@jbrowse/core 2.17.0 → 3.0.0

package/util/io/RemoteFileWithRangeCache.d.ts

@@ -1,16 +1,15 @@
-import { Buffer } from 'buffer';
-import { RemoteFile, PolyfilledResponse } from 'generic-filehandle';
+import { RemoteFile } from 'generic-filehandle2';
 export interface BinaryRangeResponse {
     headers: Record<string, string>;
     requestDate: Date;
     responseDate: Date;
-    buffer: Buffer;
+    buffer: Uint8Array;
 }
 export declare function clearCache(): void;
 export declare class RemoteFileWithRangeCache extends RemoteFile {
-    fetch(url: RequestInfo, init?: RequestInit): Promise<PolyfilledResponse>;
+    fetch(url: string | RequestInfo, init?: RequestInit): Promise<Response>;
     fetchBinaryRange(url: string, start: number, end: number, options?: {
         headers?: HeadersInit;
-        signal?: AbortSignal;
+        stopToken?: string;
     }): Promise<BinaryRangeResponse>;
 }

package/util/io/RemoteFileWithRangeCache.js

@@ -3,8 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.RemoteFileWithRangeCache = void 0;
 exports.clearCache = clearCache;
 const http_range_fetcher_1 = require("@gmod/http-range-fetcher");
-const buffer_1 = require("buffer");
-const generic_filehandle_1 = require("generic-filehandle");
+const generic_filehandle2_1 = require("generic-filehandle2");
 const fetchers = {};
 function binaryRangeFetch(url, start, end, options = {}) {
     const fetcher = fetchers[url];
@@ -15,21 +14,20 @@ function binaryRangeFetch(url, start, end, options = {}) {
 }
 const globalRangeCache = new http_range_fetcher_1.HttpRangeFetcher({
     fetch: binaryRangeFetch,
-    size: 500 * 1024 ** 2, // 500MiB
-    chunkSize: 128 * 1024, // 128KiB
-    maxFetchSize: 100 * 1024 ** 2, // 100MiB
-    minimumTTL: 24 * 60 * 60 * 1000, // 1 day
+    size: 500 * 1024 ** 2,
+    chunkSize: 128 * 1024,
+    maxFetchSize: 100 * 1024 ** 2,
+    minimumTTL: 24 * 60 * 60 * 1000,
 });
 function clearCache() {
     globalRangeCache.reset();
 }
-class RemoteFileWithRangeCache extends generic_filehandle_1.RemoteFile {
+class RemoteFileWithRangeCache extends generic_filehandle2_1.RemoteFile {
     async fetch(url, init) {
         const str = String(url);
         if (!fetchers[str]) {
             fetchers[str] = this.fetchBinaryRange.bind(this);
         }
-        // if it is a range request, route it through the range cache
         const range = new Headers(init === null || init === void 0 ? void 0 : init.headers).get('range');
         if (range) {
             const rangeParse = /bytes=(\d+)-(\d+)/.exec(range);
@@ -38,8 +36,11 @@ class RemoteFileWithRangeCache extends generic_filehandle_1.RemoteFile {
                 const s = Number.parseInt(start, 10);
                 const e = Number.parseInt(end, 10);
                 const len = e - s;
-                const { buffer, headers } = (await globalRangeCache.getRange(url, s, len + 1, { signal: init === null || init === void 0 ? void 0 : init.signal }));
-                return new Response(buffer, { status: 206, headers });
+                const { buffer, headers } = (await globalRangeCache.getRange(`${url}`, s, len + 1));
+                return new Response(buffer, {
+                    status: 206,
+                    headers,
+                });
             }
         }
         return super.fetch(url, init);
@@ -59,19 +60,16 @@ class RemoteFileWithRangeCache extends generic_filehandle_1.RemoteFile {
             const hint = ' (should be 206 for range requests)';
             throw new Error(`${errorMessage}${res.status === 200 ? hint : ''}`);
         }
-        // translate the Headers object into a regular key -> value object.
-        // will miss duplicate headers of course
         const headers = {};
         for (const [k, v] of res.headers.entries()) {
             headers[k] = v;
         }
-        // return the response headers, and the data buffer
         const arrayBuffer = await res.arrayBuffer();
         return {
             headers,
             requestDate,
             responseDate,
-            buffer: buffer_1.Buffer.from(arrayBuffer),
+            buffer: new Uint8Array(arrayBuffer),
         };
     }
 }

