@jbrowse/core 2.16.1 → 2.17.0

package/ui/AssemblySelector.js

@@ -57,9 +57,12 @@ const AssemblySelector = (0, mobx_react_1.observer)(function ({ session, onChang
         }
     }, [selection, onChange, selected]);
     const error = assemblyNames.length ? '' : 'No configured assemblies';
-    return (react_1.default.createElement(material_1.TextField, { select: true, label: "Assembly", variant: "outlined", helperText: error || helperText, value: selection || '', inputProps: { 'data-testid': 'assembly-selector' }, onChange: event => {
+    return (react_1.default.createElement(material_1.TextField, { select: true, label: "Assembly", variant: "outlined", helperText: error || helperText, value: selection || '', onChange: event => {
             setLastSelected(event.target.value);
-        }, error: !!error, InputProps: InputProps, disabled: !!error, className: classes.importFormEntry, ...TextFieldProps }, assemblyNames.map(name => {
+        }, error: !!error, disabled: !!error, className: classes.importFormEntry, ...TextFieldProps, slotProps: {
+            input: InputProps,
+            htmlInput: { 'data-testid': 'assembly-selector' },
+        } }, assemblyNames.map(name => {
         const assembly = assemblyManager.get(name);
         const displayName = assembly ? (0, configuration_1.getConf)(assembly, 'displayName') : '';
         return (react_1.default.createElement(material_1.MenuItem, { key: name, value: name }, displayName || name));

package/ui/FileSelector/UrlChooser.js

@@ -8,11 +8,13 @@ const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
 const types_1 = require("../../util/types");
 const UrlChooser = (0, mobx_react_1.observer)(function ({ location, setLocation, label, }) {
-    return (react_1.default.createElement(material_1.TextField, { fullWidth: true, variant: "outlined", inputProps: { 'data-testid': 'urlInput' }, defaultValue: location && (0, types_1.isUriLocation)(location) ? location.uri : '', label: label || 'Enter URL', onChange: event => {
+    return (react_1.default.createElement(material_1.TextField, { fullWidth: true, variant: "outlined", defaultValue: location && (0, types_1.isUriLocation)(location) ? location.uri : '', label: label || 'Enter URL', onChange: event => {
             setLocation({
                 uri: event.target.value.trim(),
                 locationType: 'UriLocation',
             });
+        }, slotProps: {
+            htmlInput: { 'data-testid': 'urlInput' },
         } }));
 });
 exports.default = UrlChooser;

package/ui/SanitizedHTML.js

@@ -68,9 +68,12 @@ function SanitizedHTML({ html: pre, className, }) {
         // see https://github.com/cure53/DOMPurify/issues/317
         // only have to add this once, and can't do it globally because dompurify
         // not yet initialized at global scope
-        dompurify_1.default.addHook('afterSanitizeAttributes', (node) => {
+        dompurify_1.default.addHook('afterSanitizeAttributes', node => {
+            // @ts-expect-error
             if (node.tagName === 'A') {
+                // @ts-expect-error
                 node.setAttribute('rel', 'noopener noreferrer');
+                // @ts-expect-error
                 node.setAttribute('target', '_blank');
             }
         });

