@genome-spy/core 0.75.0 → 0.77.0

package/dist/src/view/viewSelectors.js

@@ -13,13 +13,15 @@ import {
  */
 
 /**
- * @typedef {{ scope: string[], view: string }} ViewSelector
- * @typedef {{ scope: string[], param: string }} ParamSelector
+ * @typedef {import("./viewUtilTypes.d.ts").ViewSelector} ViewSelector
+ * @typedef {import("./viewUtilTypes.d.ts").ParamSelector} ParamSelector
  * @typedef {{ view: import("./view.js").default, param: import("../spec/parameter.js").Parameter, selector: ParamSelector }} BookmarkableParamEntry
  * @typedef {{ message: string, scope: string[] }} SelectorValidationIssue
  * @typedef {{ name: string | null }} ImportScopeInfo
  * @typedef {"exclude" | "excludeSubtree"} AddressableOverride
+ * @typedef {"exclude" | "excludeSubtree"} ChromeOverride
  * @typedef {{ skipSubtree?: boolean }} AddressableOptions
+ * @typedef {{ skipSubtree?: boolean }} ChromeOptions
  * @typedef {{ view: import("./view.js").default, param: import("../spec/parameter.js").Parameter }} ResolvedParam
  */
 
@@ -31,6 +33,9 @@ const importScopes = new WeakMap();
 /** @type {WeakMap<import("./view.js").default, AddressableOverride>} */
 const addressableOverrides = new WeakMap();
 
+/** @type {WeakMap<import("./view.js").default, ChromeOverride>} */
+const chromeOverrides = new WeakMap();
+
 /**
  * Marks a view as the root of an import scope.
  *
@@ -67,6 +72,28 @@ export function markViewAsNonAddressable(view, options = {}) {
     addressableOverrides.set(view, behavior);
 }
 
+/**
+ * Marks a view as decorative chrome.
+ *
+ * @param {import("./view.js").default} view
+ * @param {ChromeOptions} [options]
+ */
+export function markViewAsChrome(view, options = {}) {
+    const skipSubtree = options.skipSubtree ?? false;
+    const behavior = skipSubtree ? "excludeSubtree" : "exclude";
+    chromeOverrides.set(view, behavior);
+}
+
+/**
+ * Returns whether a view has been marked as decorative chrome.
+ *
+ * @param {import("./view.js").default} view
+ * @returns {boolean}
+ */
+export function isChromeView(view) {
+    return chromeOverrides.has(view);
+}
+
 /**
  * Returns the import scope chain for a view, using named import instances.
  *
@@ -158,6 +185,44 @@ export function getAddressableViews(root) {
     return views;
 }
 
+/**
+ * Visits all non-chrome views in the hierarchy.
+ *
+ * @param {import("./view.js").default} root
+ * @param {import("./view.js").Visitor} visitor
+ */
+export function visitNonChromeViews(root, visitor) {
+    root.visit((view) => {
+        const behavior = chromeOverrides.get(view);
+        if (behavior === "excludeSubtree") {
+            return VISIT_SKIP;
+        }
+
+        if (behavior === "exclude") {
+            return;
+        }
+
+        return visitor(view);
+    });
+}
+
+/**
+ * Returns non-chrome views in the hierarchy.
+ *
+ * @param {import("./view.js").default} root
+ * @returns {import("./view.js").default[]}
+ */
+export function getNonChromeViews(root) {
+    /** @type {import("./view.js").default[]} */
+    const views = [];
+
+    visitNonChromeViews(root, (view) => {
+        views.push(view);
+    });
+
+    return views;
+}
+
 /**
  * Visits all addressable views in the hierarchy.
  *

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

@@ -0,0 +1,15 @@
+/**
+ * Structured view address used by selectors.
+ */
+export interface ViewSelector {
+    scope: string[];
+    view: string;
+}
+
+/**
+ * Structured parameter address used by selectors.
+ */
+export interface ParamSelector {
+    scope: string[];
+    param: string;
+}

