@genome-spy/app 0.83.1 → 0.85.0

package/dist/{esm-D8vvQAP3.js → esm-CcDLRSvC.js}

@@ -1,5 +1,5 @@
-import { n as e, r as t } from "./esm-CGLz7idZ.js";
-import { t as n } from "./esm-VvpZ9hsq.js";
+import { t as e } from "./esm-VvpZ9hsq.js";
+import { i as t, r as n } from "./esm-BA6yMcc-.js";
 import { n as r, r as i } from "./esm-BdT7qUL-.js";
 import { t as a } from "./AbortablePromiseCache-BTmAcN-t.js";
 //#region ../core/node_modules/@gmod/tabix/esm/chunk.js
@@ -132,13 +132,13 @@ var b = class extends s {
 			coordinateType: i
 		};
 	}
-	async _parse(t = {}) {
-		let n = await e(await this.filehandle.readFile(t)), r = new DataView(n.buffer), i;
+	async _parse(e = {}) {
+		let t = await n(await this.filehandle.readFile(e)), r = new DataView(t.buffer), i;
 		if (r.getUint32(0, !0) === h) i = 1;
 		else if (r.getUint32(0, !0) === g) i = 2;
 		else throw Error("Not a CSI file");
 		this.minShift = r.getInt32(4, !0), this.depth = r.getInt32(8, !0), this.maxBinNumber = ((1 << (this.depth + 1) * 3) - 1) / 7;
-		let a = 2 ** (this.minShift + this.depth * 3), s = r.getInt32(12, !0), c = s && s >= 30 ? this.parseAuxData(n, 16) : {
+		let a = 2 ** (this.minShift + this.depth * 3), s = r.getInt32(12, !0), c = s && s >= 30 ? this.parseAuxData(t, 16) : {
 			refIdToName: [],
 			refNameToId: {},
 			metaChar: void 0,
@@ -152,25 +152,25 @@ var b = class extends s {
 		}, l = r.getInt32(16 + s, !0), u, d = 16 + s + 4, f = Array(l).fill(0).map(() => {
 			let e = r.getInt32(d, !0);
 			d += 4;
-			let t = {}, i;
+			let n = {}, i;
 			for (let a = 0; a < e; a += 1) {
 				let e = r.getUint32(d, !0);
-				if (e > this.maxBinNumber) i = this.parsePseudoBin(n, d + 4), d += 48;
+				if (e > this.maxBinNumber) i = this.parsePseudoBin(t, d + 4), d += 48;
 				else {
-					let i = m(n, d + 4);
+					let i = m(t, d + 4);
 					u = this._findFirstData(u, i);
 					let a = r.getInt32(d + 12, !0);
 					d += 16;
 					let s = Array(a);
-					for (let t = 0; t < a; t += 1) {
-						let r = m(n, d), i = m(n, d + 8);
-						d += 16, s[t] = new o(r, i, e);
+					for (let n = 0; n < a; n += 1) {
+						let r = m(t, d), i = m(t, d + 8);
+						d += 16, s[n] = new o(r, i, e);
 					}
-					t[e] = s;
+					n[e] = s;
 				}
 			}
 			return {
-				binIndex: t,
+				binIndex: n,
 				stats: i
 			};
 		});
@@ -226,8 +226,8 @@ var w = class extends s {
 		let n = await this.parse(t), r = n.refNameToId[e];
 		return r === void 0 || !n.indices[r] ? -1 : n.indices[r].stats?.lineCount ?? -1;
 	}
-	async _parse(t = {}) {
-		let n = await e(await this.filehandle.readFile(t)), r = new DataView(n.buffer);
+	async _parse(e = {}) {
+		let t = await n(await this.filehandle.readFile(e)), r = new DataView(t.buffer);
 		if (r.getUint32(0, !0) !== x) throw Error("Not a TBI file");
 		let i = r.getUint32(4, !0), a = r.getUint32(8, !0), s = a & 65536 ? "zero-based-half-open" : "1-based-closed", c = {