package/util/io/index.d.ts

@@ -1,7 +1,6 @@
-import { GenericFilehandle, Fetcher } from 'generic-filehandle';
-import { FileLocation, UriLocation } from '../types';
-import PluginManager from '../../PluginManager';
-/** if a UriLocation has a baseUri, resolves its uri with respect to that base */
+import type PluginManager from '../../PluginManager';
+import type { FileLocation, UriLocation } from '../types';
+import type { Fetcher, GenericFilehandle } from 'generic-filehandle2';
 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;

package/util/io/index.js

@@ -7,20 +7,18 @@ exports.RemoteFileWithRangeCache = void 0;
 exports.resolveUriLocation = resolveUriLocation;
 exports.openLocation = openLocation;
 exports.getFetcher = getFetcher;
-const generic_filehandle_1 = require("generic-filehandle");
 const detect_node_1 = __importDefault(require("detect-node"));
-// locals
+const generic_filehandle2_1 = require("generic-filehandle2");
 const RemoteFileWithRangeCache_1 = require("./RemoteFileWithRangeCache");
-const types_1 = require("../types");
-const tracks_1 = require("../tracks");
 const __1 = require("../");
+const tracks_1 = require("../tracks");
+const types_1 = require("../types");
 function isLocalPathLocation(location) {
     return 'localPath' in 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 }
@@ -32,36 +30,30 @@ function openLocation(location, pluginManager) {
             throw new Error('No local path provided');
         }
         if (detect_node_1.default || __1.isElectron) {
-            return new generic_filehandle_1.LocalFile(location.localPath);
+            return new generic_filehandle2_1.LocalFile(location.localPath);
         }
         else {
             throw new Error("can't use local files in the browser");
         }
     }
     if (isBlobLocation(location)) {
-        // special case where blob is not directly stored on the model, use a getter
         const blob = (0, tracks_1.getBlob)(location.blobId);
         if (!blob) {
             throw new Error(`file ("${location.name}") was opened locally from a previous session. To restore it, go to track settings and reopen the file`);
         }
-        return new generic_filehandle_1.BlobFile(blob);
+        return new generic_filehandle2_1.BlobFile(blob);
     }
     if ((0, types_1.isUriLocation)(location)) {
-        // Check for empty string
         if (!location.uri) {
             throw new Error('No URI provided');
         }
-        // Resolve any relative URLs to absolute URLs
         const absoluteLocation = resolveUriLocation(location);
-        // If there is a plugin manager, we can try internet accounts
         if (pluginManager) {
             const internetAccount = getInternetAccount(location, pluginManager);
-            // If an internetAccount was found, use it to open the location
             if (internetAccount) {
                 return internetAccount.openLocation(absoluteLocation);
             }
         }
-        // Otherwise fall back on usual open
         return new RemoteFileWithRangeCache_1.RemoteFileWithRangeCache(absoluteLocation.uri, {
             fetch: checkAuthNeededFetch,
         });
@@ -82,12 +74,9 @@ function getFetcher(location, pluginManager) {
 }
 function getInternetAccount(location, pluginManager) {
     const { rootModel } = pluginManager;
-    // If there is an appRootModel, use it to find the internetAccount
     if (rootModel && (0, types_1.isRootModelWithInternetAccounts)(rootModel)) {
         return rootModel.findAppropriateInternetAccount(location);
     }
-    // If there is no appRootModel, but there is pre-auth, create a temporary
-    // internetAccount. This is typical in a worker.
     if (location.internetAccountPreAuthorization) {
         if (!location.internetAccountPreAuthorization.authInfo.token) {
             throw new Error('Failed to obtain token from internet account. Try reloading the page');
@@ -101,9 +90,6 @@ function getInternetAccount(location, pluginManager) {
     }
     return undefined;
 }
-// This fetch throws a special error if the response is "401" and includes a
-// "WWW-Authenticate: Basic" header. This is so downstream code can retry if
-// needed with HTTP Basic authentication included
 async function checkAuthNeededFetch(url, opts) {
     var _a;
     const response = await fetch(url, opts);

