@jbrowse/core 2.17.0 → 3.0.0

package/util/Base1DUtils.js

@@ -39,8 +39,6 @@ function moveTo(self, start, end) {
     }
     const targetBpPerPx = len / (width - interRegionPaddingWidth * numBlocksWideEnough);
     const newBpPerPx = self.zoomTo(targetBpPerPx);
-    // If our target bpPerPx was smaller than the allowed minBpPerPx, adjust
-    // the scroll so the requested range is in the middle of the screen
     let extraBp = 0;
     if (targetBpPerPx < newBpPerPx) {
         extraBp = ((newBpPerPx - targetBpPerPx) * self.width) / 2;
@@ -61,7 +59,6 @@ function moveTo(self, start, end) {
 function coord(r, bp) {
     return Math.floor(r.reversed ? r.end - bp : r.start + bp) + 1;
 }
-// manual return type since getSnapshot hard to infer here
 function pxToBp(self, px) {
     var _a;
     let bpSoFar = 0;
@@ -72,7 +69,6 @@ function pxToBp(self, px) {
         const r = displayedRegions[0];
         const snap = r;
         return {
-            // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
             ...snap,
             oob: true,
             coord: coord(r, bp),
@@ -89,7 +85,6 @@ function pxToBp(self, px) {
         if (len + bpSoFar > bp && bpSoFar <= bp) {
             const snap = r;
             return {
-                // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
                 ...snap,
                 oob: false,
                 offset,
@@ -97,8 +92,6 @@ function pxToBp(self, px) {
                 index: i,
             };
         }
-        // add the interRegionPaddingWidth if the boundary is in the screen e.g. in
-        // a static block
         if (((_a = blocks[currBlock]) === null || _a === void 0 ? void 0 : _a.regionNumber) === i) {
             bpSoFar += len + interRegionPaddingBp;
             currBlock++;
@@ -113,7 +106,6 @@ function pxToBp(self, px) {
         const offset = bp - bpSoFar + len;
         const snap = r;
         return {
-            // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
             ...snap,
             oob: true,
             offset,
@@ -151,8 +143,6 @@ function bpToPx({ refName, coord, regionNumber, self, }) {
             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
         if (((_a = blocks[currBlock]) === null || _a === void 0 ? void 0 : _a.regionNumber) === i) {
             bpSoFar += len + interRegionPaddingBp;
             currBlock++;
@@ -189,8 +179,6 @@ function bpToPxMap({ refName, coord, regionNumber, self, }) {
             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
         if (((_a = blocks[currBlock]) === null || _a === void 0 ? void 0 : _a.regionNumber) === i) {
             bpSoFar += len + interRegionPaddingBp;
             currBlock++;