 			0: "generic",
@@ -239,35 +239,35 @@ var w = class extends s {
 			ref: r.getInt32(12, !0),
 			start: r.getInt32(16, !0),
 			end: r.getInt32(20, !0)
-		}, u = r.getInt32(24, !0), d = 2 ** 29, f = u ? String.fromCharCode(u) : void 0, p = r.getInt32(28, !0), h = r.getInt32(32, !0), { refNameToId: g, refIdToName: _ } = this._parseNameBytes(n.slice(36, 36 + h)), v = 36 + h, y;
+		}, u = r.getInt32(24, !0), d = 2 ** 29, f = u ? String.fromCharCode(u) : void 0, p = r.getInt32(28, !0), h = r.getInt32(32, !0), { refNameToId: g, refIdToName: _ } = this._parseNameBytes(t.slice(36, 36 + h)), v = 36 + h, y;
 		return {
 			indices: Array(i).fill(0).map(() => {
 				let e = r.getInt32(v, !0);
 				v += 4;
-				let t = {}, i;
+				let n = {}, i;
 				for (let a = 0; a < e; a += 1) {
 					let e = r.getUint32(v, !0);
 					if (v += 4, e > 37450) throw Error("tabix index contains too many bins, please use a CSI index");
 					if (e === 37450) {
 						let e = r.getInt32(v, !0);
-						v += 4, e === 2 && (i = this.parsePseudoBin(n, v)), v += 16 * e;
+						v += 4, e === 2 && (i = this.parsePseudoBin(t, v)), v += 16 * e;
 					} else {
 						let i = r.getInt32(v, !0);
 						v += 4;
 						let a = Array(i);
-						for (let t = 0; t < i; t += 1) {
-							let r = m(n, v), i = m(n, v + 8);
-							v += 16, y = this._findFirstData(y, r), a[t] = new o(r, i, e);
+						for (let n = 0; n < i; n += 1) {
+							let r = m(t, v), i = m(t, v + 8);
+							v += 16, y = this._findFirstData(y, r), a[n] = new o(r, i, e);
 						}
-						t[e] = a;
+						n[e] = a;
 					}
 				}
 				let a = r.getInt32(v, !0);
 				v += 4;
 				let s = Array(a);
-				for (let e = 0; e < a; e += 1) s[e] = m(n, v), v += 8, y = this._findFirstData(y, s[e]);
+				for (let e = 0; e < a; e += 1) s[e] = m(t, v), v += 8, y = this._findFirstData(y, s[e]);
 				return {
-					binIndex: t,
+					binIndex: n,
 					linearIndex: s,
 					stats: i
 				};
@@ -305,11 +305,11 @@ var w = class extends s {
 		return f(l, d);
 	}
 }, T = class {
-	constructor({ path: e, filehandle: t, url: o, tbiPath: s, tbiUrl: c, tbiFilehandle: l, csiPath: u, csiUrl: d, csiFilehandle: f, renameRefSeqs: p, chunkCacheSize: m = 5 * 2 ** 20 }) {
-		this.cache = new n({ maxSize: 1e3 });
+	constructor({ path: t, filehandle: n, url: o, tbiPath: s, tbiUrl: c, tbiFilehandle: l, csiPath: u, csiUrl: d, csiFilehandle: f, renameRefSeqs: p, chunkCacheSize: m = 5 * 2 ** 20 }) {
+		this.cache = new e({ maxSize: 1e3 });
 		let h = p ?? ((e) => e);
-		if (t) this.filehandle = t;
-		else if (e) this.filehandle = new r(e);
+		if (n) this.filehandle = n;
+		else if (t) this.filehandle = new r(t);
 		else if (o) this.filehandle = new i(o);
 		else throw TypeError("must provide either filehandle or path");
 		if (l) this.index = new w({
@@ -328,8 +328,8 @@ var w = class extends s {
 			filehandle: new r(u),