package/util/jexl.js

@@ -5,23 +5,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = JexlF;
 const jexl_1 = __importDefault(require("jexl"));
-function JexlF( /* config?: any*/) {
+function JexlF() {
     const j = new jexl_1.default.Jexl();
-    // someday will make sure all of configs callbacks are added in, including
-    // ones passed in
-    // below are core functions
     j.addFunction('get', (feature, data) => feature.get(data));
     j.addFunction('parent', (feature) => feature.parent());
     j.addFunction('id', (feature) => feature.id());
-    // let user cast a jexl type into a javascript type
     j.addFunction('cast', (arg) => arg);
-    // logging
     j.addFunction('log', (thing) => {
-        console.log(thing); // eslint-disable-line no-console
+        console.log(thing);
         return thing;
     });
-    // math
-    // addfunction added in jexl 2.3 but types/jexl still on 2.2
     j.addFunction('max', Math.max);
     j.addFunction('min', Math.min);
     j.addFunction('sqrt', Math.sqrt);
@@ -32,7 +25,6 @@ function JexlF( /* config?: any*/) {
     j.addFunction('log10', Math.log10);
     j.addFunction('parseInt', Number.parseInt);
     j.addFunction('parseFloat', Number.parseFloat);
-    // string
     j.addFunction('split', (s, char) => s.split(char));
     j.addFunction('charAt', (s, index) => s.charAt(index));
     j.addFunction('charCodeAt', (s, index) => s.charCodeAt(index));
@@ -46,9 +38,7 @@ function JexlF( /* 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) => 
-    // eslint-disable-next-line unicorn/prefer-string-slice
-    s.substring(start, end));
+    j.addFunction('substring', (s, start, end) => s.substring(start, end));
     j.addFunction('toLowerCase', (s) => s.toLowerCase());
     j.addFunction('toUpperCase', (s) => s.toUpperCase());
     j.addFunction('jsonParse', (s) => JSON.parse(s));

package/util/jexlStrings.d.ts

@@ -1,7 +1 @@
-/**
- * compile a jexlExpression to a string
- *
- * @param str - string of code like `jexl:...`
- * @param options -
- */
 export declare function stringToJexlExpression(str: string, jexl?: any): any;

package/util/jexlStrings.js

@@ -6,14 +6,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.stringToJexlExpression = stringToJexlExpression;
 const jexl_1 = __importDefault(require("./jexl"));
 const compilationCache = {};
-// revert function strings back to main, create a different file for
-// jexlStrings.ts pass the jexl property of the pluginManager as a param
-/**
- * compile a jexlExpression to a string
- *
- * @param str - string of code like `jexl:...`
- * @param options -
- */
 function stringToJexlExpression(str, jexl) {
     const cacheKey = `nosig|${str}`;
     if (!compilationCache[cacheKey]) {

package/util/layouts/BaseLayout.d.ts

@@ -2,7 +2,7 @@ export type RectTuple = [number, number, number, number];
 export interface SerializedLayout {
     rectangles: Record<string, RectTuple>;
     totalHeight: number;
-    containsNoTransferables: true;
+    containsNoTransferables?: true;
     maxHeightReached: boolean;
 }
 export interface Rectangle<T> {