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

@@ -1 +1 @@
-{"version":3,"file":"viewUtils.d.ts","sourceRoot":"","sources":["../../../src/view/viewUtils.js"],"names":[],"mappings":"AAUA;;;;GAIG;AACH,qCAHW,OAAO,oBAAoB,EAAE,UAAU,GAAG,OAAO,iBAAiB,EAAE,YAAY,GAC9E,IAAI,IAAI,aAAa,CAIjC;AAED;;;;GAIG;AACH,oCAHW,OAAO,oBAAoB,EAAE,aAAa,GAAG,OAAO,iBAAiB,EAAE,YAAY,GACjF,IAAI,IAAI,YAAY,CAOhC;AAED;;;GAGG;AACH,+BAFW,IAAI,6EAMd;AAED;;;;GAIG;AACH,wCAFW,IAAI,8CASd;AAED;;GAEG;AACH,kDAFW,IAAI,QAiBd;AAED;;;;;;;GAOG;AACH,4CAFW,IAAI,QAUd;AAED;;;;GAIG;AACH,0DAJW,OAAO,CAAC,OAAO,kBAAkB,EAAE,OAAO,CAAC,EAAE,mBAC7C,MAAM,OAAO,GACX,OAAO,CAAC,IAAI,CAAC,CAmBzB;AAED;;;GAGG;AACH,wCAFW,IAAI;UAGO,QAAQ;aAAW,OAAO,oBAAoB,EAAE,OAAO;WAAS,OAAO,oBAAoB,EAAE,KAAK;UAAQ,OAAO,oBAAoB,EAAE,IAAI;IAwDhK;AAED;;;;;GAKG;AACH,2CALW,OAAO,iBAAiB,EAAE,UAAU,WACpC,MAAM,eACN,OAAO,yBAAyB,EAAE,OAAO,GACvC,OAAO,CAAC,OAAO,iBAAiB,EAAE,QAAQ,CAAC,CAqCvD;AAED;;GAEG;AACH,yCAFW,CAAS,IAAI,EAAJ,IAAI,EAAE,IAAM,EAAN,IAAI,EAAE,KAAE,IAAI,+BAkBrC;AAED;;;GAGG;AACH,0CAFW,IAAI,eAqBd;AAED;;GAEG;AACH,8CAFW,OAAO,WAAW,EAAE,OAAO;;;EAoBrC;iBA9R4C,WAAW;qBAFnC,eAAe"}
+{"version":3,"file":"viewUtils.d.ts","sourceRoot":"","sources":["../../../src/view/viewUtils.js"],"names":[],"mappings":"AAUA;;;;GAIG;AACH,qCAHW,OAAO,oBAAoB,EAAE,UAAU,GAAG,OAAO,iBAAiB,EAAE,YAAY,GAC9E,IAAI,IAAI,aAAa,CAIjC;AAED;;;;GAIG;AACH,oCAHW,OAAO,oBAAoB,EAAE,aAAa,GAAG,OAAO,iBAAiB,EAAE,YAAY,GACjF,IAAI,IAAI,YAAY,CAOhC;AAED;;;GAGG;AACH,+BAFW,IAAI,6EAMd;AAED;;;;GAIG;AACH,wCAFW,IAAI,8CASd;AAED;;GAEG;AACH,kDAFW,IAAI,QAiBd;AAED;;;;;;;GAOG;AACH,4CAFW,IAAI,QAUd;AAED;;;;GAIG;AACH,0DAJW,OAAO,CAAC,OAAO,kBAAkB,EAAE,OAAO,CAAC,EAAE,mBAC7C,MAAM,OAAO,GACX,OAAO,CAAC,IAAI,CAAC,CAmBzB;AAED;;;GAGG;AACH,wCAFW,IAAI;UAGO,QAAQ;aAAW,OAAO,oBAAoB,EAAE,OAAO;WAAS,OAAO,oBAAoB,EAAE,KAAK;UAAQ,OAAO,oBAAoB,EAAE,IAAI;IAkEhK;AAED;;;;;GAKG;AACH,2CALW,OAAO,iBAAiB,EAAE,UAAU,WACpC,MAAM,eACN,OAAO,yBAAyB,EAAE,OAAO,GACvC,OAAO,CAAC,OAAO,iBAAiB,EAAE,QAAQ,CAAC,CAqCvD;AAED;;GAEG;AACH,yCAFW,CAAS,IAAI,EAAJ,IAAI,EAAE,IAAM,EAAN,IAAI,EAAE,KAAE,IAAI,+BAkBrC;AAED;;;GAGG;AACH,0CAFW,IAAI,eAqBd;AAED;;GAEG;AACH,8CAFW,OAAO,WAAW,EAAE,OAAO;;;EAoBrC;iBAxS4C,WAAW;qBAFnC,eAAe"}

package/dist/src/view/viewUtils.js

@@ -149,6 +149,16 @@ export function findEncodedFields(view) {
                             definition.type
                         ),
                     });
+                } else if (
+                    isFieldDef(definition) &&
+                    channel === "semanticScore"
+                ) {
+                    fieldInfos.push({
+                        view,
+                        channel,
+                        field: definition.field,
+                        type: "quantitative",
+                    });
                 }
 
                 if ("condition" in definition) {

package/package.json

@@ -7,7 +7,7 @@
   },
   "contributors": [],
   "license": "MIT",
-  "version": "0.75.0",
+  "version": "0.77.0",
   "jsdelivr": "dist/bundle/index.js",
   "unpkg": "dist/bundle/index.js",
   "browser": "dist/bundle/index.js",
@@ -46,7 +46,7 @@
   },
   "dependencies": {
     "@gmod/bam": "^7.1.19",
-    "@gmod/bbi": "^9.0.0",
+    "@gmod/bbi": "^9.2.0",
     "@gmod/bed": "^2.1.10",
     "@gmod/indexedfasta": "^5.0.2",
     "@gmod/tabix": "^3.2.2",
@@ -78,5 +78,5 @@
   "devDependencies": {
     "@types/long": "^4.0.1"
   },
-  "gitHead": "c641f51070e075b989f29c8b9c6ad1879ce77a6f"
+  "gitHead": "2851e22e2069a70d7d02e3ab707b7556573aa17e"
 }