 			renameRefSeqs: h
 		});
-		else if (e) this.index = new w({
-			filehandle: new r(`${e}.tbi`),
+		else if (t) this.index = new w({
+			filehandle: new r(`${t}.tbi`),
 			renameRefSeqs: h
 		});
 		else if (d) this.index = new b({ filehandle: new i(d) });
@@ -337,7 +337,7 @@ var w = class extends s {
 		else if (o) this.index = new w({ filehandle: new i(`${o}.tbi`) });
 		else throw TypeError("must provide one of tbiFilehandle, tbiPath, csiFilehandle, csiPath, tbiUrl, csiUrl");
 		this.renameRefSeq = h, this.hasCustomRenameRefSeq = p !== void 0, this.chunkCache = new a({
-			cache: new n({ maxSize: Math.floor(m / 65536) }),
+			cache: new e({ maxSize: Math.floor(m / 65536) }),
 			fill: (e, t) => this.readChunk(e, { signal: t })
 		});
 	}
@@ -386,8 +386,8 @@ var w = class extends s {
 	async getMetadata(e = {}) {
 		return this.index.getMetadata(e);
 	}
-	async getHeaderBuffer(t = {}) {
-		let { firstDataLine: n, metaChar: r, maxBlockSize: i } = await this.getMetadata(t), a = (n?.blockPosition || 0) + i, o = await e(await this.filehandle.read(a, 0, t));
+	async getHeaderBuffer(e = {}) {
+		let { firstDataLine: t, metaChar: r, maxBlockSize: i } = await this.getMetadata(e), a = (t?.blockPosition || 0) + i, o = await n(await this.filehandle.read(a, 0, e));
 		if (r) {
 			let e = -1, t = r.charCodeAt(0);
 			for (let n = 0, r = o.length; n < r; n++) {

package/dist/{esm-BeV56E_5.js → esm-CfYZhLHN.js}

@@ -1,5 +1,5 @@
-import { n as e, r as t } from "./esm-CGLz7idZ.js";
-import { t as n } from "./esm-VvpZ9hsq.js";
+import { t as e } from "./esm-VvpZ9hsq.js";
+import { i as t, r as n } from "./esm-BA6yMcc-.js";
 import { n as r, r as i } from "./esm-BdT7qUL-.js";
 //#region ../../node_modules/@gmod/bam/esm/chunk.js
 var a = class {
@@ -142,12 +142,12 @@ function b(e, t, n, r, i = []) {
 }
 //#endregion
 //#region ../../node_modules/@gmod/bam/esm/indexFile.js
-function x(e, t = 5) {
-	let r = new n({ maxSize: t });
-	return (t) => {
-		if (r.has(t)) return r.get(t);
-		let n = e(t);
-		return n && r.set(t, n), n;
+function x(t, n = 5) {
+	let r = new e({ maxSize: n });
+	return (e) => {
+		if (r.has(e)) return r.get(e);
+		let n = t(e);
+		return n && r.set(e, n), n;
 	};
 }
 var S = class {
@@ -611,50 +611,50 @@ var L = class extends S {
 			...m(e.subarray(t + 28, t + 28 + u), this.renameRefSeq)
 		};
 	}
-	async _parse(t) {
-		let n = await e(await this.filehandle.readFile(t)), r = new DataView(n.buffer), i, o = r.getUint32(0, !0);
+	async _parse(e) {
+		let t = await n(await this.filehandle.readFile(e)), r = new DataView(t.buffer), i, o = r.getUint32(0, !0);
 		if (o === M) i = 1;
 		else if (o === N) i = 2;
 		else throw Error(`Not a CSI file ${o}`);
 		this.minShift = r.getInt32(4, !0), this.depth = r.getInt32(8, !0), this.maxBinNumber = ((1 << (this.depth + 1) * 3) - 1) / 7;
