@jbrowse/core 2.4.0 → 2.4.2

package/util/Base1DUtils.js

@@ -70,7 +70,7 @@ function pxToBp(self, px) {
     if (bp < 0) {
         const r = displayedRegions[0];
         const snap = (0, mobx_state_tree_1.getSnapshot)(r);
-        // @ts-ignore
+        // @ts-expect-error
         return {
             // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
             ...snap,
@@ -88,7 +88,7 @@ function pxToBp(self, px) {
         const offset = bp - bpSoFar;
         if (len + bpSoFar > bp && bpSoFar <= bp) {
             const snap = (0, mobx_state_tree_1.getSnapshot)(r);
-            // @ts-ignore
+            // @ts-expect-error
             return {
                 // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
                 ...snap,
@@ -108,12 +108,12 @@ function pxToBp(self, px) {
             bpSoFar += len;
         }
     }
-    if (bp >= bpSoFar && displayedRegions.length) {
+    if (bp >= bpSoFar && displayedRegions.length > 0) {
         const r = displayedRegions[displayedRegions.length - 1];
         const len = r.end - r.start;
         const offset = bp - bpSoFar + len;
         const snap = (0, mobx_state_tree_1.getSnapshot)(r);
-        // @ts-ignore
+        // @ts-expect-error
         return {
             // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
             ...snap,
@@ -147,11 +147,12 @@ function bpToPx({ refName, coord, regionNumber, self, }) {
     for (; i < displayedRegions.length; i++) {
         const r = displayedRegions[i];
         const len = r.end - r.start;
-        if (refName === r.refName && coord >= r.start && coord <= r.end) {
-            if (regionNumber ? regionNumber === i : true) {
-                bpSoFar += r.reversed ? r.end - coord : coord - r.start;
-                break;
-            }
+        if (refName === r.refName &&
+            coord >= r.start &&
+            coord <= r.end &&
+            (regionNumber ? regionNumber === i : true)) {
+            bpSoFar += r.reversed ? r.end - coord : coord - r.start;
+            break;
         }
         // add the interRegionPaddingWidth if the boundary is in the screen e.g. in
         // a static block
@@ -185,11 +186,12 @@ function bpToPxMap({ refName, coord, regionNumber, self, }) {
     for (; i < displayedRegions.length; i++) {
         const r = displayedRegions[i];
         const len = r.end - r.start;
-        if (refName === r.refName && coord >= r.start && coord <= r.end) {
-            if (regionNumber !== undefined ? regionNumber === i : true) {
-                bpSoFar += r.reversed ? r.end - coord : coord - r.start;
-                break;
-            }
+        if (refName === r.refName &&
+            coord >= r.start &&
+            coord <= r.end &&
+            (regionNumber === undefined ? true : regionNumber === i)) {
+            bpSoFar += r.reversed ? r.end - coord : coord - r.start;
+            break;
         }
         // add the interRegionPaddingWidth if the boundary is in the screen e.g. in
         // a static block

package/util/Base1DViewModel.d.ts

@@ -119,7 +119,7 @@ declare const Base1DView: import("mobx-state-tree").IModelType<{
     /**
      * #action
      */
-    zoomTo(newBpPerPx: number, offset?: number): number;
+    zoomTo(bpPerPx: number, offset?: number): number;
     /**
      * #action
      */

package/util/Base1DViewModel.js

@@ -180,15 +180,16 @@ const Base1DView = mobx_state_tree_1.types
     /**
      * #action
      */
-    zoomTo(newBpPerPx, offset = self.width / 2) {
-        const bpPerPx = newBpPerPx;
-        if (bpPerPx === self.bpPerPx) {
-            return self.bpPerPx;
-        }
+    zoomTo(bpPerPx, offset = self.width / 2) {
+        const newBpPerPx = (0, index_1.clamp)(bpPerPx, 'minBpPerPx' in self ? self.minBpPerPx : 0, 'maxBpPerPx' in self ? self.maxBpPerPx : Infinity);
         const oldBpPerPx = self.bpPerPx;
-        self.bpPerPx = bpPerPx;
-        // tweak the offset so that the center of the view remains at the same coordinate
-        self.offsetPx = (0, index_1.clamp)(Math.round(((self.offsetPx + offset) * oldBpPerPx) / bpPerPx - offset), self.minOffset, self.maxOffset);
+        if (Math.abs(oldBpPerPx - newBpPerPx) < 0.000001) {
+            return oldBpPerPx;
+        }
+        self.bpPerPx = newBpPerPx;
+        // tweak the offset so that the center of the view remains at the same
+        // coordinate
+        self.offsetPx = (0, index_1.clamp)(Math.round(((self.offsetPx + offset) * oldBpPerPx) / newBpPerPx - offset), self.minOffset, self.maxOffset);
         return self.bpPerPx;
     },
     /**

