@genome-spy/core 0.77.0 → 0.79.0

package/dist/src/view/viewSelectors.d.ts

@@ -5,6 +5,16 @@
  * @param {string | null} scopeName
  */
 export function registerImportInstance(view: import("./view.js").default, scopeName: string | null): void;
+/**
+ * Marks a view as the root of a named selector scope.
+ *
+ * Import instances and dynamically inserted views share the same selector scope
+ * model, even though imports were the original use case.
+ *
+ * @param {import("./view.js").default} view
+ * @param {string | null} scopeName
+ */
+export function registerViewScope(view: import("./view.js").default, scopeName: string | null): void;
 /**
  * Returns import scope info for a view, if it is an import root.
  *

package/dist/src/view/viewSelectors.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"viewSelectors.d.ts","sourceRoot":"","sources":["../../../src/view/viewSelectors.js"],"names":[],"mappings":"AAsCA;;;;;GAKG;AACH,6CAHW,OAAO,WAAW,EAAE,OAAO,aAC3B,MAAM,GAAG,IAAI,QAIvB;AAED;;;;;;;;GAQG;AACH,wCAHW,OAAO,WAAW,EAAE,OAAO,aAC3B,MAAM,GAAG,IAAI,QAIvB;AAeD;;;;;GAKG;AACH,yCAHW,OAAO,WAAW,EAAE,OAAO,GACzB,eAAe,GAAG,SAAS,CAIvC;AAED;;;;;GAKG;AACH,+CAHW,OAAO,WAAW,EAAE,OAAO,YAC3B,kBAAkB,QAM5B;AAED;;;;;GAKG;AACH,uCAHW,OAAO,WAAW,EAAE,OAAO,YAC3B,aAAa,QAMvB;AAED;;;;;GAKG;AACH,mCAHW,OAAO,WAAW,EAAE,OAAO,GACzB,OAAO,CAInB;AAED;;;;;GAKG;AACH,wCAHW,OAAO,WAAW,EAAE,OAAO,GACzB,MAAM,EAAE,CAgBpB;AAED;;;;;GAKG;AACH,sCAHW,OAAO,WAAW,EAAE,OAAO,GACzB,YAAY,CAYxB;AAED;;;;;;GAMG;AACH,uCAJW,OAAO,WAAW,EAAE,OAAO,aAC3B,MAAM,GACJ,aAAa,CAazB;AAED;;;;;GAKG;AACH,+CAHW,aAAa,GACX,MAAM,CAQlB;AAED;;;;;GAKG;AACH,0CAHW,OAAO,WAAW,EAAE,OAAO,GACzB,OAAO,WAAW,EAAE,OAAO,EAAE,CAWzC;AAED;;;;;GAKG;AACH,0CAHW,OAAO,WAAW,EAAE,OAAO,WAC3B,OAAO,WAAW,EAAE,OAAO,QAerC;AAED;;;;;GAKG;AACH,wCAHW,OAAO,WAAW,EAAE,OAAO,GACzB,OAAO,WAAW,EAAE,OAAO,EAAE,CAWzC;AAED;;;;;GAKG;AACH,4CAHW,OAAO,WAAW,EAAE,OAAO,WAC3B,OAAO,WAAW,EAAE,OAAO,QAerC;AAED;;;;;;GAMG;AACH,0CAJW,OAAO,WAAW,EAAE,OAAO,YAC3B,YAAY,GACV,OAAO,WAAW,EAAE,OAAO,GAAG,SAAS,CAoCnD;AAED;;;;;;GAMG;AACH,2CAJW,OAAO,WAAW,EAAE,OAAO,YAC3B,aAAa,GACX,aAAa,GAAG,SAAS,CAuCrC;AAED;;;;;GAKG;AACH,8CAHW,OAAO,WAAW,EAAE,OAAO,WAC3B,CAAC,KAAK,EAAE,sBAAsB,KAAK,IAAI,QAyBjD;AAED;;;;;GAKG;AACH,4CAHW,OAAO,WAAW,EAAE,OAAO,GACzB,sBAAsB,EAAE,CAOpC;AAED;;;;;GAKG;AACH,kDAHW,OAAO,WAAW,EAAE,OAAO,GACzB,uBAAuB,EAAE,CAarC;AA5ZD;;;;;;GAMG;AAEH;;;;;;;;;;;GAWG;AAEH,wCAAyC,IAAI,CAAC;2BAZjC,OAAO,sBAAsB,EAAE,YAAY;4BAC3C,OAAO,sBAAsB,EAAE,aAAa;qCAC5C;IAAE,IAAI,EAAE,OAAO,WAAW,EAAE,OAAO,CAAC;IAAC,KAAK,EAAE,OAAO,sBAAsB,EAAE,SAAS,CAAC;IAAC,QAAQ,EAAE,aAAa,CAAA;CAAE;sCAC/G;IAAE,OAAO,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,EAAE,CAAA;CAAE;8BACpC;IAAE,IAAI,EAAE,MAAM,GAAG,IAAI,CAAA;CAAE;kCACvB,SAAS,GAAG,gBAAgB;6BAC5B,SAAS,GAAG,gBAAgB;iCAC5B;IAAE,WAAW,CAAC,EAAE,OAAO,CAAA;CAAE;4BACzB;IAAE,WAAW,CAAC,EAAE,OAAO,CAAA;CAAE;4BACzB;IAAE,IAAI,EAAE,OAAO,WAAW,EAAE,OAAO,CAAC;IAAC,KAAK,EAAE,OAAO,sBAAsB,EAAE,SAAS,CAAA;CAAE"}

