@jbrowse/core 2.1.7 → 2.2.1

package/util/Base1DViewModel.js

@@ -9,13 +9,37 @@ const mst_1 = require("./types/mst");
 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 Base1DView = mobx_state_tree_1.types
     .model('Base1DView', {
+    /**
+     * #property
+     */
     id: mst_1.ElementId,
+    /**
+     * #property
+     */
     displayedRegions: mobx_state_tree_1.types.array(mst_1.Region),
+    /**
+     * #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(() => ({
@@ -23,38 +47,65 @@ 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(region => region.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 self.displayedRegions
             .map(a => a.end - a.start)
@@ -62,12 +113,21 @@ const Base1DView = mobx_state_tree_1.types
     },
 }))
     .views(self => ({
+    /**
+     * #getter
+     */
     get dynamicBlocks() {
         return (0, calculateDynamicBlocks_1.default)(self);
     },
+    /**
+     * #getter
+     */
     get staticBlocks() {
         return (0, calculateStaticBlocks_1.default)(self);
     },
+    /**
+     * #getter
+     */
     get currBp() {
         return this.dynamicBlocks
             .map(a => a.end - a.start)
@@ -75,30 +135,51 @@ const Base1DView = mobx_state_tree_1.types
     },
 }))
     .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;
     },
-    // this makes a zoomed out view that shows all displayedRegions
-    // that makes the overview bar square with the scale bar
+    /**
+     * #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(newBpPerPx, offset = self.width / 2) {
         const bpPerPx = newBpPerPx;
         if (bpPerPx === self.bpPerPx) {
@@ -110,11 +191,17 @@ const Base1DView = mobx_state_tree_1.types
         self.offsetPx = (0, index_1.clamp)(Math.round(((self.offsetPx + offset) * oldBpPerPx) / bpPerPx - 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;
@@ -128,9 +215,12 @@ 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;
-        // the scroll is clamped to keep the linear genome on the main screen
         const newOffsetPx = (0, index_1.clamp)(self.offsetPx + distance, self.minOffset, self.maxOffset);
         self.offsetPx = newOffsetPx;
         return newOffsetPx - oldOffsetPx;
@@ -138,6 +228,7 @@ 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
      *

package/util/blockTypes.d.ts

@@ -1,4 +1,4 @@
-declare type Func<T> = (value: BaseBlock, index: number, array: BaseBlock[]) => T;
+type Func<T> = (value: BaseBlock, index: number, array: BaseBlock[]) => T;
 export declare class BlockSet {
     blocks: BaseBlock[];
     constructor(blocks?: BaseBlock[]);

package/util/calculateDynamicBlocks.js

@@ -75,7 +75,7 @@ function calculateDynamicBlocks(model, padding = true, elision = true) {
                 isRightEndOfDisplayedRegion,
                 key: '',
             };
-            blockData.key = `${(0, _1.assembleLocString)(blockData)}-${regionNumber}${reversed ? '-reversed' : ''}`;
+            blockData.key = `${(0, _1.assembleLocStringFast)(blockData)}-${regionNumber}${reversed ? '-reversed' : ''}`;
             if (padding && blocks.length === 0 && isLeftEndOfDisplayedRegion) {
                 blocks.push(new blockTypes_1.InterRegionPaddingBlock({
                     key: `${blockData.key}-beforeFirstRegion`,

package/util/calculateStaticBlocks.js

@@ -59,7 +59,7 @@ function calculateStaticBlocks(model, padding = true, elision = true, extra = 0,
                 isRightEndOfDisplayedRegion,
                 key: '',
             };
-            blockData.key = `${(0, _1.assembleLocString)(blockData)}-${regionNumber}${reversed ? '-reversed' : ''}`;
+            blockData.key = `${(0, _1.assembleLocStringFast)(blockData)}-${regionNumber}${reversed ? '-reversed' : ''}`;
             if (padding && regionNumber === 0 && blockNum === 0) {
                 blocks.push(new blockTypes_1.InterRegionPaddingBlock({
                     key: `${blockData.key}-beforeFirstRegion`,