package/util/Base1DViewModel.d.ts

@@ -1,7 +1,7 @@
-import { Instance } from 'mobx-state-tree';
-import { Feature } from './simpleFeature';
-import { Region as IRegion } from './types';
-import { BpOffset } from './Base1DUtils';
+import type { BpOffset } from './Base1DUtils';
+import type { Feature } from './simpleFeature';
+import type { Region as IRegion } from './types';
+import type { Instance } from 'mobx-state-tree';
 declare const Base1DView: import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<IRegion[], IRegion[], IRegion[]>, [undefined]>;
@@ -13,60 +13,21 @@ declare const Base1DView: import("mobx-state-tree").IModelType<{
     features: undefined | Feature[];
     volatileWidth: number;
 } & {
-    /**
-     * #action
-     */
     setDisplayedRegions(regions: IRegion[]): void;
-    /**
-     * #action
-     */
     setBpPerPx(val: number): void;
-    /**
-     * #action
-     */
     setVolatileWidth(width: number): void;
 } & {
-    /**
-     * #getter
-     */
     readonly width: number;
-    /**
-     * #getter
-     */
     readonly assemblyNames: string[];
-    /**
-     * #getter
-     */
     readonly displayedRegionsTotalPx: number;
-    /**
-     * #getter
-     */
     readonly maxOffset: number;
-    /**
-     * #getter
-     */
     readonly minOffset: number;
-    /**
-     * #getter
-     */
     readonly totalBp: number;
 } & {
-    /**
-     * #getter
-     */
     readonly dynamicBlocks: import("./blockTypes").BlockSet;
-    /**
-     * #getter
-     */
     readonly staticBlocks: import("./blockTypes").BlockSet;
-    /**
-     * #getter
-     */
     readonly currBp: number;
 } & {
-    /**
-     * #method
-     */
     pxToBp(px: number): {
         coord: number;
         index: number;
@@ -78,59 +39,21 @@ declare const Base1DView: import("mobx-state-tree").IModelType<{
         end: number;
         reversed?: boolean;
     };
-    /**
-     * #method
-     */
     bpToPx({ refName, coord, regionNumber, }: {
         refName: string;
         coord: number;
         regionNumber?: number;
     }): number | undefined;
 } & {
-    /**
-     * #action
-     */
     setFeatures(features: Feature[]): void;
-    /**
-     * #action
-     * this makes a zoomed out view that shows all displayedRegions that makes
-     * the overview bar square with the scale bar
-     */
     showAllRegions(): void;
-    /**
-     * #action
-     */
     zoomOut(): void;
-    /**
-     * #action
-     */
     zoomIn(): void;
-    /**
-     * #action
-     */
     zoomTo(bpPerPx: number, offset?: number): number;
-    /**
-     * #action
-     */
     scrollTo(offsetPx: number): number;
-    /**
-     * #action
-     */
     centerAt(coord: number, refName: string | undefined, regionNumber: number): void;
-    /**
-     * #action
-     * note: the scroll is clamped to keep the view on the main screen
-     */
     scroll(distance: number): number;
 } & {
-    /**
-     * #action
-     * offset is the base-pair-offset in the displayed region, index is the
-     * index of the displayed region in the linear genome view
-     *
-     * @param start - object as `{start, end, offset, index}`
-     * @param end - object as `{start, end, offset, index}`
-     */
     moveTo(start?: BpOffset, end?: BpOffset): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type Base1DViewStateModel = typeof Base1DView;