package/util/aborting.js

@@ -75,6 +75,6 @@ function isAbortException(exception) {
             // Error: aborted
             // AbortError: aborted
             // AbortError: The user aborted a request.
-            !!exception.message.match(/\b(aborted|AbortError)\b/i)));
+            !!/\b(aborted|aborterror)\b/i.test(exception.message)));
 }
 exports.isAbortException = isAbortException;

package/util/analytics.js

@@ -83,7 +83,7 @@ async function writeGAAnalytics(rootModel, initialTimestamp) {
     analyticsScript += `ga('jbrowseTracker.send', 'pageview',${JSON.stringify(gaData)});`;
     const analyticsScriptNode = document.createElement('script');
     analyticsScriptNode.innerHTML = analyticsScript;
-    document.getElementsByTagName('head')[0].appendChild(analyticsScriptNode);
+    document.getElementsByTagName('head')[0].append(analyticsScriptNode);
 }
 exports.writeGAAnalytics = writeGAAnalytics;
 function doAnalytics(rootModel, initialTimestamp, initialSessionQuery) {

package/util/blockTypes.js

@@ -6,13 +6,11 @@ class BlockSet {
         this.blocks = blocks;
     }
     push(block) {
-        if (block instanceof ElidedBlock) {
-            if (this.blocks.length) {
-                const lastBlock = this.blocks[this.blocks.length - 1];
-                if (lastBlock instanceof ElidedBlock) {
-                    lastBlock.push(block);
-                    return;
-                }
+        if (block instanceof ElidedBlock && this.blocks.length > 0) {
+            const lastBlock = this.blocks[this.blocks.length - 1];
+            if (lastBlock instanceof ElidedBlock) {
+                lastBlock.push(block);
+                return;
             }
         }
         this.blocks.push(block);
@@ -24,21 +22,23 @@ class BlockSet {
         return this.blocks.map(block => block.toRegion());
     }
     map(func, thisarg) {
+        // eslint-disable-next-line unicorn/no-array-method-this-argument
         return this.blocks.map(func, thisarg);
     }
     forEach(func, thisarg) {
+        // eslint-disable-next-line unicorn/no-array-method-this-argument
         return this.blocks.forEach(func, thisarg);
     }
     get length() {
         return this.blocks.length;
     }
     get totalWidthPx() {
-        return this.blocks.length
+        return this.blocks.length > 0
             ? this.blocks.map(blocks => blocks.widthPx).reduce((a, b) => a + b)
             : 0;
     }
     get totalWidthPxWithoutBorders() {
-        return this.blocks.length
+        return this.blocks.length > 0
             ? this.blocks
                 .filter(block => block.variant !== 'boundary')
                 .map(blocks => blocks.widthPx)
@@ -46,7 +46,7 @@ class BlockSet {
             : 0;
     }
     get offsetPx() {
-        return this.blocks.length ? this.blocks[0].offsetPx : 0;
+        return this.blocks.length > 0 ? this.blocks[0].offsetPx : 0;
     }
     get contentBlocks() {
         return this.blocks.filter(block => block instanceof ContentBlock);