-		let s = this.maxBinNumber, c = r.getInt32(12, !0), l = c >= 30 ? this.parseAuxData(n, 16) : void 0, f = r.getInt32(16 + c, !0), m = 16 + c + 4, h, g = [];
+		let s = this.maxBinNumber, c = r.getInt32(12, !0), l = c >= 30 ? this.parseAuxData(t, 16) : void 0, f = r.getInt32(16 + c, !0), m = 16 + c + 4, h, g = [];
 		for (let e = 0; e < f; e++) {
 			g.push(m);
 			let e = r.getInt32(m, !0);
 			m += 4;
-			for (let t = 0; t < e; t++) {
+			for (let n = 0; n < e; n++) {
 				let e = r.getUint32(m, !0);
 				if (m += 4, e > this.maxBinNumber) m += 44;
 				else {
 					m += 8;
 					let e = r.getInt32(m, !0);
 					m += 4;
-					for (let t = 0; t < e; t += 1) {
-						let e = w(n, m);
+					for (let n = 0; n < e; n += 1) {
+						let e = w(t, m);
 						m += 8, m += 8, h = p(h, e);
 					}
 				}
 			}
 		}
 		function _(e) {
-			let t = g[e];
-			if (t === void 0) return;
-			let i = r.getInt32(t, !0);
-			t += 4;
+			let n = g[e];
+			if (n === void 0) return;
+			let i = r.getInt32(n, !0);
+			n += 4;
 			let o = {}, c;
 			for (let e = 0; e < i; e++) {
-				let e = r.getUint32(t, !0);
-				if (t += 4, e > s) c = u(n, t + 28), t += 44;
+				let e = r.getUint32(n, !0);
+				if (n += 4, e > s) c = u(t, n + 28), n += 44;
 				else {
-					t += 8;
-					let i = r.getInt32(t, !0);
-					t += 4;
+					n += 8;
+					let i = r.getInt32(n, !0);
+					n += 4;
 					let s = Array(i);
 					for (let r = 0; r < i; r += 1) {
-						let i = w(n, t);
-						t += 8;
-						let o = w(n, t);
-						t += 8, s[r] = new a(i, o, e);
+						let i = w(t, n);
+						n += 8;
+						let o = w(t, n);
+						n += 8, s[r] = new a(i, o, e);
 					}
 					o[e] = s;
 				}
@@ -1158,7 +1158,7 @@ var Z = class {
 	index;
 	htsget = !1;
 	headerP;
-	chunkFeatureCache = new n({ maxSize: 100 });
+	chunkFeatureCache = new e({ maxSize: 100 });
 	RecordClass;
 	constructor({ bamFilehandle: e, bamPath: t, bamUrl: n, baiPath: r, baiFilehandle: i, baiUrl: a, csiPath: o, csiFilehandle: s, csiUrl: c, htsget: l, renameRefSeqs: u = (e) => e, recordClass: d }) {
 		this.renameRefSeq = u, this.RecordClass = d ?? K;
@@ -1171,14 +1171,14 @@ var Z = class {
 		else if (m) this.index = new k({ filehandle: m });
 		else if (!l) throw Error("no index source: pass csi*/bai* options or a bamPath/bamUrl so the .bai sibling can be inferred");
 	}
-	async getHeaderPre(t = {}) {
+	async getHeaderPre(e = {}) {
 		if (!this.index) return;
-		let n = await this.index.parse(t), r = n.firstDataLine === void 0 ? void 0 : n.firstDataLine.blockPosition + J, i = await e(r === void 0 ? await this.bam.readFile() : await this.bam.read(r, 0)), a = new DataView(i.buffer);
+		let t = await this.index.parse(e), r = t.firstDataLine === void 0 ? void 0 : t.firstDataLine.blockPosition + J, i = await n(r === void 0 ? await this.bam.readFile() : await this.bam.read(r, 0)), a = new DataView(i.buffer);
 		if (a.getInt32(0, !0) !== 21840194) throw Error("Not a BAM file");