package/util/Base1DViewModel.js

@@ -4,42 +4,19 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const mobx_state_tree_1 = require("mobx-state-tree");
-const index_1 = require("./index");
-const mst_1 = require("./types/mst");
+const Base1DUtils_1 = require("./Base1DUtils");
 const calculateDynamicBlocks_1 = __importDefault(require("./calculateDynamicBlocks"));
 const calculateStaticBlocks_1 = __importDefault(require("./calculateStaticBlocks"));
-const Base1DUtils_1 = require("./Base1DUtils");
-/**
- * #stateModel Base1DView
- * used in non-lgv view representations of a 1d view e.g. the two axes of the
- * dotplot use this
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const index_1 = require("./index");
+const mst_1 = require("./types/mst");
+function x() { }
 const Base1DView = mobx_state_tree_1.types
     .model('Base1DView', {
-    /**
-     * #property
-     */
     id: mst_1.ElementId,
-    /**
-     * #property
-     */
     displayedRegions: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.frozen(), []),
-    /**
-     * #property
-     */
     bpPerPx: 0,
-    /**
-     * #property
-     */
     offsetPx: 0,
-    /**
-     * #property
-     */
     interRegionPaddingWidth: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
-    /**
-     * #property
-     */
     minimumBlockWidth: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
 })
     .volatile(() => ({
@@ -47,133 +24,72 @@ const Base1DView = mobx_state_tree_1.types
     volatileWidth: 0,
 }))
     .actions(self => ({
-    /**
-     * #action
-     */
     setDisplayedRegions(regions) {
         self.displayedRegions = (0, mobx_state_tree_1.cast)(regions);
     },
-    /**
-     * #action
-     */
     setBpPerPx(val) {
         self.bpPerPx = val;
     },
-    /**
-     * #action
-     */
     setVolatileWidth(width) {
         self.volatileWidth = width;
     },
 }))
     .views(self => ({
-    /**
-     * #getter
-     */
     get width() {
         return self.volatileWidth;
     },
-    /**
-     * #getter
-     */
     get assemblyNames() {
         return [...new Set(self.displayedRegions.map(r => r.assemblyName))];
     },
-    /**
-     * #getter
-     */
     get displayedRegionsTotalPx() {
         return this.totalBp / self.bpPerPx;
     },
-    /**
-     * #getter
-     */
     get maxOffset() {
-        // objectively determined to keep the linear genome on the main screen
         const leftPadding = 10;
         return this.displayedRegionsTotalPx - leftPadding;
     },
-    /**
-     * #getter
-     */
     get minOffset() {
-        // objectively determined to keep the linear genome on the main screen
         const rightPadding = 30;
         return -this.width + rightPadding;
     },
-    /**
-     * #getter
-     */
     get totalBp() {
         return (0, index_1.sum)(self.displayedRegions.map(a => a.end - a.start));
     },
 }))
     .views(self => ({
-    /**
-     * #getter
-     */
     get dynamicBlocks() {
         return (0, calculateDynamicBlocks_1.default)(self);
     },
-    /**
-     * #getter
-     */
     get staticBlocks() {
         return (0, calculateStaticBlocks_1.default)(self);
     },
-    /**
-     * #getter
-     */
     get currBp() {
         return (0, index_1.sum)(this.dynamicBlocks.map(a => a.end - a.start));
     },
 }))
     .views(self => ({
-    /**
-     * #method
-     */
     pxToBp(px) {
         return (0, Base1DUtils_1.pxToBp)(self, px);
     },
-    /**
-     * #method
-     */
     bpToPx({ refName, coord, regionNumber, }) {
         var _a;
         return (_a = (0, Base1DUtils_1.bpToPx)({ refName, coord, regionNumber, self })) === null || _a === void 0 ? void 0 : _a.offsetPx;
     },
 }))
     .actions(self => ({
-    /**
-     * #action
-     */
     setFeatures(features) {
         self.features = features;
     },
-    /**
-     * #action
-     * this makes a zoomed out view that shows all displayedRegions that makes
-     * the overview bar square with the scale bar
-     */
     showAllRegions() {
         self.bpPerPx = self.totalBp / self.width;
         self.offsetPx = 0;
     },
-    /**
-     * #action
-     */
     zoomOut() {
         this.zoomTo(self.bpPerPx * 2);
     },
-    /**
-     * #action
-     */
     zoomIn() {
         this.zoomTo(self.bpPerPx / 2);
     },
-    /**
-     * #action
-     */
     zoomTo(bpPerPx, offset = self.width / 2) {
         const newBpPerPx = (0, index_1.clamp)(bpPerPx, 'minBpPerPx' in self ? self.minBpPerPx : 0, 'maxBpPerPx' in self
             ? self.maxBpPerPx
@@ -183,22 +99,14 @@ const Base1DView = mobx_state_tree_1.types
             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;
     },
-    /**
-     * #action
-     */
     scrollTo(offsetPx) {
         const newOffsetPx = (0, index_1.clamp)(offsetPx, self.minOffset, self.maxOffset);
         self.offsetPx = newOffsetPx;
         return newOffsetPx;
     },
-    /**
-     * #action
-     */
     centerAt(coord, refName, regionNumber) {
         if (!refName) {
             return;
@@ -212,10 +120,6 @@ const Base1DView = mobx_state_tree_1.types
             this.scrollTo(Math.round(centerPx - self.width / 2));
         }
     },
-    /**
-     * #action
-     * note: the scroll is clamped to keep the view on the main screen
-     */
     scroll(distance) {
         const oldOffsetPx = self.offsetPx;
         const newOffsetPx = (0, index_1.clamp)(self.offsetPx + distance, self.minOffset, self.maxOffset);
@@ -224,14 +128,6 @@ const Base1DView = mobx_state_tree_1.types
     },
 }))
     .actions(self => ({
-    /**
-     * #action
-     * offset is the base-pair-offset in the displayed region, index is the
-     * index of the displayed region in the linear genome view
-     *
-     * @param start - object as `{start, end, offset, index}`
-     * @param end - object as `{start, end, offset, index}`
-     */
     moveTo(start, end) {
         (0, Base1DUtils_1.moveTo)(self, start, end);
     },

package/util/QuickLRU.js

@@ -1,12 +1,5 @@
 "use strict";
-// vendored from quick-lru@6.1.1, didn't like being compiled as a 'pure-esm' nodejs dependency
-// the license is reproduced below https://github.com/sindresorhus/quick-lru/blob/main/license
-// MIT License
 Object.defineProperty(exports, "__esModule", { value: true });
-// Copyright (c) Sindre Sorhus <sindresorhus@gmail.com> (https://sindresorhus.com)
-// Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
-// The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
-// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 class QuickLRU extends Map {
     constructor(options = {}) {
         super();
@@ -16,7 +9,6 @@ class QuickLRU extends Map {
         if (typeof options.maxAge === 'number' && options.maxAge === 0) {
             throw new TypeError('`maxAge` must be a number greater than 0');
         }
-        // TODO: Use private class fields when ESLint supports them.
         this.maxSize = options.maxSize;
         this.maxAge = options.maxAge || Number.POSITIVE_INFINITY;
         this.onEviction = options.onEviction;
@@ -24,7 +16,6 @@ class QuickLRU extends Map {
         this.oldCache = new Map();
         this._size = 0;
     }
-    // TODO: Use private class methods when targeting Node.js 16.
     _emitEvictions(cache) {
         if (typeof this.onEviction !== 'function') {
             return;

