@jbrowse/core 3.1.0 → 3.3.0

package/ui/DataGridFlexContainer.d.ts

@@ -0,0 +1,3 @@
+export default function DataGridFlexContainer({ children, }: {
+    children: React.ReactNode;
+}): import("react/jsx-runtime").JSX.Element;

package/ui/DataGridFlexContainer.js

@@ -0,0 +1,15 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = DataGridFlexContainer;
+const jsx_runtime_1 = require("react/jsx-runtime");
+const mui_1 = require("tss-react/mui");
+const useStyles = (0, mui_1.makeStyles)()({
+    flexContainer: {
+        display: 'flex',
+        flexDirection: 'column',
+    },
+});
+function DataGridFlexContainer({ children, }) {
+    const { classes } = useStyles();
+    return (0, jsx_runtime_1.jsx)("div", { className: classes.flexContainer, children: children });
+}

package/ui/theme.js

@@ -10,8 +10,8 @@ const colors_1 = require("@mui/material/colors");
 const styles_1 = require("@mui/material/styles");
 const deepmerge_1 = __importDefault(require("deepmerge"));
 const refTheme = (0, styles_1.createTheme)();
-const midnight = '#0D233F';
-const grape = '#721E63';
+const midnight = refTheme.palette.augmentColor({ color: { main: '#0D233F' } });
+const grape = refTheme.palette.augmentColor({ color: { main: '#721E63' } });
 const forest = refTheme.palette.augmentColor({ color: { main: '#135560' } });
 const mandarin = refTheme.palette.augmentColor({ color: { main: '#FFB11D' } });
 const lightgrey = refTheme.palette.augmentColor({ color: { main: '#aaa' } });
@@ -47,6 +47,9 @@ const hardclip = '#f00';
 const softclip = '#00f';
 const skip = '#97b8c9';
 const defaults = {
+    primary: midnight,
+    secondary: grape,
+    tertiary: forest,
     quaternary: mandarin,
     highlight: mandarin,
     stopCodon,
@@ -65,9 +68,6 @@ function stockTheme() {
         palette: {
             ...defaults,
             mode: undefined,
-            primary: { main: midnight },
-            secondary: { main: grape },
-            tertiary: forest,
         },
         components: {
             MuiLink: {

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/cluster.d.ts

@@ -0,0 +1,17 @@
+export declare function euclideanDistance(a: number[], b: number[]): number;
+export declare function averageDistance(setA: number[], setB: number[], distances: number[][]): number;
+export declare function clusterData({ data, distance, linkage, onProgress, stopToken, }: {
+    data: number[][];
+    distance?: (a: number[], b: number[]) => number;
+    linkage?: (a: number[], b: number[], distances: number[][]) => number;
+    onProgress?: (a: string) => void;
+    stopToken?: string;
+}): {
+    clusters: {
+        height: number;
+        indexes: number[];
+    } | undefined;
+    distances: number[][];
+    order: number[];
+    clustersGivenK: number[][][];
+};

package/util/cluster.js

@@ -0,0 +1,96 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.euclideanDistance = euclideanDistance;
+exports.averageDistance = averageDistance;
+exports.clusterData = clusterData;
+const stopToken_1 = require("@jbrowse/core/util/stopToken");
+function toP(n) {
+    return Number.parseFloat((n * 100).toFixed(1));
+}
+function euclideanDistance(a, b) {
+    const size = Math.min(a.length, b.length);
+    let sum = 0;
+    for (let index = 0; index < size; index++) {
+        sum += (a[index] - b[index]) * (a[index] - b[index]);
+    }
+    return Math.sqrt(sum);
+}
+function averageDistance(setA, setB, distances) {
+    let distance = 0;
+    const lenA = setA.length;
+    const lenB = setB.length;
+    for (let i = 0; i < lenA; i++) {
+        for (let j = 0; j < lenB; j++) {
+            distance += distances[setA[i]][setB[j]];
+        }
+    }
+    return distance / setA.length / setB.length;
+}
+function clusterData({ data, distance = euclideanDistance, linkage = averageDistance, onProgress, stopToken, }) {
+    let start = performance.now();
+    const distances = [];
+    for (let i = 0; i < data.length; i++) {
+        if (performance.now() - start > 400) {
+            (0, stopToken_1.checkStopToken)(stopToken);
+            start = performance.now();
+        }
+        if (onProgress) {
+            onProgress(`Making distance matrix: ${toP(i / (data.length - 1))}%`);
+        }
+        const row = [];
+        for (let j = 0; j < data.length; j++) {
+            row.push(distance(data[i], data[j]));
+        }
+        distances.push(row);
+    }
+    const clusters = data.map((_datum, index) => ({
+        height: 0,
+        indexes: [Number(index)],
+    }));
+    let clustersGivenK = [];
+    start = performance.now();
+    for (let iteration = 0; iteration < data.length; iteration++) {
+        if (performance.now() - start > 400) {
+            (0, stopToken_1.checkStopToken)(stopToken);
+            start = performance.now();
+        }
+        if (onProgress) {
+            onProgress(`Clustering: ${toP((iteration + 1) / data.length)}%`);
+        }
+        clustersGivenK.push(clusters.map(cluster => cluster.indexes));
+        if (iteration >= data.length - 1) {
+            break;
+        }
+        let nearestDistance = Infinity;
+        let nearestRow = 0;
+        let nearestCol = 0;
+        for (let row = 0; row < clusters.length; row++) {
+            for (let col = row + 1; col < clusters.length; col++) {
+                const distance = linkage(clusters[row].indexes, clusters[col].indexes, distances);
+                if (distance < nearestDistance) {
+                    nearestDistance = distance;
+                    nearestRow = row;
+                    nearestCol = col;
+                }
+            }
+        }
+        const newCluster = {
+            indexes: [
+                ...clusters[nearestRow].indexes,
+                ...clusters[nearestCol].indexes,
+            ],
+            height: nearestDistance,
+            children: [clusters[nearestRow], clusters[nearestCol]],
+        };
+        clusters.splice(Math.max(nearestRow, nearestCol), 1);
+        clusters.splice(Math.min(nearestRow, nearestCol), 1);
+        clusters.push(newCluster);
+    }
+    clustersGivenK = [[], ...clustersGivenK.reverse()];
+    return {
+        clusters: clusters[0],
+        distances: distances,
+        order: clusters[0].indexes,
+        clustersGivenK: clustersGivenK,
+    };
+}