package/util/color/index.d.ts

@@ -1,5 +1,3 @@
-import { namedColorToHex, isNamedColor } from './cssColorsLevel4';
-export { namedColorToHex, isNamedColor };
 /**
  * Algorithmically pick a contrasting text color that will
  * be visible on top of the given background color. Either
@@ -22,3 +20,4 @@ export declare function contrastingTextColor(color: string): string;
  */
 export declare function emphasize(color: string, coefficient?: number): string;
 export declare function makeContrasting(foreground: string, background?: string, minContrastRatio?: number): string;
+export { isNamedColor, namedColorToHex } from './cssColorsLevel4';

package/util/color/index.js

@@ -1,10 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.makeContrasting = exports.emphasize = exports.contrastingTextColor = exports.isNamedColor = exports.namedColorToHex = void 0;
+exports.namedColorToHex = exports.isNamedColor = exports.makeContrasting = exports.emphasize = exports.contrastingTextColor = void 0;
 const styles_1 = require("@mui/material/styles");
 const cssColorsLevel4_1 = require("./cssColorsLevel4");
-Object.defineProperty(exports, "namedColorToHex", { enumerable: true, get: function () { return cssColorsLevel4_1.namedColorToHex; } });
-Object.defineProperty(exports, "isNamedColor", { enumerable: true, get: function () { return cssColorsLevel4_1.isNamedColor; } });
 /**
  * Algorithmically pick a contrasting text color that will
  * be visible on top of the given background color. Either
@@ -67,3 +65,6 @@ function makeContrasting(foreground, background = 'white', minContrastRatio = 3)
     return convertedForeground;
 }
 exports.makeContrasting = makeContrasting;
+var cssColorsLevel4_2 = require("./cssColorsLevel4");
+Object.defineProperty(exports, "isNamedColor", { enumerable: true, get: function () { return cssColorsLevel4_2.isNamedColor; } });
+Object.defineProperty(exports, "namedColorToHex", { enumerable: true, get: function () { return cssColorsLevel4_2.namedColorToHex; } });

package/util/idMaker.js

@@ -7,17 +7,14 @@ const _1 = require("./");
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function idMaker(args, id = '') {
     const keys = Object.keys(args);
-    for (let i = 0; i < keys.length; i++) {
-        const key = keys[i];
+    for (const key of keys) {
         if (id.length > 5000) {
             break;
         }
-        if (typeof args[key] === 'object' && args[key]) {
-            id += idMaker(args[key], id);
-        }
-        else {
-            id += `${key}-${args[key]};`;
-        }
+        id +=
+            typeof args[key] === 'object' && args[key]
+                ? idMaker(args[key], id)
+                : `${key}-${args[key]};`;
     }
     return (0, _1.hashCode)(id);
 }