package/util/index.d.ts

@@ -63,6 +63,7 @@ export declare function getContainingDisplay(node: IAnyStateTreeNode): import(".
  * ```
  */
 export declare function assembleLocString(region: ParsedLocString): string;
+export declare function assembleLocStringFast(region: ParsedLocString, cb?: (n: number) => string | number): string;
 export interface ParsedLocString {
     assemblyName?: string;
     refName: string;
@@ -196,6 +197,7 @@ export declare function renameRegionsIfNeeded<ARGTYPE extends {
     })[];
 }>;
 export declare function minmax(a: number, b: number): number[];
+export declare function shorten(name: string, max?: number, short?: number): string;
 export declare function stringify({ refName, coord, oob, }: {
     coord: number;
     refName?: string;
@@ -296,7 +298,7 @@ interface Block {
 export declare function bytesForRegions(regions: Region[], index: {
     blocksForRange: (ref: string, start: number, end: number) => Promise<Block[]>;
 }): Promise<number>;
-export declare type ViewSnap = {
+export type ViewSnap = {
     bpPerPx: number;
     interRegionPaddingWidth: number;
     minimumBlockWidth: number;

package/util/index.js

@@ -29,8 +29,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getBpDisplayStr = 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.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.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.getEnv = exports.measureGridWidth = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = exports.toLocale = void 0;
+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.getEnv = exports.measureGridWidth = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = exports.toLocale = exports.getBpDisplayStr = exports.supportedIndexingAdapters = void 0;
 /* eslint-disable @typescript-eslint/no-explicit-any */
 const react_1 = require("react");
 const is_object_1 = __importDefault(require("is-object"));
@@ -237,11 +237,18 @@ exports.getContainingDisplay = getContainingDisplay;
  * ```
  */
 function assembleLocString(region) {
+    return assembleLocStringFast(region, toLocale);
+}
+exports.assembleLocString = assembleLocString;
+// same as assembleLocString above, but does not perform toLocaleString which
+// can slow down the speed of block calculations which use assembleLocString
+// for block.key
+function assembleLocStringFast(region, cb = (n) => n) {
     const { assemblyName, refName, start, end, reversed } = region;
     const assemblyNameString = assemblyName ? `{${assemblyName}}` : '';
     let startString;
     if (start !== undefined) {
-        startString = `:${(start + 1).toLocaleString('en-US')}`;
+        startString = `:${cb(start + 1)}`;
     }
     else if (end !== undefined) {
         startString = ':1';
@@ -251,10 +258,7 @@ function assembleLocString(region) {
     }
     let endString;
     if (end !== undefined) {
-        endString =
-            start !== undefined && start + 1 === end
-                ? ''
-                : `..${end.toLocaleString('en-US')}`;
+        endString = start !== undefined && start + 1 === end ? '' : `..${cb(end)}`;
     }
     else {
         endString = start !== undefined ? '..' : '';
@@ -265,7 +269,7 @@ function assembleLocString(region) {
     }
     return `${assemblyNameString}${refName}${startString}${endString}${rev}`;
 }
-exports.assembleLocString = assembleLocString;
+exports.assembleLocStringFast = assembleLocStringFast;
 function parseLocStringOneBased(locString, isValidRefName) {
     if (!locString) {
         throw new Error('no location string provided, could not parse');
@@ -647,9 +651,15 @@ function minmax(a, b) {
     return [Math.min(a, b), Math.max(a, b)];
 }
 exports.minmax = minmax;
+function shorten(name, max = 70, short = 30) {
+    return name.length > max
+        ? name.slice(0, short) + '...' + name.slice(-short)
+        : name;
+}
+exports.shorten = shorten;
 function stringify({ refName, coord, oob, }) {
     return refName
-        ? `${refName}:${coord.toLocaleString('en-US')}${oob ? ' (out of bounds)' : ''}`
+        ? `${shorten(refName)}:${toLocale(coord)}${oob ? ' (out of bounds)' : ''}`
         : '';
 }
 exports.stringify = stringify;