package/dist/src/view/viewSelectors.js

@@ -43,8 +43,30 @@ const chromeOverrides = new WeakMap();
  * @param {string | null} scopeName
  */
 export function registerImportInstance(view, scopeName) {
+    registerScope(view, scopeName, "Import");
+}
+
+/**
+ * Marks a view as the root of a named selector scope.
+ *
+ * Import instances and dynamically inserted views share the same selector scope
+ * model, even though imports were the original use case.
+ *
+ * @param {import("./view.js").default} view
+ * @param {string | null} scopeName
+ */
+export function registerViewScope(view, scopeName) {
+    registerScope(view, scopeName, "View");
+}
+
+/**
+ * @param {import("./view.js").default} view
+ * @param {string | null} scopeName
+ * @param {string} scopeKind
+ */
+function registerScope(view, scopeName, scopeKind) {
     if (scopeName !== null && typeof scopeName !== "string") {
-        throw new Error("Import scope name must be a string or null.");
+        throw new Error(scopeKind + " scope name must be a string or null.");
     }
 
     importScopes.set(view, { name: scopeName });

package/package.json

@@ -7,7 +7,7 @@
   },
   "contributors": [],
   "license": "MIT",
-  "version": "0.77.0",
+  "version": "0.79.0",
   "jsdelivr": "dist/bundle/index.js",
   "unpkg": "dist/bundle/index.js",
   "browser": "dist/bundle/index.js",
@@ -49,7 +49,7 @@
     "@gmod/bbi": "^9.2.0",
     "@gmod/bed": "^2.1.10",
     "@gmod/indexedfasta": "^5.0.2",
-    "@gmod/tabix": "^3.2.2",
+    "@gmod/tabix": "3.2.2",
     "@gmod/vcf": "^7.0.0",
     "@types/d3-array": "^3.2.2",
     "@types/d3-dsv": "^3.0.7",
@@ -73,10 +73,10 @@
     "vega-expression": "^6.1.0",
     "vega-loader": "^5.1.0",
     "vega-scale": "^8.1.0",
-    "vega-util": "^2.1.0"
+    "vega-util": "2.1.0"
   },
   "devDependencies": {
     "@types/long": "^4.0.1"
   },
-  "gitHead": "2851e22e2069a70d7d02e3ab707b7556573aa17e"
+  "gitHead": "fbc253e91871c75151711b3c13373e3d7881dd5c"
 }