package/util/index.d.ts

@@ -1,7 +1,8 @@
+/// <reference types="react" />
 import PluginManager from '../PluginManager';
 import { IAnyStateTreeNode, IStateTreeNode } from 'mobx-state-tree';
 import { IReactionPublic, IReactionOptions } from 'mobx';
-import SimpleFeature, { Feature, SimpleFeatureSerialized, isFeature } from './simpleFeature';
+import { Feature } from './simpleFeature';
 import { AssemblyManager, Region, TypeTestedByPredicate } from './types';
 import { BaseBlock } from './blockTypes';
 export * from './types';
@@ -9,19 +10,19 @@ export * from './aborting';
 export * from './when';
 export * from './range';
 export * from './dedupe';
-export { SimpleFeature, isFeature };
-export type { Feature, SimpleFeatureSerialized };
 export * from './offscreenCanvasPonyfill';
 export * from './offscreenCanvasUtils';
 export declare const inDevelopment: boolean;
 export declare const inProduction: boolean;
 export declare function useDebounce<T>(value: T, delay: number): T;
+export declare function useWidthSetter(view: {
+    setWidth: (arg: number) => void;
+}, padding: string): import("react").RefObject<HTMLDivElement>;
 export declare function useDebouncedCallback<T>(callback: (...args: T[]) => void, wait?: number): (...args: T[]) => void;
 /** find the first node in the hierarchy that matches the given predicate */
 export declare function findParentThat(node: IAnyStateTreeNode, predicate: (thing: IAnyStateTreeNode) => boolean): IAnyStateTreeNode;
 export declare function springAnimate(fromValue: number, toValue: number, setValue: (value: number) => void, onFinish?: () => void, precision?: number, tension?: number, friction?: number): (() => void)[];
-/** find the first node in the hierarchy that matches the given 'is' typescript type guard predicate */
-export declare function findParentThatIs<PREDICATE extends (thing: IAnyStateTreeNode) => boolean>(node: IAnyStateTreeNode, predicate: PREDICATE): TypeTestedByPredicate<PREDICATE> & IAnyStateTreeNode;
+export declare function findParentThatIs<T extends (a: IAnyStateTreeNode) => boolean>(node: IAnyStateTreeNode, predicate: T): TypeTestedByPredicate<T> & IAnyStateTreeNode;
 /** get the current JBrowse session model, starting at any node in the state tree */
 export declare function getSession(node: IAnyStateTreeNode): import("./types").AbstractSessionModel & IAnyStateTreeNode;
 /** get the state model of the view in the state tree that contains the given node */
@@ -286,7 +287,7 @@ export declare const defaultCodonTable: {
 export declare function generateCodonTable(table: any): {
     [key: string]: string;
 };
-export declare function updateStatus<U>(msg: string, cb: (arg: string) => void, fn: () => U): Promise<U>;
+export declare function updateStatus<U>(msg: string, cb: (arg: string) => void, fn: () => U | Promise<U>): Promise<U>;
 export declare function hashCode(str: string): number;
 export declare function objectHash(obj: Record<string, any>): string;
 interface VirtualOffset {
@@ -324,8 +325,8 @@ export declare function getTickDisplayStr(totalBp: number, bpPerPx: number): str
 export declare function getViewParams(model: IAnyStateTreeNode, exportSVG?: boolean): {
     offsetPx: number;
     offsetPx1: number;
-    start: any;
-    end: any;
+    start: number;
+    end: number;
 };
 export declare function getLayoutId({ sessionId, layoutId, }: {
     sessionId: string;
@@ -337,7 +338,7 @@ export declare function getUriLink(value: {
     baseUri?: string;
 }): string;
 export declare function getStr(obj: unknown): string;
-export declare function measureGridWidth(elements: string[], args?: {
+export declare function measureGridWidth(elements: unknown[], args?: {
     minWidth?: number;
     fontSize?: number;
     maxWidth?: number;
@@ -353,3 +354,4 @@ export declare function max(arr: number[], init?: number): number;
 export declare function min(arr: number[], init?: number): number;
 export declare function sum(arr: number[]): number;
 export declare function avg(arr: number[]): number;
+export { default as SimpleFeature, type Feature, type SimpleFeatureSerialized, isFeature, } from './simpleFeature';