package/dist/bundle/browser-BTgw5ieH.js

@@ -1,126 +0,0 @@
-import { t as e } from "./chunk-DmhlhrBa.js";
-//#region ../../node_modules/generic-filehandle2/esm/blobFile.js
-var t = class {
-	constructor(e) {
-		this.blob = e;
-	}
-	async read(e, t = 0) {
-		if (!e) return new Uint8Array();
-		let n = t, r = n + e, i = this.blob.slice(n, r);
-		return i.bytes ? i.bytes() : new Uint8Array(await i.arrayBuffer());
-	}
-	async readFile(e) {
-		let t = typeof e == "string" ? e : e?.encoding;
-		if (t === "utf8") return this.blob.text();
-		if (t) throw Error(`unsupported encoding: ${t}`);
-		return this.blob.bytes ? this.blob.bytes() : new Uint8Array(await this.blob.arrayBuffer());
-	}
-	async stat() {
-		return { size: this.blob.size };
-	}
-	async close() {}
-};
-//#endregion
-//#region ../../node_modules/generic-filehandle2/esm/remoteFile.js
-function n(e) {
-	return (typeof e == "object" && e && "message" in e ? e.message : `${e}`).replace(/\.$/, "");
-}
-var r = class {
-	constructor(e, t = {}) {
-		this.baseOverrides = {}, this.url = e;
-		let n = t.fetch || globalThis.fetch.bind(globalThis);
-		t.overrides && (this.baseOverrides = t.overrides), this.fetchImplementation = n;
-	}
-	async fetch(e, t) {
-		let r = (t) => Error(`${n(t)} fetching ${e}`, { cause: t }), i;
-		try {
-			i = await this.fetchImplementation(e, t);
-		} catch (n) {
-			if (`${n}`.includes("Failed to fetch")) {
-				console.warn(`generic-filehandle: refetching ${e} to attempt to work around chrome CORS header caching bug`);
-				try {
-					i = await this.fetchImplementation(e, {
-						...t,
-						cache: "reload"
-					});
-				} catch (e) {
-					throw r(e);
-				}
-			} else throw r(n);
-		}
-		return i;
-	}
-	async read(e, t, n = {}) {
-		if (e === 0) return new Uint8Array();
-		let { headers: r = {}, signal: i, overrides: a = {} } = n;
-		e < Infinity ? r.range = `bytes=${t}-${t + e - 1}` : e === Infinity && t !== 0 && (r.range = `bytes=${t}-`);
-		let o = await this.fetch(this.url, {
-			...this.baseOverrides,
-			...a,
-			headers: {
-				...this.baseOverrides.headers,
-				...a.headers,
-				...r
-			},
-			method: "GET",
-			redirect: "follow",
-			mode: "cors",
-			signal: i
-		});
-		if (!o.ok) throw Error(`HTTP ${o.status} fetching ${this.url}`);
-		if (o.status === 200 && t === 0 || o.status === 206) {
-			let t = o.headers.get("content-range"), n = /\/(\d+)$/.exec(t || "");
-			n?.[1] && (this._stat = { size: parseInt(n[1], 10) });
-			let r = o.bytes ? await o.bytes() : new Uint8Array(await o.arrayBuffer());
-			return r.byteLength <= e ? r : r.subarray(0, e);
-		}
-		throw Error(o.status === 200 ? `${this.url} fetch returned status 200, expected 206` : `HTTP ${o.status} fetching ${this.url}`);
-	}
-	async readFile(e = {}) {
-		let t, n;
-		if (typeof e == "string") t = e, n = {};
-		else {
-			t = e.encoding;
-			let { encoding: r, ...i } = e;
-			n = i;
-		}
-		let { headers: r = {}, signal: i, overrides: a = {} } = n, o = await this.fetch(this.url, {
-			...this.baseOverrides,
-			...a,
-			headers: {
-				...this.baseOverrides.headers,
-				...a.headers,
-				...r
-			},
-			method: "GET",
-			redirect: "follow",
-			mode: "cors",
-			signal: i
-		});
-		if (!o.ok) throw Error(`HTTP ${o.status} fetching ${this.url}`);
-		if (t === "utf8") return o.text();
-		if (t) throw Error(`unsupported encoding: ${t}`);
-		return o.bytes ? o.bytes() : new Uint8Array(await o.arrayBuffer());
-	}
-	async stat() {
-		if (!this._stat && (await this.read(10, 0), !this._stat)) throw Error(`unable to determine size of file at ${this.url}`);
-		return this._stat;
-	}
-	async close() {}
-}, i = /* @__PURE__ */ e({
-	BlobFile: () => t,
-	LocalFile: () => a,
-	RemoteFile: () => r
-}), a = class {
-	readFile() {
-		throw Error("unimplemented");
-	}
-	read() {
-		throw Error("unimplemented");
-	}
-	close() {
-		throw Error("unimplemented");
-	}
-};
-//#endregion
-export { i as n, r, a as t };