@jbrowse/core 2.11.0 → 2.11.2

package/ui/ErrorMessageStackTraceDialog.js

@@ -28,6 +28,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
 const source_map_js_1 = require("source-map-js");
 const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
 // locals
@@ -90,7 +91,7 @@ async function mapStackTrace(stack) {
             mappedStack.push(line);
             continue;
         }
-        mappedStack.push(`${originalPosition.source}:${originalPosition.line}:${originalPosition.column + 1}`);
+        mappedStack.push(`${originalPosition.source}:${originalPosition.line}:${originalPosition.column + 1} (${match[1].trim()})`);
     }
     return mappedStack.join('\n');
 }
@@ -107,7 +108,17 @@ function stripMessage(trace, error) {
         return trace;
     }
 }
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    pre: {
+        background: (0, material_1.alpha)(theme.palette.error.main, 0.2),
+        border: `1px solid ${theme.palette.divider}`,
+        overflow: 'auto',
+        margin: 20,
+        maxHeight: 300,
+    },
+}));
 function Contents({ text, extra }) {
+    const { classes } = useStyles();
     const err = encodeURIComponent([
         'I got this error from JBrowse, here is the stack trace:\n',
         '```',
@@ -129,13 +140,7 @@ function Contents({ text, extra }) {
             " or send an email to ",
             react_1.default.createElement(Link2, { href: emailLink }, email),
             ' '),
-        react_1.default.createElement("pre", { style: {
-                background: 'lightgrey',
-                border: '1px solid black',
-                overflow: 'auto',
-                margin: 20,
-                maxHeight: 300,
-            } }, err2)));
+        react_1.default.createElement("pre", { className: classes.pre }, err2)));
 }
 function ErrorMessageStackTraceDialog({ error, onClose, extra, }) {
     const [mappedStackTrace, setMappedStackTrace] = (0, react_1.useState)();

package/ui/index.d.ts

@@ -11,7 +11,6 @@ export { default as FileSelector } from './FileSelector';
 export { default as LoadingEllipses } from './LoadingEllipses';
 export { default as Menu } from './Menu';
 export { default as PrerenderedCanvas } from './PrerenderedCanvas';
-export { default as Tooltip } from './Tooltip';
 export { default as ReturnToImportFormDialog } from './ReturnToImportFormDialog';
 export { default as ResizeHandle } from './ResizeHandle';
 export { default as SanitizedHTML } from './SanitizedHTML';

package/ui/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.SanitizedHTML = exports.ResizeHandle = exports.ReturnToImportFormDialog = exports.Tooltip = exports.PrerenderedCanvas = exports.Menu = exports.LoadingEllipses = exports.FileSelector = exports.FatalErrorDialog = exports.FactoryResetDialog = exports.ErrorMessage = exports.EditableTypography = exports.Dialog = exports.CascadingMenu = exports.AssemblySelector = exports.Logomark = exports.LogoFull = void 0;
+exports.SanitizedHTML = exports.ResizeHandle = exports.ReturnToImportFormDialog = exports.PrerenderedCanvas = exports.Menu = exports.LoadingEllipses = exports.FileSelector = exports.FatalErrorDialog = exports.FactoryResetDialog = exports.ErrorMessage = exports.EditableTypography = exports.Dialog = exports.CascadingMenu = exports.AssemblySelector = exports.Logomark = exports.LogoFull = void 0;
 __exportStar(require("./theme"), exports);
 var Logo_1 = require("./Logo");
 Object.defineProperty(exports, "LogoFull", { enumerable: true, get: function () { return Logo_1.LogoFull; } });
@@ -44,8 +44,6 @@ var Menu_1 = require("./Menu");
 Object.defineProperty(exports, "Menu", { enumerable: true, get: function () { return __importDefault(Menu_1).default; } });
 var PrerenderedCanvas_1 = require("./PrerenderedCanvas");
 Object.defineProperty(exports, "PrerenderedCanvas", { enumerable: true, get: function () { return __importDefault(PrerenderedCanvas_1).default; } });
-var Tooltip_1 = require("./Tooltip");
-Object.defineProperty(exports, "Tooltip", { enumerable: true, get: function () { return __importDefault(Tooltip_1).default; } });
 var ReturnToImportFormDialog_1 = require("./ReturnToImportFormDialog");
 Object.defineProperty(exports, "ReturnToImportFormDialog", { enumerable: true, get: function () { return __importDefault(ReturnToImportFormDialog_1).default; } });
 var ResizeHandle_1 = require("./ResizeHandle");