package/util/TimeTraveller.js

@@ -1,6 +1,5 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-// adapted from https://github.com/mobxjs/mobx-state-tree/blob/master/packages/mst-middlewares/src/time-traveller.ts
 const mobx_state_tree_1 = require("mobx-state-tree");
 const MAX_HISTORY_LENGTH = 20;
 function debounce(func, timeout = 300) {
@@ -34,11 +33,9 @@ const TimeTraveller = mobx_state_tree_1.types
     let snapshotDisposer;
     let skipNextUndoState = false;
     return {
-        // allows user code to (temporarily) stop tracking undo states
         stopTrackingUndo() {
             self.notTrackingUndo = true;
         },
-        // allows user code to resume tracking undo states
         resumeTrackingUndo() {
             self.notTrackingUndo = false;
         },
@@ -47,7 +44,6 @@ const TimeTraveller = mobx_state_tree_1.types
                 return;
             }
             if (skipNextUndoState) {
-                // skip recording if this state was caused by undo / redo
                 skipNextUndoState = false;
                 return;
             }

package/util/aborting.d.ts

@@ -2,29 +2,9 @@ import { Observable } from 'rxjs';
 declare class AbortError extends Error {
     code: string | undefined;
 }
-/**
- * properly check if the given AbortSignal is aborted.
- * per the standard, if the signal reads as aborted,
- * this function throws either a DOMException AbortError, or a regular error
- * with a `code` attribute set to `ERR_ABORTED`.
- *
- * for convenience, passing `undefined` is a no-op
- *
- * @param signal -
- * @returns nothing
- */
 export declare function checkAbortSignal(signal?: AbortSignal): void;
-/**
- * Skips to the next tick, then runs `checkAbortSignal`.
- * Await this to inside an otherwise synchronous loop to
- * provide a place to break when an abort signal is received.
- */
 export declare function abortBreakPoint(signal?: AbortSignal): Promise<void>;
 export declare function makeAbortError(): AbortError | DOMException;
 export declare function observeAbortSignal(signal?: AbortSignal): Observable<Event>;
-/**
- * check if the given exception was caused by an operation being intentionally aborted
- * @param exception -
- */
 export declare function isAbortException(exception: unknown): boolean;
 export {};

package/util/aborting.js

@@ -8,17 +8,6 @@ exports.isAbortException = isAbortException;
 const rxjs_1 = require("rxjs");
 class AbortError extends Error {
 }
-/**
- * properly check if the given AbortSignal is aborted.
- * per the standard, if the signal reads as aborted,
- * this function throws either a DOMException AbortError, or a regular error
- * with a `code` attribute set to `ERR_ABORTED`.
- *
- * for convenience, passing `undefined` is a no-op
- *
- * @param signal -
- * @returns nothing
- */
 function checkAbortSignal(signal) {
     if (!signal) {
         return;
@@ -33,16 +22,7 @@ function checkAbortSignal(signal) {
 function timeout(ms) {
     return new Promise(resolve => setTimeout(resolve, ms));
 }
-/**
- * Skips to the next tick, then runs `checkAbortSignal`.
- * Await this to inside an otherwise synchronous loop to
- * provide a place to break when an abort signal is received.
- */
 async function abortBreakPoint(signal) {
-    // it was observed that an actual timeout is needed to get the aborting (wrap
-    // hicrenderer in a try catch, console.error the error, and rethrow the error
-    // to see). using await Promise.resolve() did not appear to allow aborting to
-    // occur
     await timeout(1);
     checkAbortSignal(signal);
 }
@@ -60,20 +40,9 @@ function observeAbortSignal(signal) {
     }
     return (0, rxjs_1.fromEvent)(signal, 'abort');
 }
-/**
- * check if the given exception was caused by an operation being intentionally aborted
- * @param exception -
- */
 function isAbortException(exception) {
     return (exception instanceof Error &&
-        // DOMException
         (exception.name === 'AbortError' ||
-            // standard-ish non-DOM abort exception
             exception.code === 'ERR_ABORTED' ||
-            // message contains aborted for bubbling through RPC
-            // things we have seen that we want to catch here
-            // Error: aborted
-            // AbortError: aborted
-            // AbortError: The user aborted a request.
             !!/\b(aborted|aborterror)\b/i.test(exception.message)));
 }