 		let o = a.getInt32(4, !0);
 		this.header = new TextDecoder("utf8").decode(i.subarray(8, 8 + o));
 		let s = o + 8, c = f(i, s, this.renameRefSeq);
-		if (c ||= (i = await e(await this.bam.readFile()), f(i, s, this.renameRefSeq)), !c) throw Error("Insufficient data for reference sequences");
+		if (c ||= (i = await n(await this.bam.readFile()), f(i, s, this.renameRefSeq)), !c) throw Error("Insufficient data for reference sequences");
 		return this.chrToIndex = c.chrToIndex, this.indexToChr = c.indexToChr, q(this.header);
 	}
 	getHeader(e) {
@@ -1329,8 +1329,8 @@ async function re({ url: e, headers: t }, n) {
 	});
 	return new Uint8Array(await a.arrayBuffer());
 }
-async function $(t, n) {
-	return h(await Promise.all(t.map(async (t) => e(await re(t, n)))));
+async function $(e, t) {
+	return h(await Promise.all(e.map(async (e) => n(await re(e, t)))));
 }
 var ie = class extends Z {
 	baseUrl;

package/dist/{esm-DQ3lJSQN.js → esm-JAiZmFIS.js}

@@ -1,4 +1,4 @@
-import { t as e } from "./esm-CGLz7idZ.js";
+import { n as e } from "./esm-BA6yMcc-.js";
 import { n as t } from "./esm-BdT7qUL-.js";
 //#region ../core/node_modules/@gmod/indexedfasta/esm/fetchableSmallFasta.js
 var n = new TextDecoder("utf8");

package/dist/framebufferReadback-CCLOjStu.js

@@ -0,0 +1,148 @@
+import { i as e } from "./color-W5zffv-z.js";
+import { y as t } from "./twgl-full.module-DB2UdP1k.js";
+import { a as n, n as r, o as i } from "./clipOptions-gqdb3fvW.js";
+import { t as a } from "./viewRenderingContext-HtpqwS_x.js";
+//#region ../core/src/view/renderingContext/bufferedViewRenderingContext.js
+var o = class extends a {
+	#e = [
+		0,
+		0,
+		0,
+		0
+	];
+	#t;
+	#n = [];
+	#r;
+	#i;
+	#a = /* @__PURE__ */ new Set();
+	#o;
+	#s = void 0;
+	#c = 1;
+	#l = {
+		width: 0,
+		height: 0
+	};
+	#u;
+	constructor(t, n) {
+		if (super(t), this.#i = n.webGLHelper, this.#r = n.framebufferInfo, this.#c = n.devicePixelRatio, this.#l = n.canvasSize, this.#o = n.markPredicate ?? (() => !0), this.#u = n.pixelOffset, n.clearColor) {
+			let t = e(n.clearColor).rgb();
+			this.#e = [
+				t.r / 255,
+				t.g / 255,
+				t.b / 255,
+				t.opacity
+			];
+		}
+	}
+	getDevicePixelRatio() {
+		return this.#c;
+	}
+	pushView(e, t) {
+		this.#a.add(e), this.#s = t;
+	}
+	renderMark(e, t) {
+		if (!this.#o(e) || this.globalOptions.picking && !e.isPickingParticipant()) return;
+		let r = e.render(t);
+		if (r) {
+			let a = n(t);
+			this.#n.push({
+				mark: e,
+				callback: r,
+				coords: this.#s,
+				clip: i(a, e.properties.clip, this.#s),
+				cullClip: a
+			});
+		}
+	}
+	render() {
+		if (this.#t || this.#d(), this.#t.length == 0) return;
+		let e = this.#i.gl, t = this.#r;
+		t ? (e.bindFramebuffer(e.FRAMEBUFFER, t.framebuffer), e.viewport(0, 0, t.width, t.height)) : e.viewport(0, 0, e.drawingBufferWidth, e.drawingBufferHeight), e.disable(e.SCISSOR_TEST), e.clearColor(...this.#e), e.clear(e.COLOR_BUFFER_BIT);