package/ui/theme.js

@@ -14,6 +14,7 @@ const midnight = '#0D233F';
 const grape = '#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' } });
 const bases = {
     A: refTheme.palette.augmentColor({ color: colors_1.green }),
     C: refTheme.palette.augmentColor({ color: colors_1.blue }),
@@ -372,58 +373,37 @@ function createJBrowseBaseTheme(theme) {
 }
 function createJBrowseTheme(configTheme = {}, themes = exports.defaultThemes, themeName = 'default') {
     return (0, styles_1.createTheme)(createJBrowseBaseTheme(themeName === 'default'
-        ? (0, deepmerge_1.default)(themes.default, augmentTheme(configTheme), {
+        ? (0, deepmerge_1.default)(themes.default, augmentThemeColors(configTheme), {
             arrayMerge: overwriteArrayMerge,
         })
-        : augmentThemePlus(themes[themeName])));
+        : addMissingColors(themes[themeName])));
 }
-function augmentTheme(theme = {}) {
-    var _a, _b;
-    if ((_a = theme.palette) === null || _a === void 0 ? void 0 : _a.tertiary) {
-        theme = (0, deepmerge_1.default)(theme, {
-            palette: {
-                tertiary: refTheme.palette.augmentColor('color' in theme.palette.tertiary
-                    ? theme.palette.tertiary
-                    : { color: theme.palette.tertiary }),
-            },
-        });
-    }
-    if ((_b = theme.palette) === null || _b === void 0 ? void 0 : _b.quaternary) {
-        theme = (0, deepmerge_1.default)(theme, {
-            palette: {
-                quaternary: refTheme.palette.augmentColor('color' in theme.palette.quaternary
-                    ? theme.palette.quaternary
-                    : { color: theme.palette.quaternary }),
-            },
-        });
+// MUI by default allows strings like '#f00' for primary and secondary and
+// augments them to have light and dark variants but not for anything else, so
+// we augment them here
+function augmentThemeColors(theme = {}) {
+    var _a;
+    for (const entry of ['tertiary', 'quaternary', 'highlight']) {
+        if ((_a = theme.palette) === null || _a === void 0 ? void 0 : _a[entry]) {
+            theme = (0, deepmerge_1.default)(theme, {
+                palette: {
+                    [entry]: refTheme.palette.augmentColor('color' in theme.palette[entry]
+                        ? theme.palette[entry]
+                        : { color: theme.palette[entry] }),
+                },
+            });
+        }
     }
     return theme;
 }
-// creates some blank quaternary/tertiary colors if unsupplied by a user theme
-function augmentThemePlus(theme = {}) {
-    var _a, _b;
-    theme = augmentTheme(theme);
-    if (!((_a = theme.palette) === null || _a === void 0 ? void 0 : _a.quaternary)) {
-        theme = (0, deepmerge_1.default)(theme, {
-            palette: {
-                quaternary: refTheme.palette.augmentColor({
-                    color: {
-                        main: '#aaa',
-                    },
-                }),
-            },
-        });
-    }
-    if (!((_b = theme.palette) === null || _b === void 0 ? void 0 : _b.tertiary)) {
-        theme = (0, deepmerge_1.default)(theme, {
-            palette: {
-                tertiary: refTheme.palette.augmentColor({
-                    color: {
-                        main: '#aaa',
-                    },
-                }),
-            },
-        });
-    }
-    return theme;
+// adds missing colors to users theme
+function addMissingColors(theme = {}) {
+    var _a, _b, _c;
+    return augmentThemeColors((0, deepmerge_1.default)(theme, {
+        palette: {
+            quaternary: ((_a = theme.palette) === null || _a === void 0 ? void 0 : _a.quaternary) || lightgrey,
+            tertiary: ((_b = theme.palette) === null || _b === void 0 ? void 0 : _b.tertiary) || lightgrey,
+            highlight: ((_c = theme.palette) === null || _c === void 0 ? void 0 : _c.highlight) || mandarin,
+        },
+    }));
 }

