@genome-spy/app 0.72.0 → 0.74.0

package/dist/esm-CuMSzCHy.js

@@ -0,0 +1,298 @@
+//#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) {
+	if (e.length === 0 || e === ".") return {};
+	let n = {}, r = e.length;
+	e[r - 1] === "\n" && (r = e[r - 2] === "\r" ? r - 2 : r - 1, e = e.slice(0, r));
+	let i = 0;
+	for (; i < r;) {
+		let a = e.indexOf(";", i);
+		if (a === -1 && (a = r), a > i) {
+			let r = e.indexOf("=", i);
+			if (r !== -1 && r < a && r + 1 < a) {
+				let o = e.slice(i, r), s = n[o];
+				s || (s = [], n[o] = s);
+				let c = r + 1;
+				for (; c < a;) {
+					let n = e.indexOf(",", c);
+					if ((n === -1 || n > a) && (n = a), n > c) {
+						let r = e.slice(c, n);
+						s.push(t(r));
+					}
+					c = n + 1;
+				}
+			}
+		}
+		i = a + 1;
+	}
+	return n;
+}
+function r(e) {
+	if (e.length === 0 || e === ".") return {};
+	let t = {}, n = e.length;
+	e[n - 1] === "\n" && (n = e[n - 2] === "\r" ? n - 2 : n - 1, e = e.slice(0, n));
+	let r = 0;
+	for (; r < n;) {
+		let i = e.indexOf(";", r);
+		if (i === -1 && (i = n), i > r) {
+			let n = e.indexOf("=", r);
+			if (n !== -1 && n < i && n + 1 < i) {
+				let a = e.slice(r, n), o = t[a];
+				o || (o = [], t[a] = o);
+				let s = n + 1;
+				for (; s < i;) {
+					let t = e.indexOf(",", s);
+					(t === -1 || t > i) && (t = i), t > s && o.push(e.slice(s, t)), s = t + 1;
+				}
+			}
+		}
+		r = i + 1;
+	}
+	return t;
+}
+function i(e) {
+	return e.length === 0 || e === "." ? null : t(e);
+}
+function a(e) {
+	return e.length === 0 || e === "." ? null : e;
+}
+function o(e) {
+	let t = e.split("	"), r = t[0], o = t[1], s = t[2], c = t[3], l = t[4], u = t[5], d = t[6], f = t[7], p = t[8];
+	return {
+		seq_id: i(r),
+		source: i(o),
+		type: i(s),
+		start: c.length === 0 || c === "." ? null : +c,
+		end: l.length === 0 || l === "." ? null : +l,
+		score: u.length === 0 || u === "." ? null : +u,
+		strand: a(d),
+		phase: a(f),
+		attributes: p.length === 0 || p === "." ? null : n(p)
+	};
+}
+function s(e) {
+	let t = e.split("	"), n = t[0], i = t[1], o = t[2], s = t[3], c = t[4], l = t[5], u = t[6], d = t[7], f = t[8];
+	return {
+		seq_id: a(n),
+		source: a(i),
+		type: a(o),
+		start: s.length === 0 || s === "." ? null : +s,
+		end: c.length === 0 || c === "." ? null : +c,
+		score: l.length === 0 || l === "." ? null : +l,
+		strand: a(u),
+		phase: a(d),
+		attributes: f.length === 0 || f === "." ? null : r(f)
+	};
+}
+var c = new Set([
+	"start",
+	"end",
+	"seq_id",
+	"score",
+	"type",
+	"source",
+	"phase",
+	"strand"
+]);
+function l(e) {
+	if (e === "+") return 1;
+	if (e === "-") return -1;
+	if (e === ".") return 0;
+}
+function u(e, n) {
+	if (e.length === 0 || e === ".") return;
+	let r = e.length;
+	e[r - 1] === "\n" && (r = e[r - 2] === "\r" ? r - 2 : r - 1, e = e.slice(0, r));
+	let i = 0;
+	for (; i < r;) {
+		let a = e.indexOf(";", i);
+		if (a === -1 && (a = r), a > i) {
+			let r = e.indexOf("=", i);
+			if (r !== -1 && r < a && r + 1 < a) {
+				let o = e.slice(i, r);
+				if (o === "_lineHash") {
+					i = a + 1;
+					continue;
+				}
+				let s = o.toLowerCase();
+				c.has(s) && (s += "2");
+				let l = [], u = r + 1;
+				for (; u < a;) {
+					let n = e.indexOf(",", u);
+					if ((n === -1 || n > a) && (n = a), n > u) {
+						let r = e.slice(u, n);
+						l.push(t(r));
+					}
+					u = n + 1;
+				}
+				n[s] = l.length === 1 ? l[0] : l;
+			}
+		}
+		i = a + 1;
+	}
+}
+function d(e, t) {
+	if (e.length === 0 || e === ".") return;
+	let n = e.length;
+	e[n - 1] === "\n" && (n = e[n - 2] === "\r" ? n - 2 : n - 1, e = e.slice(0, n));
+	let r = 0;
+	for (; r < n;) {
+		let i = e.indexOf(";", r);
+		if (i === -1 && (i = n), i > r) {
+			let n = e.indexOf("=", r);
+			if (n !== -1 && n < i && n + 1 < i) {
+				let a = e.slice(r, n);
+				if (a === "_lineHash") {
+					r = i + 1;
+					continue;