+		for (let e of this.#a) e.onBeforeRender();
+		for (let e of this.#t) e();
+		this.#r && e.bindFramebuffer(e.FRAMEBUFFER, null);
+	}
+	#d() {
+		this.#t = [];
+		let e = !0, n = !0, i = (t) => () => {
+			e && t();
+		}, a = (t) => () => {
+			e && n && t();
+		}, o = t(this.#n.reverse(), (e) => e.mark);
+		for (let [t, s] of [...o.entries()].reverse()) {
+			if (!t.isReady()) continue;
+			this.#t.push(() => {
+				e = t.unitView.getEffectiveOpacity() > 0;
+			}), this.#t.push(...t.prepareRender(this.globalOptions).map((e) => i(e)));
+			let o, c, l;
+			for (let e of s) {
+				let s = e.coords;
+				(!s.equals(o) || !r(e.clip, c) || !r(e.cullClip, l)) && this.#t.push(i(() => {
+					n = t.setViewport(this.#l, this.#c, s, e.clip, e.cullClip, this.#u);
+				})), this.#t.push(a(e.callback)), o = e.coords, c = e.clip, l = e.cullClip;
+			}
+		}
+	}
+};
+//#endregion
+//#region ../core/src/gl/framebufferReadback.js
+function s(e, t, n = {}) {
+	let r = n.x ?? 0, i = n.y ?? 0, a = n.width ?? t.width, o = n.height ?? t.height;
+	f(t, r, i, a, o);
+	let s = new Uint8Array(a * o * 4);
+	e.bindFramebuffer(e.FRAMEBUFFER, t.framebuffer);
+	try {
+		e.readPixels(r, t.height - i - o, a, o, e.RGBA, e.UNSIGNED_BYTE, s);
+	} finally {
+		e.bindFramebuffer(e.FRAMEBUFFER, null);
+	}
+	return {
+		pixels: d(s, a, o, n.unpremultiplyAlpha ?? !1),
+		width: a,
+		height: o
+	};
+}
+function c(e, t, n = "image/png", r = {}) {
+	return u(e, t, r).toDataURL(n);
+}
+function l(e, t, n = "image/png", r = {}) {
+	let i = u(e, t, r);
+	return new Promise((e, t) => {
+		i.toBlob((r) => {
+			r ? e(r) : t(/* @__PURE__ */ Error(`Could not encode framebuffer as ${n}.`));
+		}, n);
+	});
+}
+function u(e, t, n) {
+	let { pixels: r, width: i, height: a } = s(e, t, n), o = document.createElement("canvas");
+	o.width = i, o.height = a;
+	let c = o.getContext("2d"), l = c.createImageData(i, a);
+	return l.data.set(r), c.putImageData(l, 0, 0), o;
+}
+function d(e, t, n, r) {
+	let i = new Uint8ClampedArray(e.length), a = t * 4;
+	for (let t = 0; t < n; t++) {
+		let r = (n - t - 1) * a, o = t * a;
+		i.set(e.subarray(r, r + a), o);
+	}
+	if (r) for (let e = 0; e < i.length; e += 4) {
+		let t = i[e + 3];
+		if (t == 0) i[e] = 0, i[e + 1] = 0, i[e + 2] = 0;
+		else if (t < 255) {
+			let n = 255 / t;
+			i[e] = Math.round(i[e] * n), i[e + 1] = Math.round(i[e + 1] * n), i[e + 2] = Math.round(i[e + 2] * n);
+		}
+	}
+	return i;
+}
+function f(e, t, n, r, i) {
+	if (![
+		t,
+		n,
+		r,
+		i
+	].every(Number.isInteger)) throw RangeError("Framebuffer readback bounds must be integers.");
+	if (t < 0 || n < 0 || r <= 0 || i <= 0 || t + r > e.width || n + i > e.height) throw RangeError("Framebuffer readback bounds are out of range.");
+}
+//#endregion
+export { c as n, o as r, l as t };