package/util/index.d.ts

@@ -7,6 +7,8 @@ import { Feature } from './simpleFeature';
 import { AssemblyManager, Region, TypeTestedByPredicate } from './types';
 import type { Region as MUIRegion } from './types/mst';
 import { BaseBlock } from './blockTypes';
+import { GenericFilehandle } from 'generic-filehandle';
+import { BaseOptions } from '../data_adapters/BaseAdapter';
 export * from './types';
 export * from './aborting';
 export * from './when';
@@ -163,21 +165,17 @@ export declare function polarToCartesian(rho: number, theta: number): [number, n
  * @returns [rho, theta]
  */
 export declare function cartesianToPolar(x: number, y: number): [number, number];
-export declare function featureSpanPx(feature: Feature, region: {
+interface MinimalRegion {
     start: number;
     end: number;
     reversed?: boolean;
-}, bpPerPx: number): [number, number];
-export declare function bpSpanPx(leftBp: number, rightBp: number, region: {
-    start: number;
-    end: number;
-    reversed?: boolean;
-}, bpPerPx: number): [number, number];
+}
+export declare function featureSpanPx(feature: Feature, region: MinimalRegion, bpPerPx: number): readonly [number, number];
+export declare function bpSpanPx(leftBp: number, rightBp: number, region: MinimalRegion, bpPerPx: number): readonly [number, number];
 export declare function iterMap<T, U>(iter: Iterable<T>, func: (arg: T) => U, sizeHint?: number): U[];
 /**
  * Returns the index of the last element in the array where predicate is true,
- * and -1 otherwise.
- * Based on https://stackoverflow.com/a/53187807
+ * and -1 otherwise. Based on https://stackoverflow.com/a/53187807
  *
  * @param array - The source array to search in
  *
@@ -231,9 +229,10 @@ export declare function stringify({ refName, coord, assemblyName, oob, }: {
     oob?: boolean;
 }, useAssemblyName?: boolean): string;
 export declare const isElectron: boolean;
-export declare function revcom(seqString: string): string;
-export declare function reverse(seqString: string): string;
-export declare const complement: (seqString: string) => string;
+export declare const complementTable: Record<string, string>;
+export declare function revcom(str: string): string;
+export declare function reverse(str: string): string;
+export declare function complement(str: string): string;
 export declare const rIC: (((callback: IdleRequestCallback, options?: IdleRequestOptions) => number) & typeof requestIdleCallback) | ((cb: () => void) => void);
 export declare function measureText(str: unknown, fontSize?: number): number;
 export type Frame = 1 | 2 | 3 | -1 | -2 | -3;
@@ -406,5 +405,6 @@ export declare function renderToStaticMarkup(node: React.ReactElement, createRoo
     render: (node: React.ReactElement) => unknown;
 }): string;
 export declare function isGzip(buf: Buffer): boolean;
-export { default as SimpleFeature, type Feature, type SimpleFeatureSerialized, isFeature, } from './simpleFeature';
+export declare function fetchAndMaybeUnzip(loc: GenericFilehandle, opts?: BaseOptions): Promise<Buffer>;
+export { isFeature, default as SimpleFeature, type Feature, type SimpleFeatureSerialized, type SimpleFeatureSerializedNoId, } from './simpleFeature';
 export { blobToDataURL } from './blobToDataURL';