package/util/blockTypes.d.ts

@@ -21,6 +21,7 @@ export declare class BlockSet {
     get totalBp(): number;
 }
 export declare class BaseBlock {
+    type: string;
     regionNumber?: number;
     reversed?: boolean;
     refName: string;
@@ -45,12 +46,14 @@ export declare class BaseBlock {
     };
 }
 export declare class ContentBlock extends BaseBlock {
+    type: string;
 }
 /**
  * marker block representing one or more blocks that are
  * too small to be shown at the current zoom level
  */
 export declare class ElidedBlock extends BaseBlock {
+    type: string;
     widthPx: number;
     elidedBlockCount: number;
     constructor(data: Record<string, any>);
@@ -61,5 +64,6 @@ export declare class ElidedBlock extends BaseBlock {
  * and provides a thick border between them
  */
 export declare class InterRegionPaddingBlock extends BaseBlock {
+    type: string;
 }
 export {};

package/util/blockTypes.js

@@ -7,9 +7,10 @@ class BlockSet {
         this.blocks = blocks;
     }
     push(block) {
-        if (block instanceof ElidedBlock && this.blocks.length > 0) {
+        if (block.type === 'ElidedBlock' && this.blocks.length > 0) {
             const lastBlock = this.blocks.at(-1);
-            if (lastBlock instanceof ElidedBlock) {
+            if ((lastBlock === null || lastBlock === void 0 ? void 0 : lastBlock.type) === 'ElidedBlock') {
+                ;
                 lastBlock.push(block);
                 return;
             }
@@ -49,7 +50,7 @@ class BlockSet {
         return this.blocks.length > 0 ? this.blocks[0].offsetPx : 0;
     }
     get contentBlocks() {
-        return this.blocks.filter(block => block instanceof ContentBlock);
+        return this.blocks.filter(block => block.type === 'ContentBlock');
     }
     get totalBp() {
         return (0, _1.sum)(this.contentBlocks.map(block => block.end - block.start));
@@ -62,6 +63,7 @@ class BaseBlock {
      */
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
     constructor(data) {
+        this.type = 'BaseBlock';
         this.widthPx = 0;
         Object.assign(this, data);
         this.assemblyName = data.assemblyName;
@@ -83,6 +85,10 @@ class BaseBlock {
 }
 exports.BaseBlock = BaseBlock;
 class ContentBlock extends BaseBlock {
+    constructor() {
+        super(...arguments);
+        this.type = 'ContentBlock';
+    }
 }
 exports.ContentBlock = ContentBlock;
 /**
@@ -93,6 +99,7 @@ class ElidedBlock extends BaseBlock {
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
     constructor(data) {
         super(data);
+        this.type = 'ElidedBlock';
         this.elidedBlockCount = 0;
         this.widthPx = data.widthPx;
     }
@@ -112,5 +119,9 @@ exports.ElidedBlock = ElidedBlock;
  * and provides a thick border between them
  */
 class InterRegionPaddingBlock extends BaseBlock {
+    constructor() {
+        super(...arguments);
+        this.type = 'InterRegionPaddingBlock';
+    }
 }
 exports.InterRegionPaddingBlock = InterRegionPaddingBlock;