+				}
+				let o = a.toLowerCase();
+				c.has(o) && (o += "2");
+				let s = [], l = n + 1;
+				for (; l < i;) {
+					let t = e.indexOf(",", l);
+					(t === -1 || t > i) && (t = i), t > l && s.push(e.slice(l, t)), l = t + 1;
+				}
+				t[o] = s.length === 1 ? s[0] : s;
+			}
+		}
+		r = i + 1;
+	}
+}
+function f(e) {
+	let n = e.split("	"), r = n[0], i = n[1], a = n[2], o = n[3], s = n[4], c = n[5], d = n[6], f = n[7], p = n[8], m = {
+		refName: r.length === 0 || r === "." ? "" : t(r),
+		source: i.length === 0 || i === "." ? null : t(i),
+		type: a.length === 0 || a === "." ? null : t(a),
+		start: o.length === 0 || o === "." ? 0 : o - 1,
+		end: s.length === 0 || s === "." ? 0 : +s,
+		score: c.length === 0 || c === "." ? void 0 : +c,
+		strand: l(d),
+		phase: f.length === 0 || f === "." ? void 0 : +f,
+		subfeatures: []
+	};
+	return u(p, m), m;
+}
+function p(e) {
+	let t = e.split("	"), n = t[0], r = t[1], i = t[2], a = t[3], o = t[4], s = t[5], c = t[6], u = t[7], f = t[8], p = {
+		refName: n.length === 0 || n === "." ? "" : n,
+		source: r.length === 0 || r === "." ? null : r,
+		type: i.length === 0 || i === "." ? null : i,
+		start: a.length === 0 || a === "." ? 0 : a - 1,
+		end: o.length === 0 || o === "." ? 0 : +o,
+		score: s.length === 0 || s === "." ? void 0 : +s,
+		strand: l(c),
+		phase: u.length === 0 || u === "." ? void 0 : +u,
+		subfeatures: []
+	};
+	return d(f, p), p;
+}
+//#endregion
+//#region ../../node_modules/gff-nostream/esm/api.js
+function m(e) {
+	return _(g(e));
+}
+function h(e) {
+	return v(g(e));
+}
+function g(e) {
+	let t = e.split(/\r?\n/), n = [];
+	for (let e = 0; e < t.length; e++) {
+		let r = t[e];
+		if (r.length === 0 || r[0] === "#") {
+			if (r.startsWith("##FASTA")) break;
+			continue;
+		}
+		if (r[0] === ">") break;
+		n.push({
+			line: r,
+			start: 0,
+			end: 0,
+			hasEscapes: r.includes("%")
+		});
+	}
+	return n;
+}
+function _(e) {
+	let t = [], n = /* @__PURE__ */ new Map(), r = /* @__PURE__ */ new Map();
+	for (let i = 0; i < e.length; i++) {
+		let a = e[i], c = a.hasEscapes ? o(a.line) : s(a.line);
+		c.child_features = [], c.derived_features = [], a.lineHash !== void 0 && (c.attributes ||= {}, c.attributes._lineHash = [String(a.lineHash)]);
+		let l = c.attributes, u = l?.ID, d = l?.Parent;
+		if (!u && !d) {
+			t.push([c]);
+			continue;
+		}
+		let f;
+		if (u) {
+			let e = u[0], i = n.get(e);
+			if (i) i.push(c), f = i;
+			else {
+				f = [c], d || t.push(f), n.set(e, f);
+				let i = r.get(e);
+				if (i) {
+					for (let e = 0; e < i.length; e++) c.child_features.push(i[e]);
+					r.delete(e);
+				}
+			}
+		} else f = [c];
+		if (d) for (let e = 0; e < d.length; e++) {
+			let t = d[e], i = n.get(t);
+			if (i) for (let e = 0; e < i.length; e++) i[e].child_features.push(f);
+			else {
+				let e = r.get(t);
+				e || (e = [], r.set(t, e)), e.push(f);
+			}
+		}
+	}
+	return t;
+}
+function v(e) {
+	let t = [], n = /* @__PURE__ */ new Map(), r = /* @__PURE__ */ new Map();
+	for (let i = 0; i < e.length; i++) {
+		let a = e[i], o = a.hasEscapes ? f(a.line) : p(a.line);
+		a.lineHash !== void 0 && (o._lineHash = String(a.lineHash));
+		let s = o.id, c = o.parent;
+		if (!s && !c) {
+			t.push(o);
+			continue;
+		}
+		if (s && !n.get(s)) {
+			c || t.push(o), n.set(s, o);
+			let e = r.get(s);
+			if (e) {
+				for (let t = 0; t < e.length; t++) o.subfeatures.push(e[t]);
+				r.delete(s);
+			}
+		}
+		if (c) {
+			let e = Array.isArray(c) ? c : [c];
+			for (let t = 0; t < e.length; t++) {
+				let i = e[t], a = n.get(i);
+				if (a) a.subfeatures.push(o);
+				else {
+					let e = r.get(i);
+					e || (e = [], r.set(i, e)), e.push(o);
+				}
+			}
+		}
+	}
+	return t;
+}
+//#endregion
+export { _ as parseRecords, v as parseRecordsJBrowse, m as parseStringSync, h as parseStringSyncJBrowse };