package/util/index.js

@@ -10,18 +10,6 @@ var __createBinding = (this && this.__createBinding) || (Object.create ? (functi
     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 __exportStar = (this && this.__exportStar) || function(m, exports) {
     for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
 };
@@ -29,19 +17,17 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.bytesForRegions = exports.objectHash = exports.hashCode = exports.updateStatus = exports.generateCodonTable = exports.defaultCodonTable = exports.defaultStops = exports.defaultStarts = exports.measureText = exports.rIC = exports.blobToDataURL = exports.complement = exports.reverse = exports.revcom = exports.isElectron = exports.stringify = exports.shorten = exports.minmax = exports.renameRegionsIfNeeded = exports.renameRegionIfNeeded = exports.makeAbortableReaction = 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.useDebounce = exports.inProduction = exports.inDevelopment = exports.isFeature = exports.SimpleFeature = void 0;
-exports.avg = exports.sum = exports.min = exports.max = exports.localStorageSetItem = exports.localStorageGetItem = exports.getEnv = exports.measureGridWidth = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = exports.toLocale = exports.getBpDisplayStr = exports.supportedIndexingAdapters = void 0;
+exports.supportedIndexingAdapters = exports.bytesForRegions = exports.objectHash = exports.hashCode = exports.updateStatus = exports.generateCodonTable = exports.defaultCodonTable = exports.defaultStops = exports.defaultStarts = exports.measureText = exports.rIC = exports.blobToDataURL = exports.complement = exports.reverse = exports.revcom = exports.isElectron = exports.stringify = exports.shorten = exports.minmax = exports.renameRegionsIfNeeded = exports.renameRegionIfNeeded = exports.makeAbortableReaction = 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 = exports.inProduction = exports.inDevelopment = void 0;
+exports.isFeature = exports.SimpleFeature = exports.avg = exports.sum = exports.min = exports.max = exports.localStorageSetItem = exports.localStorageGetItem = exports.getEnv = exports.measureGridWidth = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = exports.toLocale = exports.getBpDisplayStr = void 0;
 /* eslint-disable @typescript-eslint/no-explicit-any */
 const react_1 = require("react");
 const is_object_1 = __importDefault(require("is-object"));
 const mobx_state_tree_1 = require("mobx-state-tree");
 const mobx_1 = require("mobx");
-const simpleFeature_1 = __importStar(require("./simpleFeature"));
-exports.SimpleFeature = simpleFeature_1.default;
-Object.defineProperty(exports, "isFeature", { enumerable: true, get: function () { return simpleFeature_1.isFeature; } });
 const types_1 = require("./types");
 const aborting_1 = require("./aborting");
 const types_2 = require("./types");
+const useMeasure_1 = __importDefault(require("@jbrowse/core/util/useMeasure"));
 __exportStar(require("./types"), exports);
 __exportStar(require("./aborting"), exports);
 __exportStar(require("./when"), exports);
@@ -66,6 +52,20 @@ function useDebounce(value, delay) {
     return debouncedValue;
 }
 exports.useDebounce = useDebounce;
+// used in ViewContainer files to get the width
+function useWidthSetter(view, padding) {
+    const [ref, { width }] = (0, useMeasure_1.default)();
+    (0, react_1.useEffect)(() => {
+        if (width && (0, mobx_state_tree_1.isAlive)(view)) {
+            // sets after a requestAnimationFrame
+            // https://stackoverflow.com/a/58701523/2129219
+            // avoids ResizeObserver loop error being shown during development
+            requestAnimationFrame(() => view.setWidth(width - Number.parseInt(padding, 10) * 2));
+        }
+    }, [padding, view, width]);
+    return ref;
+}
+exports.useWidthSetter = useWidthSetter;
 // https://stackoverflow.com/questions/56283920/
 function useDebouncedCallback(callback, wait = 400) {
     // track args & timeout handle between calls
@@ -159,7 +159,7 @@ function springAnimate(fromValue, toValue, setValue, onFinish = () => { }, preci
     ];
 }
 exports.springAnimate = springAnimate;
-/** find the first node in the hierarchy that matches the given 'is' typescript type guard predicate */
+// find the first node in the hierarchy that matches the given 'is' typescript type guard predicate
 function findParentThatIs(node, predicate) {
     return findParentThat(node, predicate);
 }
@@ -278,12 +278,12 @@ function parseLocStringOneBased(locString, isValidRefName) {
     let reversed = false;
     if (locString.endsWith('[rev]')) {
         reversed = true;
-        locString = locString.replace(/\[rev\]$/, '');
+        locString = locString.replace(/\[rev]$/, '');
     }
     // remove any whitespace
     locString = locString.replace(/\s/, '');
     // refNames can have colons, ref https://samtools.github.io/hts-specs/SAMv1.pdf Appendix A
-    const assemblyMatch = locString.match(/(\{(.+)\})?(.+)/);
+    const assemblyMatch = locString.match(/({(.+)})?(.+)/);
     if (!assemblyMatch) {
         throw new Error(`invalid location string: "${locString}"`);
     }
@@ -465,8 +465,8 @@ function bpToPx(bp, { reversed, end = 0, start = 0, }, bpPerPx) {
     return roundToNearestPointOne((reversed ? end - bp : bp - start) / bpPerPx);
 }
 exports.bpToPx = bpToPx;
-const oneEightyOverPi = 180.0 / Math.PI;
-const piOverOneEighty = Math.PI / 180.0;
+const oneEightyOverPi = 180 / Math.PI;
+const piOverOneEighty = Math.PI / 180;
 function radToDeg(radians) {
     return (radians * oneEightyOverPi) % 360;
 }
@@ -505,7 +505,7 @@ function bpSpanPx(leftBp, rightBp, region, bpPerPx) {
 exports.bpSpanPx = bpSpanPx;
 // do an array map of an iterable
 function iterMap(iter, func, sizeHint) {
-    const results = sizeHint ? new Array(sizeHint) : [];