package/util/index.js

@@ -17,7 +17,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.blobToDataURL = exports.isFeature = exports.SimpleFeature = exports.defaultCodonTable = exports.defaultStops = exports.defaultStarts = exports.rIC = exports.complement = exports.isElectron = void 0;
+exports.blobToDataURL = exports.SimpleFeature = exports.isFeature = exports.defaultCodonTable = exports.defaultStops = exports.defaultStarts = exports.rIC = exports.complementTable = exports.isElectron = void 0;
 exports.useDebounce = useDebounce;
 exports.useWidthSetter = useWidthSetter;
 exports.useDebouncedCallback = useDebouncedCallback;
@@ -53,6 +53,7 @@ exports.shorten = shorten;
 exports.stringify = stringify;
 exports.revcom = revcom;
 exports.reverse = reverse;
+exports.complement = complement;
 exports.measureText = measureText;
 exports.getFrame = getFrame;
 exports.generateCodonTable = generateCodonTable;
@@ -88,6 +89,7 @@ exports.getStrokeProps = getStrokeProps;
 exports.getFillProps = getFillProps;
 exports.renderToStaticMarkup = renderToStaticMarkup;
 exports.isGzip = isGzip;
+exports.fetchAndMaybeUnzip = fetchAndMaybeUnzip;
 const react_1 = require("react");
 const is_object_1 = __importDefault(require("is-object"));
 const mobx_state_tree_1 = require("mobx-state-tree");
@@ -100,6 +102,7 @@ const useMeasure_1 = __importDefault(require("@jbrowse/core/util/useMeasure"));
 const colord_1 = require("./colord");
 // eslint-disable-next-line react/no-deprecated
 const react_dom_1 = require("react-dom");
+const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 __exportStar(require("./types"), exports);
 __exportStar(require("./aborting"), exports);
 __exportStar(require("./when"), exports);
@@ -607,8 +610,7 @@ function iterMap(iter, func, sizeHint) {
 }
 /**
  * Returns the index of the last element in the array where predicate is true,
- * and -1 otherwise.
- * Based on https://stackoverflow.com/a/53187807
+ * and -1 otherwise. Based on https://stackoverflow.com/a/53187807
  *
  * @param array - The source array to search in
  *
@@ -766,55 +768,67 @@ function stringify({ refName, coord, assemblyName, oob, }, useAssemblyName) {
 // const isElectron = process.versions.electron
 // const i2 = process.versions.hasOwnProperty('electron')
 exports.isElectron = /electron/i.test(typeof navigator !== 'undefined' ? navigator.userAgent : '');
-function revcom(seqString) {
-    return reverse((0, exports.complement)(seqString));
-}
-function reverse(seqString) {
-    return seqString.split('').reverse().join('');
-}
-exports.complement = (() => {
-    const complementRegex = /[ACGT]/gi;
-    // from bioperl: tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/
-    // generated with:
-    // perl -MJSON -E '@l = split "","acgtrymkswhbvdnxACGTRYMKSWHBVDNX"; print to_json({ map { my $in = $_; tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/; $in => $_ } @l})'
-    const complementTable = {
-        S: 'S',
-        w: 'w',
-        T: 'A',
-        r: 'y',
-        a: 't',
-        N: 'N',
-        K: 'M',
-        x: 'x',
-        d: 'h',
-        Y: 'R',
-        V: 'B',
-        y: 'r',
-        M: 'K',
-        h: 'd',
-        k: 'm',
-        C: 'G',
-        g: 'c',
-        t: 'a',
-        A: 'T',
-        n: 'n',
-        W: 'W',
-        X: 'X',
-        m: 'k',
-        v: 'b',
-        B: 'V',
-        s: 's',
-        H: 'D',
-        c: 'g',
-        D: 'H',
-        b: 'v',
-        R: 'Y',
-        G: 'C',
-    };
-    return (seqString) => {
-        return seqString.replaceAll(complementRegex, m => complementTable[m] || '');
-    };
-})();
+// from bioperl: tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/
+// generated with:
+// perl -MJSON -E '@l = split "","acgtrymkswhbvdnxACGTRYMKSWHBVDNX"; print to_json({ map { my $in = $_; tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/; $in => $_ } @l})'
+exports.complementTable = {
+    S: 'S',
+    w: 'w',
+    T: 'A',
+    r: 'y',
+    a: 't',
+    N: 'N',
+    K: 'M',
+    x: 'x',
+    d: 'h',
+    Y: 'R',
+    V: 'B',
+    y: 'r',
+    M: 'K',
+    h: 'd',
+    k: 'm',
+    C: 'G',
+    g: 'c',
+    t: 'a',
+    A: 'T',
+    n: 'n',
+    W: 'W',
+    X: 'X',
+    m: 'k',
+    v: 'b',
+    B: 'V',
+    s: 's',
+    H: 'D',
+    c: 'g',
+    D: 'H',
+    b: 'v',
+    R: 'Y',
+    G: 'C',
+};
+function revcom(str) {
+    var _a;
+    let revcomped = '';
+    for (let i = str.length - 1; i >= 0; i--) {
+        revcomped += (_a = exports.complementTable[str[i]]) !== null && _a !== void 0 ? _a : str[i];
+    }
+    return revcomped;
+}
+function reverse(str) {
+    let reversed = '';
+    for (let i = str.length - 1; i >= 0; i--) {
+        reversed += str[i];
+    }
+    return reversed;
+}
+function complement(str) {
+    var _a;
+    let comp = '';
+    // eslint-disable-next-line @typescript-eslint/prefer-for-of
+    for (let i = 0; i < str.length; i++) {
+        comp += (_a = exports.complementTable[str[i]]) !== null && _a !== void 0 ? _a : str[i];
+    }
+    return comp;
+}
 // requires immediate execution in jest environment, because (hypothesis) it
 // otherwise listens for prerendered_canvas but reads empty pixels, and doesn't
 // get the contents of the canvas
@@ -1213,8 +1227,15 @@ function renderToStaticMarkup(node, createRootFn) {
 function isGzip(buf) {
     return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
 }
+async function fetchAndMaybeUnzip(loc, opts) {
+    const { statusCallback = () => { } } = opts || {};
+    const buf = (await updateStatus('Downloading file', statusCallback, () => loc.readFile(opts)));
+    return isGzip(buf)
+        ? await updateStatus('Unzipping', statusCallback, () => (0, bgzf_filehandle_1.unzip)(buf))
+        : buf;
+}
 var simpleFeature_1 = require("./simpleFeature");
-Object.defineProperty(exports, "SimpleFeature", { enumerable: true, get: function () { return __importDefault(simpleFeature_1).default; } });
 Object.defineProperty(exports, "isFeature", { enumerable: true, get: function () { return simpleFeature_1.isFeature; } });
+Object.defineProperty(exports, "SimpleFeature", { enumerable: true, get: function () { return __importDefault(simpleFeature_1).default; } });
 var blobToDataURL_1 = require("./blobToDataURL");
 Object.defineProperty(exports, "blobToDataURL", { enumerable: true, get: function () { return blobToDataURL_1.blobToDataURL; } });