package/util/layouts/GranularRectLayout.d.ts

@@ -1,4 +1,4 @@
-import { RectTuple, SerializedLayout, Rectangle, BaseLayout } from './BaseLayout';
+import type { BaseLayout, RectTuple, Rectangle, SerializedLayout } from './BaseLayout';
 export default class GranularRectLayout<T> implements BaseLayout<T> {
     private pitchX;
     private pitchY;
@@ -9,11 +9,6 @@ export default class GranularRectLayout<T> implements BaseLayout<T> {
     private maxHeight;
     private displayMode;
     private pTotalHeight;
-    /**
-     * pitchX - layout grid pitch in the X direction
-     * pitchY - layout grid pitch in the Y direction
-     * maxHeight - maximum layout height, default Infinity (no max)
-     */
     constructor({ pitchX, pitchY, maxHeight, hardRowLimit, displayMode, }?: {
         pitchX?: number;
         pitchY?: number;
@@ -21,21 +16,10 @@ export default class GranularRectLayout<T> implements BaseLayout<T> {
         displayMode?: string;
         hardRowLimit?: number;
     });
-    /**
-     * @returns top position for the rect, or Null if laying
-     *  out the rect would exceed maxHeight
-     */
     addRect(id: string, left: number, right: number, height: number, data?: T): number | null;
     collides(rect: Rectangle<T>, top: number): boolean;
-    /**
-     * make a subarray if it does not exist
-     */
     private autovivifyRow;
     addRectToBitmap(rect: Rectangle<T>): void;
-    /**
-     *  Given a range of X coordinates, deletes all data dealing with
-     *  the features.
-     */
     discardRange(left: number, right: number): void;
     hasSeen(id: string): boolean;
     getByCoord(x: number, y: number): string | Record<string, T> | undefined;