+    const results = Array.from({ length: sizeHint || 0 });
     let counter = 0;
     for (const item of iter) {
         results[counter] = func(item);
@@ -552,7 +552,7 @@ exports.findLastIndex = findLastIndex;
  * @param errorFunction -
  */
 function makeAbortableReaction(self, dataFunction, asyncReactionFunction, 
-// @ts-ignore
+// @ts-expect-error
 reactionOptions, startedFunction, successFunction, errorFunction) {
     let inProgress;
     function handleError(error) {
@@ -585,7 +585,7 @@ reactionOptions, startedFunction, successFunction, errorFunction) {
         startedFunction(thisInProgress);
         try {
             const result = await asyncReactionFunction(data, thisInProgress.signal, self, 
-            // @ts-ignore
+            // @ts-expect-error
             mobxReactionHandle);
             (0, aborting_1.checkAbortSignal)(thisInProgress.signal);
             if ((0, mobx_state_tree_1.isAlive)(self)) {
@@ -610,15 +610,12 @@ function renameRegionIfNeeded(refNameMap, region) {
     if ((0, mobx_state_tree_1.isStateTreeNode)(region) && !(0, mobx_state_tree_1.isAlive)(region)) {
         return region;
     }
-    if (region && refNameMap && refNameMap[region.refName]) {
+    if (region && (refNameMap === null || refNameMap === void 0 ? void 0 : refNameMap[region.refName])) {
         // clone the region so we don't modify it
-        if ((0, mobx_state_tree_1.isStateTreeNode)(region)) {
-            // @ts-ignore
-            region = { ...(0, mobx_state_tree_1.getSnapshot)(region) };
-        }
-        else {
-            region = { ...region };
-        }
+        region = (0, mobx_state_tree_1.isStateTreeNode)(region)
+            ? // @ts-expect-error
+                { ...(0, mobx_state_tree_1.getSnapshot)(region) }
+            : { ...region };
         // modify it directly in the container
         const newRef = refNameMap[region.refName];
         if (newRef) {
@@ -634,7 +631,7 @@ async function renameRegionsIfNeeded(assemblyManager, args) {
         throw new Error('sessionId is required');
     }
     const assemblyNames = regions.map(region => region.assemblyName);
-    const assemblyMaps = Object.fromEntries(await Promise.all(assemblyNames.map(async (assemblyName) => {
+    const assemblyMaps = Object.fromEntries(await Promise.all([...new Set(assemblyNames)].map(async (assemblyName) => {
         return [
             assemblyName,
             await assemblyManager.getRefNameMapForAdapter(adapterConfig, assemblyName, args),
@@ -741,11 +738,9 @@ exports.blobToDataURL = blobToDataURL;
 // otherwise listens for prerendered_canvas but reads empty pixels, and doesn't
 // get the contents of the canvas
 exports.rIC = typeof jest === 'undefined'
-    ? // @ts-ignore
-        typeof window !== 'undefined' && window.requestIdleCallback
-            ? // @ts-ignore
-                window.requestIdleCallback
-            : (cb) => setTimeout(() => cb(), 1)
+    ? typeof window !== 'undefined' && window.requestIdleCallback
+        ? window.requestIdleCallback
+        : (cb) => setTimeout(() => cb(), 1)
     : (cb) => cb();
 // prettier-ignore
 const widths = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.2796875, 0.2765625, 0.3546875, 0.5546875, 0.5546875, 0.8890625, 0.665625, 0.190625, 0.3328125, 0.3328125, 0.3890625, 0.5828125, 0.2765625, 0.3328125, 0.2765625, 0.3015625, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.2765625, 0.2765625, 0.584375, 0.5828125, 0.584375, 0.5546875, 1.0140625, 0.665625, 0.665625, 0.721875, 0.721875, 0.665625, 0.609375, 0.7765625, 0.721875, 0.2765625, 0.5, 0.665625, 0.5546875, 0.8328125, 0.721875, 0.7765625, 0.665625, 0.7765625, 0.721875, 0.665625, 0.609375, 0.721875, 0.665625, 0.94375, 0.665625, 0.665625, 0.609375, 0.2765625, 0.3546875, 0.2765625, 0.4765625, 0.5546875, 0.3328125, 0.5546875, 0.5546875, 0.5, 0.5546875, 0.5546875, 0.2765625, 0.5546875, 0.5546875, 0.221875, 0.240625, 0.5, 0.221875, 0.8328125, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.3328125, 0.5, 0.2765625, 0.5546875, 0.5, 0.721875, 0.5, 0.5, 0.5, 0.3546875, 0.259375, 0.353125, 0.5890625];
@@ -910,10 +905,10 @@ exports.supportedIndexingAdapters = supportedIndexingAdapters;
 function getBpDisplayStr(totalBp) {
     let str;
     if (Math.floor(totalBp / 1000000) > 0) {
-        str = `${parseFloat((totalBp / 1000000).toPrecision(3))}Mbp`;
+        str = `${Number.parseFloat((totalBp / 1000000).toPrecision(3))}Mbp`;
     }
     else if (Math.floor(totalBp / 1000) > 0) {
-        str = `${parseFloat((totalBp / 1000).toPrecision(3))}Kbp`;
+        str = `${Number.parseFloat((totalBp / 1000).toPrecision(3))}Kbp`;
     }
     else {
         str = `${toLocale(Math.floor(totalBp))}bp`;
@@ -926,18 +921,12 @@ function toLocale(n) {
 }
 exports.toLocale = toLocale;
 function getTickDisplayStr(totalBp, bpPerPx) {
-    let str;
-    if (Math.floor(bpPerPx / 1000) > 0) {
-        str = `${toLocale(parseFloat((totalBp / 1000000).toFixed(2)))}M`;
-    }
-    else {
-        str = `${toLocale(Math.floor(totalBp))}`;
-    }
-    return str;
+    return Math.floor(bpPerPx / 1000) > 0
+        ? `${toLocale(Number.parseFloat((totalBp / 1000000).toFixed(2)))}M`
+        : `${toLocale(Math.floor(totalBp))}`;
 }
 exports.getTickDisplayStr = getTickDisplayStr;
 function getViewParams(model, exportSVG) {
-    // @ts-ignore
     const { dynamicBlocks, staticBlocks, offsetPx } = getContainingView(model);
     const b = (dynamicBlocks === null || dynamicBlocks === void 0 ? void 0 : dynamicBlocks.contentBlocks[0]) || {};
     const staticblock = (staticBlocks === null || staticBlocks === void 0 ? void 0 : staticBlocks.contentBlocks[0]) || {};
@@ -1062,3 +1051,6 @@ function avg(arr) {
     return sum(arr) / arr.length;
 }
 exports.avg = avg;
+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; } });