package/util/io/RemoteFileWithRangeCache.d.ts

@@ -1,6 +1,6 @@
 /// <reference types="node" />
 import { RemoteFile, PolyfilledResponse } from 'generic-filehandle';
-interface BinaryRangeResponse {
+export interface BinaryRangeResponse {
     headers: Record<string, string>;
     requestDate: Date;
     responseDate: Date;
@@ -14,4 +14,3 @@ export declare class RemoteFileWithRangeCache extends RemoteFile {
         signal?: AbortSignal;
     }): Promise<BinaryRangeResponse>;
 }
-export {};

package/util/io/RemoteFileWithRangeCache.js

@@ -52,9 +52,9 @@ class RemoteFileWithRangeCache extends generic_filehandle_1.RemoteFile {
                 const [, start, end] = rangeParse;
                 const s = parseInt(start, 10);
                 const e = parseInt(end, 10);
-                const response = await globalRangeCache.getRange(url, s, e - s + 1, {
+                const response = (await globalRangeCache.getRange(url, s, e - s + 1, {
                     signal: init && init.signal,
-                });
+                }));
                 const { headers } = response;
                 return new Response(response.buffer, { status: 206, headers });
             }

package/util/io/index.js

@@ -82,7 +82,7 @@ exports.getFetcher = getFetcher;
 function getInternetAccount(location, pluginManager) {
     const { rootModel } = pluginManager;
     // If there is an appRootModel, use it to find the internetAccount
-    if (rootModel && (0, types_1.isAppRootModel)(rootModel)) {
+    if (rootModel && (0, types_1.isRootModelWithInternetAccounts)(rootModel)) {
         return rootModel.findAppropriateInternetAccount(location);
     }
     // If there is no appRootModel, but there is pre-auth, create a temporary
@@ -103,10 +103,10 @@ function getInternetAccount(location, pluginManager) {
 // "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);
     if (response.status === 401) {
-        const authHeaders = response.headers.get('WWW-Authenticate');
-        if (authHeaders && authHeaders.includes('Basic')) {
+        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());
         }
     }

package/util/jexl.d.ts

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

package/util/layouts/BaseLayout.d.ts

@@ -1,4 +1,4 @@
-export declare type RectTuple = [number, number, number, number];
+export type RectTuple = [number, number, number, number];
 export interface SerializedLayout {
     rectangles: Record<string, RectTuple>;
     totalHeight: number;

package/util/layouts/GranularRectLayout.d.ts

@@ -9,6 +9,11 @@ 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;
@@ -33,9 +38,9 @@ export default class GranularRectLayout<T> implements BaseLayout<T> {
      */
     discardRange(left: number, right: number): void;
     hasSeen(id: string): boolean;
-    getByCoord(x: number, y: number): Record<string, T> | string | undefined;
+    getByCoord(x: number, y: number): string | Record<string, T> | undefined;
     getByID(id: string): RectTuple | undefined;
-    getDataByID(id: string): unknown;
+    getDataByID(id: string): T | undefined;
     cleanup(): void;
     getTotalHeight(): number;
     get totalHeight(): number;