package/util/calculateDynamicBlocks.js

@@ -38,10 +38,9 @@ function calculateDynamicBlocks(model, padding = true, elision = true) {
         const displayedRegionRightPx = displayedRegionLeftPx + (regionEnd - regionStart) / bpPerPx;
         const regionWidthPx = (regionEnd - regionStart) / bpPerPx;
         const parentRegion = (0, mobx_state_tree_1.isStateTreeNode)(region) ? (0, mobx_state_tree_1.getSnapshot)(region) : region;
-        if (displayedRegionLeftPx < windowRightPx &&
-            displayedRegionRightPx > windowLeftPx) {
+        const [leftPx, rightPx] = (0, range_1.intersection2)(windowLeftPx, windowRightPx, displayedRegionLeftPx, displayedRegionRightPx);
+        if (leftPx !== undefined && rightPx !== undefined) {
             // this displayed region overlaps the view, so make a record for it
-            const [leftPx, rightPx] = (0, range_1.intersection2)(windowLeftPx, windowRightPx, displayedRegionLeftPx, displayedRegionRightPx);
             let start;
             let end;
             let isLeftEndOfDisplayedRegion;

package/util/index.d.ts

@@ -392,6 +392,14 @@ interface BasicFeature {
 }
 export declare function gatherOverlaps(regions: BasicFeature[]): BasicFeature[];
 export declare function stripAlpha(str: string): string;
+export declare function getStrokeProps(str: string): {
+    strokeOpacity: number;
+    stroke: string;
+};
+export declare function getFillProps(str: string): {
+    fillOpacity: number;
+    fill: string;
+};
 export declare function renderToStaticMarkup(node: React.ReactElement, createRootFn?: (elt: Element | DocumentFragment) => {
     render: (node: React.ReactElement) => unknown;
 }): string;

package/util/index.js

@@ -18,7 +18,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getBpDisplayStr = exports.isSupportedIndexingAdapter = exports.bytesForRegions = exports.objectHash = exports.hashCode = exports.updateStatus = exports.generateCodonTable = exports.defaultCodonTable = exports.defaultStops = exports.defaultStarts = exports.getFrame = exports.measureText = exports.rIC = exports.complement = exports.reverse = exports.revcom = exports.isElectron = exports.stringify = exports.shorten = exports.minmax = exports.renameRegionsIfNeeded = exports.renameRegionIfNeeded = exports.makeAbortableReaction = exports.findLast = exports.findLastIndex = exports.iterMap = exports.bpSpanPx = exports.featureSpanPx = exports.cartesianToPolar = exports.polarToCartesian = exports.degToRad = exports.radToDeg = exports.bpToPx = exports.clamp = exports.compareLocStrings = exports.compareLocs = exports.parseLocString = exports.parseLocStringOneBased = exports.assembleLocStringFast = exports.assembleLocString = exports.getContainingDisplay = exports.getContainingTrack = exports.getContainingView = exports.getSession = exports.findParentThatIs = exports.springAnimate = exports.findParentThat = exports.useDebouncedCallback = exports.useWidthSetter = exports.useDebounce = void 0;
-exports.blobToDataURL = exports.isFeature = exports.SimpleFeature = exports.renderToStaticMarkup = exports.stripAlpha = exports.gatherOverlaps = exports.mergeIntervals = exports.notEmpty = exports.groupBy = exports.avg = exports.sum = exports.min = exports.max = exports.localStorageSetItem = exports.localStorageGetItem = exports.getEnv = exports.measureGridWidth = exports.linkify = exports.coarseStripHTML = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = exports.toLocale = void 0;
+exports.blobToDataURL = exports.isFeature = exports.SimpleFeature = exports.renderToStaticMarkup = exports.getFillProps = exports.getStrokeProps = exports.stripAlpha = exports.gatherOverlaps = exports.mergeIntervals = exports.notEmpty = exports.groupBy = exports.avg = exports.sum = exports.min = exports.max = exports.localStorageSetItem = exports.localStorageGetItem = exports.getEnv = exports.measureGridWidth = exports.linkify = exports.coarseStripHTML = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = exports.toLocale = void 0;
 /* eslint-disable @typescript-eslint/no-explicit-any */
 const react_1 = require("react");
 const is_object_1 = __importDefault(require("is-object"));
@@ -1150,6 +1150,16 @@ function stripAlpha(str) {
     return c.alpha(1).toHex();
 }
 exports.stripAlpha = stripAlpha;
+function getStrokeProps(str) {
+    const c = (0, colord_1.colord)(str);
+    return { strokeOpacity: c.alpha(), stroke: c.alpha(1).toHex() };
+}
+exports.getStrokeProps = getStrokeProps;
+function getFillProps(str) {
+    const c = (0, colord_1.colord)(str);
+    return { fillOpacity: c.alpha(), fill: c.alpha(1).toHex() };
+}
+exports.getFillProps = getFillProps;
 // https://react.dev/reference/react-dom/server/renderToString#removing-rendertostring-from-the-client-code
 function renderToStaticMarkup(node, createRootFn) {
     const div = document.createElement('div');
@@ -1161,7 +1171,7 @@ function renderToStaticMarkup(node, createRootFn) {
             (0, react_dom_1.render)(node, div);
         }
     });
-    return div.innerHTML;
+    return div.innerHTML.replaceAll(/\brgba\((.+?),[^,]+?\)/g, 'rgb($1)');
 }
 exports.renderToStaticMarkup = renderToStaticMarkup;
 var simpleFeature_1 = require("./simpleFeature");

