} else throw n(r);
+			} else throw n(i);
 		}
-		return i;
+		return r;
 	}
-	async read(e, n, r = {}) {
-		if (e === 0) return new Uint8Array();
+	async read(e, n, i = {}) {
+		if (e === 0) return /* @__PURE__ */ new Uint8Array();
 		if (Number.isNaN(e) || Number.isNaN(n)) throw TypeError(`read() called with NaN length or position (length=${e}, position=${n}). The index file may be corrupt.`);
-		let i = await this.fetch(this.url, this.buildRequest(r, { range: `bytes=${n}-${n + e - 1}` }));
-		if (i.status === 416) return new Uint8Array();
-		if (!i.ok) throw Error(`HTTP ${i.status} fetching ${this.url}`);
-		if (i.status === 200 && n === 0 || i.status === 206) {
-			let n = i.headers.get("content-range"), r = /\/(\d+)$/.exec(n ?? "");
-			r?.[1] && (this._stat = { size: parseInt(r[1], 10) });
-			let a = await t(i);
-			return !this._stat && i.status === 200 && (this._stat = { size: a.byteLength }), a.byteLength <= e ? a : a.subarray(0, e);
+		let a = await this.fetch(this.url, this.buildRequest(i, { range: `bytes=${n}-${n + e - 1}` }));
+		if (a.status === 416) return /* @__PURE__ */ new Uint8Array();
+		if (!a.ok) throw Error(`HTTP ${a.status} fetching ${this.url}`);
+		if (a.status === 200 && n === 0 || a.status === 206) {
+			let n = a.headers.get("content-range"), o = /\/(\d+)$/.exec(n ?? "");
+			o?.[1] && (this._stat = { size: parseInt(o[1], 10) });
+			let s = i.onProgress ? await r(a, i.onProgress) : await t(a);
+			return !this._stat && a.status === 200 && (this._stat = { size: s.byteLength }), s.byteLength <= e ? s : s.subarray(0, e);
 		}
-		throw Error(i.status === 200 ? `${this.url} fetch returned status 200, expected 206` : `HTTP ${i.status} fetching ${this.url}`);
+		throw Error(a.status === 200 ? `${this.url} fetch returned status 200, expected 206` : `HTTP ${a.status} fetching ${this.url}`);
 	}
 	async readFile(e = {}) {
-		let n = typeof e == "string" ? e : e.encoding, r = typeof e == "string" ? {} : e, i = await this.fetch(this.url, this.buildRequest(r));
-		if (!i.ok) throw Error(`HTTP ${i.status} fetching ${this.url}`);
-		if (n === "utf8") return i.text();
+		let n = typeof e == "string" ? e : e.encoding, i = typeof e == "string" ? {} : e, a = await this.fetch(this.url, this.buildRequest(i));
+		if (!a.ok) throw Error(`HTTP ${a.status} fetching ${this.url}`);
+		if (n === "utf8") return a.text();
 		if (n) throw Error(`unsupported encoding: ${n}`);
-		return t(i);
+		return i.onProgress ? r(a, i.onProgress) : t(a);
 	}
 	async stat() {
 		return this._stat || await this.read(10, 0), this._stat ?? { size: 0 };
@@ -101,11 +121,11 @@ var i = class {
 	close() {
 		return Promise.resolve();
 	}
-}, a = /* @__PURE__ */ e({
-	BlobFile: () => n,
-	LocalFile: () => o,
-	RemoteFile: () => i
-}), o = class {
+}, s = /* @__PURE__ */ e({
+	BlobFile: () => i,
+	LocalFile: () => c,
+	RemoteFile: () => o
+}), c = class {
 	readFile() {
 		return Promise.reject(/* @__PURE__ */ Error("unimplemented"));
 	}
@@ -120,4 +140,4 @@ var i = class {
 	}
 };
 //#endregion
-export { a as n, i as r, o as t };