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

@@ -75,6 +75,7 @@ export declare function renameRegionsIfNeeded<ARGTYPE extends {
 }>;
 export declare function minmax(a: number, b: number): readonly [number, number];
 export declare function shorten(name: string, max?: number, short?: number): string;
+export declare function shorten2(name: string, max?: number): string;
 export declare function stringify({ refName, coord, assemblyName, oob, }: {
     assemblyName?: string;
     coord: number;
@@ -192,7 +193,8 @@ 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 +259,7 @@ 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, idx: number) => 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

@@ -49,6 +49,7 @@ exports.renameRegionIfNeeded = renameRegionIfNeeded;
 exports.renameRegionsIfNeeded = renameRegionsIfNeeded;
 exports.minmax = minmax;
 exports.shorten = shorten;
+exports.shorten2 = shorten2;
 exports.stringify = stringify;
 exports.revcom = revcom;
 exports.reverse = reverse;
@@ -63,6 +64,7 @@ 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 +96,7 @@ 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");
@@ -528,6 +531,9 @@ function shorten(name, max = 70, short = 30) {
         ? `${name.slice(0, short)}...${name.slice(-short)}`
         : name;
 }
+function shorten2(name, max = 70) {
+    return name.length > max ? `${name.slice(0, max)}...` : name;
+}
 function stringify({ refName, coord, assemblyName, oob, }, useAssemblyName) {
     return [
         assemblyName && useAssemblyName ? `{${assemblyName}}` : '',
@@ -589,8 +595,8 @@ 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 +697,7 @@ 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 +717,7 @@ function generateCodonTable(table) {
                 }
             }
         }
-    });
+    }
     return tempCodonTable;
 }
 async function updateStatus(msg, cb, fn) {
@@ -760,15 +766,29 @@ 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(totalBp / 1000) > 0) {
-        return `${Number.parseFloat((totalBp / 1000).toPrecision(3))}Kbp`;
+    else if (Math.floor(total / 1000) > 0) {
+        return `${r(total / 1000)}Kbp`;
     }
     else {
-        return `${toLocale(Math.floor(totalBp))}bp`;
+        return `${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(total / 1000) > 0) {
+        return `${r(current / 1000)}/${r(total / 1000)}Kb`;
+    }
+    else {
+        return `${r(current)}/${r(total)}}bytes`;
     }
 }
 function toLocale(n) {
@@ -988,6 +1008,17 @@ 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();
+    let i = 0;
+    for (const t of iter) {
+        if (performance.now() - start > durationMs) {
+            (0, stopToken_1.checkStopToken)(stopToken);
+            start = performance.now();
+        }
+        arg(t, i++);
+    }
+}
 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/offscreenCanvasUtils.d.ts

@@ -1,18 +1,18 @@
-export type RenderReturn = Record<string, unknown> | undefined;
-type RendererRet = Promise<RenderReturn> | RenderReturn;
-export declare function renderToAbstractCanvas(width: number, height: number, opts: {
-    exportSVG?: {
-        rasterizeLayers?: boolean;
-        scale?: number;
-    };
+interface ExportSVGOptions {
+    rasterizeLayers?: boolean;
+    scale?: number;
+}
+interface RenderToAbstractCanvasOptions {
+    exportSVG?: ExportSVGOptions;
     highResolutionScaling?: number;
-}, cb: (ctx: CanvasRenderingContext2D) => RendererRet): Promise<{
+}
+export declare function renderToAbstractCanvas<T>(width: number, height: number, opts: RenderToAbstractCanvasOptions, cb: (ctx: CanvasRenderingContext2D) => T): Promise<(Awaited<T> & {
     canvasRecordedData: any;
-} | {
+}) | (Awaited<T> & {
     reactElement: import("react/jsx-runtime").JSX.Element;
-} | {
+}) | (Awaited<T> & {
     imageData: any;
-}>;
+})>;
 export declare function getSerializedSvg(results: {
     width: number;
     height: number;

package/util/offscreenCanvasUtils.js

@@ -80,7 +80,10 @@ async function renderToAbstractCanvas(width, height, opts, cb) {
         }
         ctx.scale(s, s);
         const result = await cb(ctx);
-        return { ...result, imageData: await (0, offscreenCanvasPonyfill_1.createImageBitmap)(canvas) };
+        return {
+            ...result,
+            imageData: await (0, offscreenCanvasPonyfill_1.createImageBitmap)(canvas),
+        };
     }
 }
 async function getSerializedSvg(results) {

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;