package/util/layouts/GranularRectLayout.js

@@ -1,29 +1,15 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-/**
- * Rectangle-layout manager that lays out rectangles using bitmaps at
- * resolution that, for efficiency, may be somewhat lower than that of
- * the coordinate system for the rectangles being laid out.  `pitchX`
- * and `pitchY` are the ratios of input scale resolution to internal
- * bitmap resolution.
- */
-// minimum excess size of the array at which we garbage collect
 const minSizeToBotherWith = 10000;
 const maxFeaturePitchWidth = 20000;
 function segmentsIntersect(x1, x2, y1, y2) {
     return x2 >= y1 && y2 >= x1;
 }
-// a single row in the layout
 class LayoutRow {
     constructor() {
         this.padding = 1;
         this.widthLimit = 1000000;
     }
-    // this.rowState.bits is the array of items in the layout row, indexed by (x - this.offset)
-    // this.rowState.min is the leftmost edge of all the rectangles we have in the layout
-    // this.rowState.max is the rightmost edge of all the rectangles we have in the layout
-    // this.rowState.offset is the offset of the bits array relative to the genomic coordinates
-    //      (modified by pitchX, but we don't know that in this class)
     setAllFilled(data) {
         this.allFilled = data;
     }
@@ -56,8 +42,6 @@ class LayoutRow {
         }
         return flag;
     }
-    // NOTE: this.rowState.min, this.rowState.max, and this.rowState.offset are
-    // interbase coordinates
     initialize(left, right) {
         const rectWidth = right - left;
         return {
@@ -69,15 +53,13 @@ class LayoutRow {
     }
     addRect(rect, data) {
         const left = rect.l;
-        const right = rect.r + this.padding; // only padding on the right
+        const right = rect.r + this.padding;
         if (!this.rowState) {
             this.rowState = this.initialize(left, right);
         }
-        // or check if we need to expand to the left and/or to the right
         let oLeft = left - this.rowState.offset;
         let oRight = right - this.rowState.offset;
         const currLength = this.rowState.bits.length;
-        // expand rightward if necessary
         if (oRight >= this.rowState.bits.length) {
             const additionalLength = oRight + 1;
             if (this.rowState.bits.length + additionalLength > this.widthLimit) {
@@ -91,9 +73,7 @@ class LayoutRow {
                 ];
             }
         }
-        // expand leftward if necessary
         if (left < this.rowState.offset) {
-            // use math.min to avoid negative lengths
             const additionalLength = Math.min(currLength - oLeft, this.rowState.offset);
             if (this.rowState.bits.length + additionalLength > this.widthLimit) {
                 console.warn('Layout width limit exceeded, discarding old layout. Please be more careful about discarding unused blocks.');
@@ -123,82 +103,51 @@ class LayoutRow {
             this.rowState.max = right;
         }
     }
-    /**
-     *  Given a range of interbase coordinates, deletes all data dealing with that range
-     */
     discardRange(left, right) {
         if (this.allFilled) {
             return;
-        } // allFilled is irrevocable currently
-        // if we have no data, do nothing
+        }
         if (!this.rowState) {
             return;
         }
-        // if doesn't overlap at all, do nothing
         if (right <= this.rowState.min || left >= this.rowState.max) {
             return;
         }
-        // if completely encloses range, discard everything
         if (left <= this.rowState.min && right >= this.rowState.max) {
             this.rowState = undefined;
             return;
         }
-        // if overlaps left edge, adjust the min
         if (right > this.rowState.min && left <= this.rowState.min) {
             this.rowState.min = right;
         }
-        // if overlaps right edge, adjust the max
         if (left < this.rowState.max && right >= this.rowState.max) {
             this.rowState.max = left;
         }
-        // now trim the left, right, or both sides of the array
         if (this.rowState.offset < this.rowState.min - minSizeToBotherWith &&
             this.rowState.bits.length >
                 this.rowState.max + minSizeToBotherWith - this.rowState.offset) {
-            // trim both sides
             const leftTrimAmount = this.rowState.min - this.rowState.offset;
             const rightTrimAmount = this.rowState.bits.length -
                 1 -
                 (this.rowState.max - this.rowState.offset);
-            // if (rightTrimAmount <= 0) debugger
-            // if (leftTrimAmount <= 0) debugger
-            // this.log(`trim both sides, ${leftTrimAmount} from left, ${rightTrimAmount} from right`)
             this.rowState.bits = this.rowState.bits.slice(leftTrimAmount, this.rowState.bits.length - rightTrimAmount);
             this.rowState.offset += leftTrimAmount;
-            // if (this.rowState.offset > this.rowState.min) debugger
-            // if (this.rowState.bits.length <= this.rowState.max - this.rowState.offset) debugger
         }
         else if (this.rowState.offset < this.rowState.min - minSizeToBotherWith) {
-            // trim left side
             const desiredOffset = this.rowState.min - Math.floor(minSizeToBotherWith / 2);
             const trimAmount = desiredOffset - this.rowState.offset;
-            // this.log(`trim left side by ${trimAmount}`)
             this.rowState.bits.splice(0, trimAmount);