+export { s as n, o as r, c as t };

package/dist/bundle/esm-BdLYkz-m.js

@@ -0,0 +1,248 @@
+//#region ../../node_modules/gff-nostream/esm/util.js
+var e = {};
+for (let t = 0; t < 256; t++) {
+	let n = t.toString(16).toUpperCase().padStart(2, "0");
+	e[n] = String.fromCharCode(t), e[n.toLowerCase()] = String.fromCharCode(t);
+}
+function t(t) {
+	let n = t.indexOf("%");
+	if (n === -1) return t;
+	let r = "", i = 0, a = n;
+	for (; a < t.length;) if (t[a] === "%" && a + 2 < t.length) {
+		r += t.slice(i, a);
+		let n = e[t.slice(a + 1, a + 3)];
+		n === void 0 ? r += t.slice(a, a + 3) : r += n, a += 3, i = a;
+	} else a++;
+	return r + t.slice(i);
+}
+function n(e, n) {
+	if (e.length === 0 || e === ".") return {};
+	let r = {}, i = e.length;
+	e[i - 1] === "\n" && (i = e[i - 2] === "\r" ? i - 2 : i - 1, e = e.slice(0, i));
+	let a = 0;
+	for (; a < i;) {
+		let o = e.indexOf(";", a);
+		if (o === -1 && (o = i), o > a) {
+			let i = e.indexOf("=", a);
+			if (i !== -1 && i < o && i + 1 < o) {
+				let s = e.slice(a, i), c = r[s];
+				c || (c = [], r[s] = c);
+				let l = i + 1;
+				for (; l < o;) {
+					let r = e.indexOf(",", l);
+					if ((r === -1 || r > o) && (r = o), r > l) {
+						let i = e.slice(l, r);
+						c.push(n ? t(i) : i);
+					}
+					l = r + 1;
+				}
+			}
+		}
+		a = o + 1;
+	}
+	return r;
+}
+function r(e) {
+	return e.length === 0 || e === ".";
+}
+function i(e, n, i) {
+	return r(e) ? i : n ? t(e) : e;
+}
+function a(e) {
+	return r(e) ? null : +e;
+}
+function o(e, t) {
+	let o = e.split("	"), s = o[8];
+	return {
+		seq_id: i(o[0], t, null),
+		source: i(o[1], t, null),
+		type: i(o[2], t, null),
+		start: a(o[3]),
+		end: a(o[4]),
+		score: a(o[5]),
+		strand: i(o[6], !1, null),
+		phase: i(o[7], !1, null),
+		attributes: r(s) ? null : n(s, t)
+	};
+}
+function s(e) {
+	return o(e, !0);
+}
+function c(e) {
+	return o(e, !1);
+}
+var l = /* @__PURE__ */ new Set([
+	"start",
+	"end",
+	"seq_id",
+	"score",
+	"type",
+	"source",
+	"phase",
+	"strand"
+]), u = {
+	ID: "id",
+	Name: "name",
+	Parent: "parent",
+	Note: "note",
+	Dbxref: "dbxref",
+	Ontology_term: "ontology_term",
+	Is_circular: "is_circular",
+	Alias: "alias",
+	Target: "target",
+	Gap: "gap",
+	Derives_from: "derives_from",
+	id: "id",
+	name: "name",
+	parent: "parent",
+	note: "note",
+	dbxref: "dbxref",
+	alias: "alias",
+	target: "target",
+	gap: "gap"
+};
+function d(e, n, r) {
+	if (e.length === 0 || e === ".") return;
+	let i = e.length;
+	e[i - 1] === "\n" && (i = e[i - 2] === "\r" ? i - 2 : i - 1, e = e.slice(0, i));
+	let a = 0;
+	for (; a < i;) {
+		let o = e.indexOf(";", a);
+		if (o === -1 && (o = i), o > a) {
+			let i = e.indexOf("=", a);
+			if (i !== -1 && i < o && i + 1 < o) {
+				let s = e.slice(a, i), c = u[s];
+				c === void 0 && (c = s.toLowerCase(), l.has(c) && (c += "2"));
+				let d = [], f = i + 1;
+				for (; f < o;) {
+					let n = e.indexOf(",", f);
+					if ((n === -1 || n > o) && (n = o), n > f) {
+						let i = e.slice(f, n);
+						d.push(r ? t(i) : i);
+					}
+					f = n + 1;
+				}