package/util/simpleFeature.d.ts

@@ -10,14 +10,6 @@ export interface Feature {
     get(name: 'start' | 'end'): number;
     get(name: 'subfeatures'): Feature[] | undefined;
     get(name: string): any;
-    /**
-     * Set an item of data.
-     */
-    set(name: string, val: any): void;
-    /**
-     * Get an array listing which data keys are present in this feature.
-     */
-    tags(): string[];
     /**
      * Get the unique ID of this feature.
      */

package/util/stats.d.ts

@@ -10,6 +10,7 @@ export interface UnrectifiedQuantitativeStats {
     basesCovered: number;
 }
 export interface QuantitativeStats extends UnrectifiedQuantitativeStats {
+    currStatsBpPerPx: number;
     featureDensity: number;
     scoreMean: number;
     scoreStdDev: number;
@@ -32,14 +33,6 @@ export declare function calcStdFromSums(sum: number, sumSquares: number, n: numb
  * scoreMean, scoreStdDev, and featureDensity added
  */
 export declare function rectifyStats(s: UnrectifiedQuantitativeStats): QuantitativeStats;
-/**
- * calculates per-base scores for variable width features over a region
- *
- * @param region - object contains start, end
- * @param features - list of features with start, end, score
- * @returns array of numeric scores
- */
-export declare function calcPerBaseStats(region: NoAssemblyRegion, features: Feature[]): number[];
 /**
  * transform a list of scores to summary statistics
  *

package/util/stats.js

@@ -2,7 +2,6 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.calcStdFromSums = calcStdFromSums;
 exports.rectifyStats = rectifyStats;
-exports.calcPerBaseStats = calcPerBaseStats;
 exports.scoresToStats = scoresToStats;
 exports.blankStats = blankStats;
 const rxjs_1 = require("rxjs");
@@ -48,40 +47,6 @@ function rectifyStats(s) {
         featureDensity: (s.featureCount || 1) / s.basesCovered,
     };
 }
-/**
- * calculates per-base scores for variable width features over a region
- *
- * @param region - object contains start, end
- * @param features - list of features with start, end, score
- * @returns array of numeric scores
- */
-function calcPerBaseStats(region, features) {
-    const { start, end } = region;
-    const scores = [];
-    const feats = features.sort((a, b) => a.get('start') - b.get('start'));
-    let pos = start;
-    let currentFeat = 0;
-    let i = 0;
-    while (pos < end) {
-        while (currentFeat < feats.length &&
-            pos >= feats[currentFeat].get('end')) {
-            currentFeat += 1;
-        }
-        const f = feats[currentFeat];
-        if (!f) {
-            scores[i] = 0;
-        }
-        else if (pos >= f.get('start') && pos < f.get('end')) {
-            scores[i] = f.get('score');
-        }
-        else {
-            scores[i] = 0;
-        }
-        i += 1;
-        pos += 1;
-    }
-    return scores;
-}
 /**
  * transform a list of scores to summary statistics
  *