             this.rowState.offset += trimAmount;
-            // if (this.rowState.offset > this.rowState.min) debugger
-            // if (this.rowState.bits.length <= this.rowState.max - this.rowState.offset) debugger
         }
         else if (this.rowState.bits.length >
             this.rowState.max - this.rowState.offset + minSizeToBotherWith) {
-            // trim right side
             const desiredLength = this.rowState.max -
                 this.rowState.offset +
                 1 +
                 Math.floor(minSizeToBotherWith / 2);
-            // this.log(`trim right side by ${this.rowState.bits.length-desiredLength}`)
-            // if (desiredLength > this.rowState.bits.length) debugger
             this.rowState.bits.length = desiredLength;
-            // if (this.rowState.offset > this.rowState.min) debugger
-            // if (this.rowState.bits.length <= this.rowState.max - this.rowState.offset) debugger
         }
-        // if (this.rowState.offset > this.rowState.min) debugger
-        // if (this.rowState.bits.length <= this.rowState.max - this.rowState.offset) debugger
-        // if range now enclosed in the new bounds, loop through and clear the bits
         const oLeft = Math.max(this.rowState.min, left) - this.rowState.offset;
-        // if (oLeft < 0) debugger
-        // if (oLeft >= this.rowState.bits.length) debugger
-        // if (oRight < 0) debugger
-        // if (oRight >= this.rowState.bits.length) debugger
         const oRight = Math.min(right, this.rowState.max) - this.rowState.offset;
         for (let x = oLeft; x >= 0 && x < oRight; x += 1) {
             this.rowState.bits[x] = undefined;
@@ -206,18 +155,12 @@ class LayoutRow {
     }
 }
 class GranularRectLayout {
-    /**
-     * pitchX - layout grid pitch in the X direction
-     * pitchY - layout grid pitch in the Y direction
-     * maxHeight - maximum layout height, default Infinity (no max)
-     */
     constructor({ pitchX = 10, pitchY = 10, maxHeight = 10000, hardRowLimit = 10000, displayMode = 'normal', } = {}) {
         this.pitchX = pitchX;
         this.pitchY = pitchY;
         this.hardRowLimit = hardRowLimit;
         this.maxHeightReached = false;
         this.displayMode = displayMode;
-        // reduce the pitchY to try and pack the features tighter
         if (this.displayMode === 'compact') {
             this.pitchY = Math.round(this.pitchY / 4) || 1;
             this.pitchX = Math.round(this.pitchX / 4) || 1;
@@ -225,21 +168,14 @@ class GranularRectLayout {
         this.bitmap = [];
         this.rectangles = new Map();
         this.maxHeight = Math.ceil(maxHeight / this.pitchY);
-        this.pTotalHeight = 0; // total height, in units of bitmap squares (px/pitchY)
+        this.pTotalHeight = 0;
     }
-    /**
-     * @returns top position for the rect, or Null if laying
-     *  out the rect would exceed maxHeight
-     */
     addRect(id, left, right, height, data) {
-        // if we have already laid it out, return its layout
         const storedRec = this.rectangles.get(id);
         if (storedRec) {
             if (storedRec.top === null) {
                 return null;
             }
-            // add it to the bitmap again, since that bitmap range may have been
-            // discarded
             this.addRectToBitmap(storedRec);
             return storedRec.top * this.pitchY;
         }
@@ -287,9 +223,6 @@ class GranularRectLayout {
         }
         return false;
     }
-    /**
-     * make a subarray if it does not exist
-     */
     autovivifyRow(bitmap, y) {
         let row = bitmap[y];
         if (!row) {
@@ -308,11 +241,6 @@ class GranularRectLayout {
         const data = rect.id;
         const yEnd = rect.top + rect.h;
         if (rect.r - rect.l > maxFeaturePitchWidth) {
-            // the rect is very big in relation to the view size, just pretend, for
-            // the purposes of layout, that it extends infinitely.  this will cause
-            // weird layout if a user scrolls manually for a very, very long time
-            // along the genome at the same zoom level.  but most users will not do
-            // that.  hopefully.
             for (let y = rect.top; y < yEnd; y += 1) {
                 this.autovivifyRow(this.bitmap, y).setAllFilled(data);
             }
@@ -323,10 +251,6 @@ class GranularRectLayout {
             }
         }
     }
-    /**
-     *  Given a range of X coordinates, deletes all data dealing with
-     *  the features.
-     */
     discardRange(left, right) {
         const pLeft = Math.floor(left / this.pitchX);
         const pRight = Math.floor(right / this.pitchX);
@@ -376,7 +300,7 @@ class GranularRectLayout {
             const { l, r, originalHeight, top } = rect;
             const t = (top || 0) * this.pitchY;
             const b = t + originalHeight;
-            return [id, [l * this.pitchX, t, r * this.pitchX, b]]; // left, top, right, bottom
+            return [id, [l * this.pitchX, t, r * this.pitchX, b]];
         }));
     }
     serializeRegion(region) {
@@ -394,7 +318,6 @@ class GranularRectLayout {
                 const y2 = r * this.pitchX;
                 const x1 = region.start;
                 const x2 = region.end;
-                // add +/- pitchX to avoid resolution causing errors
                 if (segmentsIntersect(x1, x2, y1 - this.pitchX, y2 + this.pitchX)) {
                     regionRectangles[id] = [y1, t, y2, b];
                 }