package/util/analytics.js

@@ -12,7 +12,6 @@ async function writeAWSAnalytics(rootModel, initialTimeStamp, sessionQuery) {
         const savedSessionCount = Object.keys(localStorage).filter(name => name.includes('localSaved-')).length;
         const { jbrowse: config, session, version: ver } = rootModel;
         const { tracks, assemblies, plugins } = config;
-        // stats to be recorded in db
         const stats = {
             ver,
             'plugins-count': (plugins === null || plugins === void 0 ? void 0 : plugins.length) || 0,
@@ -23,29 +22,23 @@ async function writeAWSAnalytics(rootModel, initialTimeStamp, sessionQuery) {
             'open-views': (session === null || session === void 0 ? void 0 : session.views.length) || 0,
             'synteny-tracks-count': multiAssemblyTracks,
             'saved-sessions-count': savedSessionCount,
-            // field if existing session param in query before autogenerated param
             'existing-session-param-type': (sessionQuery === null || sessionQuery === void 0 ? void 0 : sessionQuery.split('-')[0]) || 'none',
-            // screen geometry
             'scn-h': window.screen.height,
             'scn-w': window.screen.width,
-            // window geometry
             'win-h': window.innerHeight,
             'win-w': window.innerWidth,
             electron: util_1.isElectron,
             loadTime: (Date.now() - initialTimeStamp) / 1000,
             jb2: true,
         };
-        // stringifies the track type counts, gets processed in lambda
         tracks.forEach((track) => {
             const key = `track-types-${track.type}`;
             stats[key] = stats[key] + 1 || 1;
         });
-        // stringifies the session track type counts, gets processed in lambda
         session === null || session === void 0 ? void 0 : session.sessionTracks.forEach((track) => {
             const key = `sessionTrack-types-${track.type}`;
             stats[key] = stats[key] + 1 || 1;
         });
-        // put stats into a query string for get request
         const qs = Object.keys(stats)
             .map(key => `${key}=${stats[key]}`)
             .join('&');
@@ -59,13 +52,12 @@ async function writeGAAnalytics(rootModel, initialTimestamp) {
     var _a;
     const jbrowseUser = 'UA-7115575-5';
     const stats = {
-        'tracks-count': rootModel.jbrowse.tracks.length, // this is all possible tracks
+        'tracks-count': rootModel.jbrowse.tracks.length,
         ver: rootModel.version,
         electron: util_1.isElectron,
         loadTime: Date.now() - initialTimestamp,
         pluginNames: ((_a = rootModel.jbrowse.plugins) === null || _a === void 0 ? void 0 : _a.map((plugin) => plugin.name)) || '',
     };
-    // create script
     let analyticsScript = "(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){";
     analyticsScript +=
         '(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),';
@@ -88,10 +80,7 @@ async function writeGAAnalytics(rootModel, initialTimestamp) {
 function doAnalytics(rootModel, initialTimestamp, initialSessionQuery) {
     if (rootModel &&
         !(0, configuration_1.readConfObject)(rootModel.jbrowse.configuration, 'disableAnalytics')) {
-        // ok if these are unhandled
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
         writeAWSAnalytics(rootModel, initialTimestamp, initialSessionQuery);
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
         writeGAAnalytics(rootModel, initialTimestamp);
     }
 }

package/util/blockTypes.d.ts

@@ -33,9 +33,6 @@ export declare class BaseBlock {
     widthPx: number;
     variant?: string;
     isLeftEndOfDisplayedRegion?: boolean;
-    /**
-     * a block that should be shown as filled with data
-     */
     constructor(data: Record<string, any>);
     toRegion(): {
         refName: string;
@@ -48,10 +45,6 @@ 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;
@@ -59,10 +52,6 @@ export declare class ElidedBlock extends BaseBlock {
     constructor(data: Record<string, any>);
     push(otherBlock: ElidedBlock): void;
 }
-/**
- * marker block that sits between two different displayed regions
- * and provides a thick border between them
- */
 export declare class InterRegionPaddingBlock extends BaseBlock {
     type: string;
 }