+				n[c] = d.length === 1 ? d[0] : d;
+			}
+		}
+		a = o + 1;
+	}
+}
+var f = {
+	"+": 1,
+	"-": -1,
+	".": 0
+};
+function p(e, t) {
+	let n = e.split("	"), a = n[3], o = n[4], s = n[5], c = n[7], l = n[8], u = {
+		refName: i(n[0], t, ""),
+		source: i(n[1], t, null),
+		type: i(n[2], t, null),
+		start: r(a) ? 0 : a - 1,
+		end: r(o) ? 0 : +o,
+		score: r(s) ? void 0 : +s,
+		strand: f[n[6]],
+		phase: r(c) ? void 0 : +c,
+		subfeatures: []
+	};
+	return d(l, u, t), u;
+}
+function m(e) {
+	return p(e, !0);
+}
+function h(e) {
+	return p(e, !1);
+}
+//#endregion
+//#region ../../node_modules/gff-nostream/esm/api.js
+function g(e) {
+	let t = e.indexOf("	"), n = e.indexOf("	", t + 1), r = e.indexOf("	", n + 1);
+	return e.slice(n + 1, r);
+}
+function _(e, t, n) {
+	let r = e.get(t);
+	r ? r.push(n) : e.set(t, [n]);
+}
+function v(e) {
+	let t = Array.isArray(e) ? e[0] : e;
+	return typeof t == "string" ? t : void 0;
+}
+function y(e) {
+	return Array.isArray(e) ? e.filter((e) => typeof e == "string") : typeof e == "string" ? [e] : [];
+}
+function b(e) {
+	return C(S(e));
+}
+function x(e) {
+	return w(S(e));
+}
+function S(e) {
+	let t = e.split(/\r?\n/), n = [];
+	for (let e of t) {
+		if (e.startsWith("##FASTA") || e.startsWith(">")) break;
+		e.length === 0 || e.startsWith("#") || n.push({
+			line: e,
+			hasEscapes: e.includes("%")
+		});
+	}
+	return n;
+}
+function C(e) {
+	let t = [], n = /* @__PURE__ */ new Map(), r = /* @__PURE__ */ new Map();
+	for (let i of e) {
+		let e = {
+			...i.hasEscapes ? s(i.line) : c(i.line),
+			child_features: [],
+			derived_features: []
+		};
+		i.lineHash !== void 0 && (e.attributes ??= {}, e.attributes._lineHash = [String(i.lineHash)]);
+		let a = e.attributes, o = a?.ID, l = a?.Parent;
+		if (!o && !l) t.push([e]);
+		else {
+			let i;
+			if (o) {
+				let a = o[0], s = n.get(a);
+				if (s) e.child_features = s[0].child_features, e.derived_features = s[0].derived_features, s.push(e), i = s;
+				else {
+					i = [e], l || t.push(i), n.set(a, i);
+					let o = r.get(a);
+					if (o) {
+						for (let t of o) e.child_features.push(t);
+						r.delete(a);
+					}
+				}
+			} else i = [e];
+			if (l) for (let e of l) {
+				let t = n.get(e);
+				t ? t[0].child_features.push(i) : _(r, e, i);
+			}
+		}
+	}
+	return t;
+}
+function w(e) {
+	let t = [], n = /* @__PURE__ */ new Map(), r = /* @__PURE__ */ new Map();
+	for (let i of e) {
+		let e = i.hasEscapes ? m(i.line) : h(i.line);
+		i.lineHash !== void 0 && (e._lineHash = String(i.lineHash));
+		let a = v(e.id), o = y(e.parent);
+		if (!a && o.length === 0) t.push(e);
+		else {
+			if (o.length === 0 && t.push(e), a && !n.has(a)) {
+				n.set(a, e);
+				let t = r.get(a);
+				if (t) {
+					for (let n of t) e.subfeatures.push(n);
+					r.delete(a);
+				}
+			}
+			for (let t of o) {
+				let i = n.get(t);
+				i ? i.subfeatures.push(e) : _(r, t, e);
+			}
+		}
+	}
+	return t;
+}
+//#endregion
+export { g as extractType, C as parseRecords, w as parseRecordsJBrowse, b as parseStringSync, x as parseStringSyncJBrowse };