package/util/io/RemoteFileWithRangeCache.js

@@ -50,8 +50,8 @@ class RemoteFileWithRangeCache extends generic_filehandle_1.RemoteFile {
             const rangeParse = /bytes=(\d+)-(\d+)/.exec(range);
             if (rangeParse) {
                 const [, start, end] = rangeParse;
-                const s = parseInt(start, 10);
-                const e = parseInt(end, 10);
+                const s = Number.parseInt(start, 10);
+                const e = Number.parseInt(end, 10);
                 const response = (await globalRangeCache.getRange(url, s, e - s + 1, {
                     signal: init && init.signal,
                 }));

package/util/io/index.d.ts

@@ -1,7 +1,8 @@
 import { GenericFilehandle, Fetcher } from 'generic-filehandle';
-import { RemoteFileWithRangeCache } from './RemoteFileWithRangeCache';
-import { FileLocation } from '../types';
+import { FileLocation, UriLocation } from '../types';
 import PluginManager from '../../PluginManager';
-export { RemoteFileWithRangeCache };
+/** if a UriLocation has a baseUri, resolves its uri with respect to that base */
+export declare function resolveUriLocation(location: UriLocation): UriLocation;
 export declare function openLocation(location: FileLocation, pluginManager?: PluginManager): GenericFilehandle;
 export declare function getFetcher(location: FileLocation, pluginManager?: PluginManager): Fetcher;
+export { RemoteFileWithRangeCache } from './RemoteFileWithRangeCache';