package/util/layouts/MultiLayout.d.ts

@@ -1,13 +1,8 @@
-import { BaseLayout, SerializedLayout } from './BaseLayout';
+import type { BaseLayout, SerializedLayout } from './BaseLayout';
 export default class MultiLayout<SUB_LAYOUT_CLASS extends BaseLayout<T>, T> {
     SubLayoutClass: new (...args: any[]) => SUB_LAYOUT_CLASS;
     subLayoutConstructorArgs: Record<string, any>;
     subLayouts: Map<string, SUB_LAYOUT_CLASS>;
-    /**
-     * layout class that just keeps a number of named sub-layouts.
-     * basically just a fancier
-     * `{ layout1: new GranularRectLayout(), layout2: new GranularRectLayout() ...}`
-     */
     constructor(SubLayoutClass: new (...args: any[]) => SUB_LAYOUT_CLASS, subLayoutConstructorArgs?: Record<string, any>);
     getDataByID(id: string): unknown;
     getSublayout(layoutName: string): SUB_LAYOUT_CLASS;

package/util/layouts/MultiLayout.js

@@ -1,11 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 class MultiLayout {
-    /**
-     * layout class that just keeps a number of named sub-layouts.
-     * basically just a fancier
-     * `{ layout1: new GranularRectLayout(), layout2: new GranularRectLayout() ...}`
-     */
     constructor(SubLayoutClass, subLayoutConstructorArgs = {}) {
         this.SubLayoutClass = SubLayoutClass;
         this.subLayoutConstructorArgs = subLayoutConstructorArgs;
@@ -13,7 +8,6 @@ class MultiLayout {
     }
     getDataByID(id) {
         for (const layout of this.subLayouts.values()) {
-            // @ts-expect-error
             const r = layout.getDataByID(id);
             if (r) {
                 return r;

package/util/layouts/PrecomputedLayout.d.ts

@@ -1,4 +1,4 @@
-import { RectTuple, SerializedLayout, BaseLayout, Rectangle } from './BaseLayout';
+import type { BaseLayout, RectTuple, Rectangle, SerializedLayout } from './BaseLayout';
 export interface Layout {
     minX: number;
     minY: number;
@@ -13,9 +13,6 @@ export default class PrecomputedLayout<T> implements BaseLayout<T> {
     private rbush;
     constructor({ rectangles, totalHeight, maxHeightReached }: SerializedLayout);
     addRect(id: string): number;
-    /**
-     * returns a Map of `feature id -> rectangle`
-     */
     getRectangles(): Map<string, RectTuple>;
     getTotalHeight(): number;
     collides(_rect: Rectangle<T>, _top: number): boolean;

package/util/layouts/PrecomputedLayout.js

@@ -7,7 +7,6 @@ const rbush_1 = __importDefault(require("rbush"));
 class PrecomputedLayout {
     constructor({ rectangles, totalHeight, maxHeightReached }) {
         this.rectangles = new Map(Object.entries(rectangles));
-        // rectangles is of the form "featureId": [leftPx, topPx, rightPx, bottomPx]
         this.totalHeight = totalHeight;
         this.maxHeightReached = maxHeightReached;
         this.rbush = new rbush_1.default();
@@ -26,12 +25,8 @@ class PrecomputedLayout {
         if (!rect) {
             throw new Error(`id ${id} not found in precomputed feature layout`);
         }
-        // left, top, right, bottom
         return rect[1];
     }
-    /**
-     * returns a Map of `feature id -> rectangle`
-     */
     getRectangles() {
         return this.rectangles;
     }

package/util/layouts/PrecomputedMultiLayout.js

@@ -12,8 +12,6 @@ class ThrowingLayout {
 }
 class PrecomputedMultiLayout extends MultiLayout_1.default {
     constructor(json) {
-        // use ThrowingLayout because there is not supposed to be any creation
-        // of new layouts in a precomputed layout
         super(ThrowingLayout);
         Object.entries(json).forEach(([layoutName, sublayoutJson]) => {
             this.subLayouts.set(layoutName, new PrecomputedLayout_1.default(sublayoutJson));

package/util/layouts/SceneGraph.d.ts

@@ -17,21 +17,9 @@ export default class SceneGraph {
     private children;
     private absoluteCache;
     parent?: SceneGraph;
-    /**
-     * note: all coordinates are inter-base or inter-pixel coordinates
-     */
     constructor(name: string, left: number, top: number, width: number, height: number, data?: Record<string, any> | undefined);
     addChild(nameOrSceneGraph: string | SceneGraph, left: number, top: number, width: number, height: number, data?: Record<string, any>): SceneGraph;
     getSubRecord(name: string): SceneGraph | undefined;
-    /**
-     * if the record does not already cover the given absolute extents, extend it
-     * to cover them
-     *
-     * @param left -
-     * @param right -
-     * @param top -
-     * @param bottom -
-     */
     expand(newLeft: number, newRight: number, newTop: number, newBottom: number): void;
     get bottom(): number;
     get right(): number;