package/util/jexl.d.ts

@@ -1,4 +1,4 @@
 import jexl from 'jexl';
 type JexlNonBuildable = Omit<typeof jexl, 'Jexl'>;
-export default function (): JexlNonBuildable;
+export default function JexlF(): JexlNonBuildable;
 export {};

package/util/jexl.js

@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const jexl_1 = __importDefault(require("jexl"));
-function default_1( /* config?: any*/) {
+function JexlF( /* config?: any*/) {
     const j = new jexl_1.default.Jexl();
     // someday will make sure all of configs callbacks are added in, including
     // ones passed in
@@ -61,4 +61,4 @@ function default_1( /* config?: any*/) {
     j.addBinaryOp('&', 15, (a, b) => a & b);
     return j;
 }
-exports.default = default_1;
+exports.default = JexlF;

package/util/range.d.ts

@@ -5,7 +5,7 @@
  *
  * @returns array of [left, right], or [] if the ranges do not intersect. the choice of [] is because it allows destructuring array assignment without check for undefined return
  */
-export declare function intersection2(left1: number, right1: number, left2: number, right2: number): number[];
+export declare function intersection2(left1: number, right1: number, left2: number, right2: number): [number, number] | [];
 /**
  * Return whether 2 interbase coordinate ranges intersect.
  *

package/util/simpleFeature.d.ts

@@ -48,6 +48,10 @@ export interface SimpleFeatureArgs {
 export interface SimpleFeatureSerializedNoId {
     [key: string]: unknown;
     parentId?: string;
+    start: number;
+    end: number;
+    refName: string;
+    type?: string;
     subfeatures?: SimpleFeatureSerializedNoId[];
 }
 export interface SimpleFeatureSerialized extends SimpleFeatureSerializedNoId {

package/BaseFeatureWidget/SequenceFeatureDetails/CDNASequence.d.ts

@@ -1,13 +0,0 @@
-import React from 'react';
-import { Feat } from '../util';
-export default function CDNASequence({ utr, cds, exons, sequence, upstream, downstream, includeIntrons, collapseIntron, intronBp, }: {
-    utr: Feat[];
-    cds: Feat[];
-    exons: Feat[];
-    sequence: string;
-    upstream?: string;
-    downstream?: string;
-    includeIntrons?: boolean;
-    collapseIntron?: boolean;
-    intronBp: number;
-}): React.JSX.Element;

package/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureSettingsDialog.d.ts

@@ -1,9 +0,0 @@
-import React from 'react';
-export default function SequenceFeatureSettingsDialog({ handleClose, intronBp: intronBpArg, upDownBp: upDownBpArg, }: {
-    handleClose: (arg?: {
-        intronBp: number;
-        upDownBp: number;
-    }) => void;
-    intronBp: number;
-    upDownBp: number;
-}): React.JSX.Element;

package/ui/ResizeBar.d.ts

@@ -1,7 +0,0 @@
-import React from 'react';
-export default function ResizeBar({ widths, setWidths, checkbox, scrollLeft, }: {
-    widths: number[];
-    setWidths: (arg: number[]) => void;
-    checkbox?: boolean;
-    scrollLeft?: number;
-}): React.JSX.Element;

