@jbrowse/core 3.1.0 → 3.2.0

package/util/Base1DUtils.js

@@ -44,7 +44,7 @@ function moveTo(self, start, end) {
         extraBp = ((newBpPerPx - targetBpPerPx) * self.width) / 2;
     }
     let bpToStart = -extraBp;
-    for (let i = 0; i < self.displayedRegions.length; i += 1) {
+    for (let i = 0; i < self.displayedRegions.length; i++) {
         const region = self.displayedRegions[i];
         if (start.index === i) {
             bpToStart += start.offset;

package/util/analytics.js

@@ -68,9 +68,9 @@ async function writeGAAnalytics(rootModel, initialTimestamp) {
     analyticsScript += `ga('create', '${jbrowseUser}', 'auto', 'jbrowseTracker');`;
     const gaData = {};
     const googleDimensions = 'tracks-count ver electron loadTime pluginNames';
-    googleDimensions.split(/\s+/).forEach((key, index) => {
+    for (const [index, key] of googleDimensions.split(/\s+/).entries()) {
         gaData[`dimension${index + 1}`] = stats[key];
-    });
+    }
     gaData.metric1 = Math.round(stats.loadTime);
     analyticsScript += `ga('jbrowseTracker.send', 'pageview',${JSON.stringify(gaData)});`;
     const analyticsScriptNode = document.createElement('script');

package/util/idMaker.d.ts

@@ -1 +1 @@
-export default function idMaker(args: Record<string, unknown>, id?: string, len?: number): number;
+export default function idMaker(args: Record<string, unknown>, id?: string, len?: number): string | number;

package/util/idMaker.js

@@ -20,5 +20,5 @@ function idMaker(args, id = '', len = 5000) {
             }
         }
     }
-    return (0, _1.hashCode)(id);
+    return `adp-${(0, _1.hashCode)(id)}`;
 }

package/util/index.d.ts

@@ -192,7 +192,8 @@ export interface ViewSnap {
     })[];
 }
 export declare function isSupportedIndexingAdapter(type?: string): boolean;
-export declare function getBpDisplayStr(totalBp: number): string;
+export declare function getBpDisplayStr(total: number): string;
+export declare function getProgressDisplayStr(current: number, total: number): string;
 export declare function toLocale(n: number): string;
 export declare function getTickDisplayStr(totalBp: number, bpPerPx: number): string;
 export declare function getViewParams(model: IAnyStateTreeNode, exportSVG?: boolean): {
@@ -257,6 +258,7 @@ export declare function fetchAndMaybeUnzipText(loc: GenericFilehandle, opts?: Ba
 export declare function isObject(x: unknown): x is Record<string | symbol | number, unknown>;
 export declare function localStorageGetNumber(key: string, defaultVal: number): number;
 export declare function localStorageGetBoolean(key: string, defaultVal: boolean): boolean;
+export declare function forEachWithStopTokenCheck<T>(iter: Iterable<T>, stopToken: string | undefined, arg: (arg: T) => void, durationMs?: number): void;
 export declare function testAdapter(fileName: string, regex: RegExp, adapterHint: string | undefined, expected: string): boolean;
 export { type Feature, type SimpleFeatureSerialized, type SimpleFeatureSerializedNoId, default as SimpleFeature, isFeature, } from './simpleFeature';
 export { blobToDataURL } from './blobToDataURL';