package/dist/bundle/esm-0dYHNV_D.js

@@ -1,121 +0,0 @@
-import { t as e } from "./esm-C49STiCR.js";
-import { t } from "./browser-KWU9rWZT.js";
-//#region node_modules/@gmod/indexedfasta/esm/indexedFasta.js
-function n(e, t, n, r) {
-	return e + t * Math.floor(r / n) + r % n;
-}
-async function r(e, t = {}) {
-	let n = new TextDecoder("utf8").decode(await e.readFile(t)), r = [], i = [], a = [], o = [], s = [], c = {}, l = 0, u = n.length, d = 0;
-	for (; l < u;) {
-		let e = n.indexOf("\n", l);
-		e === -1 && (e = u);
-		let t = n.slice(l, e);
-		if (t.endsWith("\r") && (t = t.slice(0, -1)), t = t.trim(), l = e + 1, t.length === 0) continue;
-		let f = t.indexOf("	"), p = t.indexOf("	", f + 1), m = t.indexOf("	", p + 1), h = t.indexOf("	", m + 1), g = t.slice(0, f);
-		if (g.startsWith(">")) throw Error("found > in sequence name, might have supplied FASTA file for the FASTA index");
-		r.push(g), a.push(+t.slice(f + 1, p)), i.push(+t.slice(p + 1, m)), o.push(+t.slice(m + 1, h)), s.push(+t.slice(h + 1)), c[g] = d, d++;
-	}
-	return {
-		names: r,
-		nameToIndex: c,
-		offsets: i,
-		lengths: a,
-		lineLengths: o,
-		lineBytes: s
-	};
-}
-var i = class {
-	constructor({ fasta: e, fai: n, path: r, faiPath: i }) {
-		if (e) this.fasta = e;
-		else if (r) this.fasta = new t(r);
-		else throw Error("Need to pass filehandle for fasta or path to localfile");
-		if (n) this.fai = n;
-		else if (i) this.fai = new t(i);
-		else if (r) this.fai = new t(`${r}.fai`);
-		else throw Error("Need to pass filehandle for  or path to localfile");
-	}
-	async _getIndexes(e) {
-		return this.indexes ||= r(this.fai, e).catch((e) => {
-			throw this.indexes = void 0, e;
-		}), this.indexes;
-	}
-	async getSequenceNames(e) {
-		return (await this._getIndexes(e)).names;
-	}
-	async getSequenceSizes(e) {
-		let t = await this._getIndexes(e);
-		if (!t.sizesCache) {
-			let e = {};
-			for (let n = 0; n < t.names.length; n++) e[t.names[n]] = t.lengths[n];
-			t.sizesCache = e;
-		}
-		return t.sizesCache;
-	}
-	async getSequenceSize(e, t) {
-		let n = await this._getIndexes(t), r = n.nameToIndex[e];
-		return r === void 0 ? void 0 : n.lengths[r];
-	}
-	async hasReferenceSequence(e, t) {
-		return (await this._getIndexes(t)).nameToIndex[e] !== void 0;
-	}
-	async getResiduesByName(e, t, n, r) {
-		let i = await this._getIndexes(r), a = i.nameToIndex[e];
-		if (a !== void 0) return this._fetchFromIndex(i.offsets[a], i.lineBytes[a], i.lineLengths[a], i.lengths[a], t, n, r);
-	}
-	async getSequence(e, t, n, r) {
-		return this.getResiduesByName(e, t, n, r);
-	}
-	async _fetchFromIndex(e, t, r, i, a = 0, o, s) {
-		let c = o;
-		if (a < 0) throw TypeError("regionStart cannot be less than 0");
-		if ((c === void 0 || c > i) && (c = i), a >= c) return "";
-		let l = n(e, t, r, a), u = n(e, t, r, c) - l, d = new TextDecoder("utf8").decode(await this.fasta.read(u, l, s)).replace(/\s+/g, "");
-		if (/[^\x20-\x7e]/.test(d.slice(0, 1e3))) throw Error("Non-ASCII characters detected in sequence. The file may be gzip compressed. Use BgzipIndexedFasta for bgzip files, or decompress the file.");
-		return d;
-	}
-}, a = class extends i {
-	constructor({ fasta: n, path: r, fai: i, faiPath: a, gzi: o, gziPath: s }) {
-		super({
-			fasta: n,
-			path: r,
-			fai: i,
-			faiPath: a
-		}), n && o ? this.fasta = new e({
-			filehandle: n,
-			gziFilehandle: o
-		}) : r && s && (this.fasta = new e({
-			filehandle: new t(r),
-			gziFilehandle: new t(s)
-		}));
-	}
-};
-//#endregion
-//#region node_modules/@gmod/indexedfasta/esm/index.js
-function o(e) {
-	return e.split(">").filter((e) => /\S/.test(e)).map((e) => {
-		let [t, ...n] = e.split("\n"), [r, ...i] = t.split(" "), a = n.join("").replace(/\s/g, "");
-		return {
-			id: r,
-			description: i.join(" "),
-			sequence: a
-		};
-	});
-}
-var s = class {
-	constructor({ fasta: e, path: n }) {
-		if (e) this.fasta = e;
-		else if (n) this.fasta = new t(n);
-		else throw Error("Need to pass fasta or path");
-		this.data = this.fasta.readFile().then((e) => o(new TextDecoder("utf8").decode(e)));
-	}
-	async fetch(e, t, n) {
-		let r = (await this.data).find((t) => t.id === e), i = n - t;
-		if (!r) throw Error(`no sequence with id ${e} exists`);
-		return r.sequence.slice(t, i);
-	}
-	async getSequenceNames() {
-		return (await this.data).map((e) => e.id);
-	}
-};
-//#endregion
-export { a as BgzipIndexedFasta, s as FetchableSmallFasta, i as IndexedFasta, o as parseSmallFasta };