package/util/io/index.js

@@ -3,12 +3,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getFetcher = exports.openLocation = exports.RemoteFileWithRangeCache = void 0;
+exports.RemoteFileWithRangeCache = exports.getFetcher = exports.openLocation = exports.resolveUriLocation = void 0;
 const generic_filehandle_1 = require("generic-filehandle");
 const detect_node_1 = __importDefault(require("detect-node"));
 // locals
 const RemoteFileWithRangeCache_1 = require("./RemoteFileWithRangeCache");
-Object.defineProperty(exports, "RemoteFileWithRangeCache", { enumerable: true, get: function () { return RemoteFileWithRangeCache_1.RemoteFileWithRangeCache; } });
 const types_1 = require("../types");
 const tracks_1 = require("../tracks");
 const __1 = require("../");
@@ -18,6 +17,13 @@ function isLocalPathLocation(location) {
 function isBlobLocation(location) {
     return 'blobId' in location;
 }
+/** if a UriLocation has a baseUri, resolves its uri with respect to that base */
+function resolveUriLocation(location) {
+    return location.baseUri
+        ? { ...location, uri: new URL(location.uri, location.baseUri).href }
+        : location;
+}
+exports.resolveUriLocation = resolveUriLocation;
 function openLocation(location, pluginManager) {
     if (!location) {
         throw new Error('must provide a location to openLocation');
@@ -47,9 +53,7 @@ function openLocation(location, pluginManager) {
             throw new Error('No URI provided');
         }
         // Resolve any relative URLs to absolute URLs
-        const absoluteLocation = location.baseUri
-            ? { ...location, uri: new URL(location.uri, location.baseUri).href }
-            : location;
+        const absoluteLocation = resolveUriLocation(location);
         // If there is a plugin manager, we can try internet accounts
         if (pluginManager) {
             const internetAccount = getInternetAccount(location, pluginManager);
@@ -105,10 +109,11 @@ function getInternetAccount(location, pluginManager) {
 async function checkAuthNeededFetch(url, opts) {
     var _a;
     const response = await fetch(url, opts);
-    if (response.status === 401) {
-        if ((_a = response.headers.get('WWW-Authenticate')) === null || _a === void 0 ? void 0 : _a.includes('Basic')) {
-            throw new types_1.AuthNeededError('Accessing HTTPBasic resource without authentication', url.toString());
-        }
+    if (response.status === 401 &&
+        ((_a = response.headers.get('WWW-Authenticate')) === null || _a === void 0 ? void 0 : _a.includes('Basic'))) {
+        throw new types_1.AuthNeededError('Accessing HTTPBasic resource without authentication', url.toString());
     }
     return response;
 }
+var RemoteFileWithRangeCache_2 = require("./RemoteFileWithRangeCache");
+Object.defineProperty(exports, "RemoteFileWithRangeCache", { enumerable: true, get: function () { return RemoteFileWithRangeCache_2.RemoteFileWithRangeCache; } });

package/util/jexl.js

@@ -45,7 +45,9 @@ function default_1( /* config?: any*/) {
     j.addFunction('replaceAll', (s, match, sub) => s.replaceAll(match, sub));
     j.addFunction('slice', (s, start, end) => s.slice(start, end));
     j.addFunction('startsWith', (s, search, pos) => s.startsWith(search, pos));
-    j.addFunction('substring', (s, start, end) => s.substring(start, end));
+    j.addFunction('substring', (s, start, end) => 
+    // eslint-disable-next-line unicorn/prefer-string-slice
+    s.substring(start, end));
     j.addFunction('toLowerCase', (s) => s.toLowerCase());
     j.addFunction('toUpperCase', (s) => s.toUpperCase());
     j.addFunction('trim', (s) => s.trim());