package/util/index.js

@@ -63,6 +63,7 @@ exports.objectHash = objectHash;
 exports.bytesForRegions = bytesForRegions;
 exports.isSupportedIndexingAdapter = isSupportedIndexingAdapter;
 exports.getBpDisplayStr = getBpDisplayStr;
+exports.getProgressDisplayStr = getProgressDisplayStr;
 exports.toLocale = toLocale;
 exports.getTickDisplayStr = getTickDisplayStr;
 exports.getViewParams = getViewParams;
@@ -94,6 +95,7 @@ exports.fetchAndMaybeUnzipText = fetchAndMaybeUnzipText;
 exports.isObject = isObject;
 exports.localStorageGetNumber = localStorageGetNumber;
 exports.localStorageGetBoolean = localStorageGetBoolean;
+exports.forEachWithStopTokenCheck = forEachWithStopTokenCheck;
 exports.testAdapter = testAdapter;
 const react_1 = require("react");
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
@@ -589,8 +591,8 @@ function reverse(str) {
 function complement(str) {
     var _a;
     let comp = '';
-    for (let i = 0; i < str.length; i++) {
-        comp += (_a = exports.complementTable[str[i]]) !== null && _a !== void 0 ? _a : str[i];
+    for (const element of str) {
+        comp += (_a = exports.complementTable[element]) !== null && _a !== void 0 ? _a : element;
     }
     return comp;
 }
@@ -691,7 +693,7 @@ exports.defaultCodonTable = {
 };
 function generateCodonTable(table) {
     const tempCodonTable = {};
-    Object.keys(table).forEach(codon => {
+    for (const codon of Object.keys(table)) {
         const aa = table[codon];
         const nucs = [];
         for (let i = 0; i < 3; i++) {
@@ -711,7 +713,7 @@ function generateCodonTable(table) {
                 }
             }
         }
-    });
+    }
     return tempCodonTable;
 }
 async function updateStatus(msg, cb, fn) {
@@ -760,15 +762,29 @@ function isSupportedIndexingAdapter(type = '') {
         'VcfAdapter',
     ].includes(type);
 }
-function getBpDisplayStr(totalBp) {
-    if (Math.floor(totalBp / 1000000) > 0) {
-        return `${Number.parseFloat((totalBp / 1000000).toPrecision(3))}Mbp`;
+function getBpDisplayStr(total) {
+    if (Math.floor(total / 1000000) > 0) {
+        return `${r(total / 1000000)}Mbp`;
+    }
+    else if (Math.floor(total / 1000) > 0) {
+        return `${r(total / 1000)}Kbp`;
+    }
+    else {
+        return `${Math.floor(total)}bp`;
+    }
+}
+function r(s) {
+    return toLocale(Number.parseFloat(s.toPrecision(3)));
+}
+function getProgressDisplayStr(current, total) {
+    if (Math.floor(total / 1000000) > 0) {
+        return `${r(current / 1000000)}/${r(total / 1000000)}Mb`;
     }
-    else if (Math.floor(totalBp / 1000) > 0) {
-        return `${Number.parseFloat((totalBp / 1000).toPrecision(3))}Kbp`;
+    else if (Math.floor(total / 1000) > 0) {
+        return `${r(current / 1000)}/${r(total / 1000)}Kb`;
     }
     else {
-        return `${toLocale(Math.floor(totalBp))}bp`;
+        return `${r(current)}/${r(total)}}bytes`;
     }
 }
 function toLocale(n) {
@@ -988,6 +1004,16 @@ function localStorageGetNumber(key, defaultVal) {
 function localStorageGetBoolean(key, defaultVal) {
     return Boolean(JSON.parse(localStorageGetItem(key) || JSON.stringify(defaultVal)));
 }
+function forEachWithStopTokenCheck(iter, stopToken, arg, durationMs = 400) {
+    let start = performance.now();
+    for (const t of iter) {
+        if (performance.now() - start > durationMs) {
+            (0, stopToken_1.checkStopToken)(stopToken);
+            start = performance.now();
+        }
+        arg(t);
+    }
+}
 function testAdapter(fileName, regex, adapterHint, expected) {
     return (regex.test(fileName) && !adapterHint) || adapterHint === expected;
 }

package/util/layouts/PrecomputedMultiLayout.js

@@ -13,9 +13,9 @@ class ThrowingLayout {
 class PrecomputedMultiLayout extends MultiLayout_1.default {
     constructor(json) {
         super(ThrowingLayout);
-        Object.entries(json).forEach(([layoutName, sublayoutJson]) => {
+        for (const [layoutName, sublayoutJson] of Object.entries(json)) {
             this.subLayouts.set(layoutName, new PrecomputedLayout_1.default(sublayoutJson));
-        });
+        }
     }
 }
 exports.default = PrecomputedMultiLayout;

package/util/map-obj.js

@@ -13,12 +13,12 @@ function map(object, mapper, isSeen = new WeakSet()) {
     }
     isSeen.add(object);
     const mapArray = (array) => {
-        array.forEach(element => {
+        for (const element of array) {
             mapper(element);
             if (isObject(element)) {
                 map(element, mapper, isSeen);
             }
-        });
+        }
     };
     if (Array.isArray(object)) {
         mapArray(object);

package/util/rxjs.d.ts

@@ -1,3 +1,3 @@
 import { Observable } from 'rxjs';
 import type { Observer } from 'rxjs';
-export declare function ObservableCreate<T>(func: (arg: Observer<T>) => void | Promise<void>, _stopToken?: string): Observable<T>;
+export declare function ObservableCreate<T>(func: (arg: Observer<T>) => void | Promise<void>, stopToken?: string): Observable<T>;

package/util/rxjs.js

@@ -2,7 +2,9 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.ObservableCreate = ObservableCreate;
 const rxjs_1 = require("rxjs");
-function ObservableCreate(func, _stopToken) {
+const stopToken_1 = require("./stopToken");
+function ObservableCreate(func, stopToken) {
+    (0, stopToken_1.checkStopToken)(stopToken);
     return new rxjs_1.Observable((observer) => {
         try {
             const ret = func(observer);

package/util/stopToken.d.ts

@@ -1,3 +1,3 @@
 export declare function createStopToken(): string;
 export declare function stopStopToken(stopToken: string): void;
-export declare function checkStopToken(stopToken?: string): void;
+export declare function checkStopToken(stopToken: string | undefined): void;