package/ui/ResizeBar.js

@@ -1,80 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
-const mui_1 = require("tss-react/mui");
-// locals
-const ResizeHandle_1 = __importDefault(require("./ResizeHandle"));
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    resizeBar: {
-        background: theme.palette.action.disabledBackground,
-        height: 12,
-        position: 'relative',
-        overflow: 'hidden',
-    },
-    tick: {
-        position: 'absolute',
-        height: '100%',
-        pointerEvents: 'none',
-        background: theme.palette.action.disabled,
-        width: 1,
-    },
-    hiddenTick: {
-        position: 'absolute',
-        height: '100%',
-        width: 5,
-    },
-}));
-function Tick({ left, scrollLeft, idx, onDrag, onMouseDown, }) {
-    const { classes } = useStyles();
-    const onDragCallback = (0, react_1.useCallback)((lastFrameDistance, totalDistance) => onDrag(lastFrameDistance, totalDistance, idx), [idx, onDrag]);
-    // has an invisible wider than tick mark (1px) clickable area (5px)
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(ResizeHandle_1.default, { onDrag: onDragCallback, onMouseDown: onMouseDown, vertical: true, className: classes.hiddenTick, style: { left: left - scrollLeft - 2.5 } }),
-        react_1.default.createElement("div", { style: { left: left - scrollLeft }, className: classes.tick })));
-}
-function ResizeBar({ widths, setWidths, checkbox, scrollLeft = 0, }) {
-    const { classes } = useStyles();
-    const offsets = [];
-    const [initial, setInitial] = (0, react_1.useState)();
-    let init = checkbox ? 52 : 0;
-    for (let i = 0; i < widths.length; i++) {
-        const width = widths[i];
-        offsets[i] = width + init;
-        init += width;
-    }
-    return (react_1.default.createElement("div", { className: classes.resizeBar }, offsets.map((left, i) => (react_1.default.createElement(Tick, { key: i, onMouseDown: () => {
-            setInitial([...widths]);
-        }, left: i === offsets.length - 1 ? left - 3 : left, onDrag: (_, totalDistance, idx) => {
-            const newWidths = [...widths];
-            // mui doesn't allow columns smaller than 50
-            newWidths[idx] = Math.max(initial[idx] - totalDistance, 50);
-            setWidths(newWidths);
-        }, idx: i, scrollLeft: scrollLeft })))));
-}
-exports.default = ResizeBar;

package/ui/Tooltip.d.ts

@@ -1,11 +0,0 @@
-import React from 'react';
-import { Feature } from '../util';
-import { AnyConfigurationModel } from '../configuration';
-declare const Tooltip: ({ offsetX, offsetY, configuration, feature, timeout, }: {
-    offsetX: number;
-    offsetY: number;
-    configuration: AnyConfigurationModel;
-    feature?: Feature;
-    timeout?: number;
-}) => React.JSX.Element | null;
-export default Tooltip;

package/ui/Tooltip.js

@@ -1,54 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
-const mui_1 = require("tss-react/mui");
-const mobx_react_1 = require("mobx-react");
-const configuration_1 = require("../configuration");
-const useStyles = (0, mui_1.makeStyles)()({
-    hoverLabel: {
-        border: '1px solid black',
-        position: 'absolute',
-        background: '#fffa',
-        pointerEvents: 'none',
-        zIndex: 10000,
-    },
-});
-const Tooltip = (0, mobx_react_1.observer)(function ({ offsetX, offsetY, configuration, feature, timeout = 300, }) {
-    const { classes } = useStyles();
-    const [shown, setShown] = (0, react_1.useState)(false);
-    (0, react_1.useEffect)(() => {
-        // only show the loading message after short timeout to prevent excessive
-        // flickering
-        const handle = setTimeout(() => setShown(true), timeout);
-        return () => clearTimeout(handle);
-    });
-    if (feature && shown) {
-        const text = (0, configuration_1.readConfObject)(configuration, 'mouseover', { feature });
-        return (react_1.default.createElement("div", { className: classes.hoverLabel, style: { left: offsetX, top: offsetY } }, text));
-    }
-    return null;
-});
-exports.default = Tooltip;