package/util/layouts/GranularRectLayout.js

@@ -18,66 +18,47 @@ class LayoutRow {
     constructor() {
         this.padding = 1;
         this.widthLimit = 1000000;
-        // 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)
-        // 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
     }
-    // log(msg: string): void {
-    //   // if (this.rowNumber === 0)
-    //   // eslint-disable-next-line no-console
-    //   console.log(`r${this.rowNumber}: ${msg}`)
-    // }
+    // 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;
     }
     getItemAt(x) {
+        var _a;
         if (this.allFilled) {
             return this.allFilled;
         }
-        if (!this.rowState) {
-            return undefined;
-        }
-        if (this.rowState.min === undefined) {
+        if (((_a = this.rowState) === null || _a === void 0 ? void 0 : _a.min) === undefined ||
+            x < this.rowState.min ||
+            x >= this.rowState.max) {
             return undefined;
         }
-        if (x < this.rowState.min) {
-            return undefined;
-        }
-        if (x >= this.rowState.max) {
-            return undefined;
-        }
-        const offset = x - this.rowState.offset;
-        // if (offset < 0)
-        //     debugger
-        // if (offset >= this.rowState.bits.length)
-        //     debugger
-        return this.rowState.bits[offset];
+        return this.rowState.bits[x - this.rowState.offset];
     }
     isRangeClear(left, right) {
         if (this.allFilled) {
             return false;
         }
-        if (!this.rowState) {
-            return true;
-        }
-        const { min, max } = this.rowState;
-        if (right <= min || left >= max) {
+        if (this.rowState === undefined ||
+            right <= this.rowState.min ||
+            left >= this.rowState.max) {
             return true;
         }
-        // TODO: check right and middle before looping
-        const maxX = Math.min(max, right);
-        let x = Math.max(min, left);
-        for (; x < right && x < maxX; x += 1) {
-            if (this.getItemAt(x)) {
-                return false;
-            }
+        const { min, max, offset, bits } = this.rowState;
+        const maxX = Math.min(max, right) - offset;
+        let flag = true;
+        for (let x = Math.max(min, left) - offset; x < maxX && flag; x++) {
+            flag = bits[x] === undefined;
         }
-        return true;
+        return flag;
     }
+    // NOTE: this.rowState.min, this.rowState.max, and this.rowState.offset are
+    // interbase coordinates
     initialize(left, right) {
-        // NOTE: this.rowState.min, this.rowState.max, and this.rowState.offset are interbase coordinates
         const rectWidth = right - left;
         return {
             offset: left - rectWidth,
@@ -85,7 +66,6 @@ class LayoutRow {
             max: right,
             bits: new Array(3 * rectWidth),
         };
-        // this.log(`initialize ${this.rowState.min} - ${this.rowState.max} (${this.rowState.bits.length})`)
     }
     addRect(rect, data) {
         const left = rect.l;
@@ -220,8 +200,7 @@ 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)
@@ -296,7 +275,7 @@ class GranularRectLayout {
         const maxY = top + rect.h;
         for (let y = top; y < maxY; y += 1) {
             const row = bitmap[y];
-            if (row && !row.isRangeClear(rect.l, rect.r)) {
+            if (row !== undefined && !row.isRangeClear(rect.l, rect.r)) {
                 return true;
             }
         }
@@ -370,7 +349,12 @@ class GranularRectLayout {
         const r = this.rectangles.get(id);
         if (r) {
             const t = r.top * this.pitchY;
-            return [r.l * this.pitchX, t, r.r * this.pitchX, t + r.originalHeight];
+            return [
+                r.l * this.pitchX,
+                t,
+                r.r * this.pitchX,
+                t + r.originalHeight,
+            ];
         }
         return undefined;
     }

package/util/layouts/MultiLayout.d.ts

@@ -1,14 +1,14 @@
 import { BaseLayout, SerializedLayout } from './BaseLayout';
 export default class MultiLayout<SUB_LAYOUT_CLASS extends BaseLayout<T>, T> {
     SubLayoutClass: new (...args: any[]) => SUB_LAYOUT_CLASS;
-    subLayouts: Map<string, 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, layoutArgs?: Record<string, any>);
+    constructor(SubLayoutClass: new (...args: any[]) => SUB_LAYOUT_CLASS, subLayoutConstructorArgs?: Record<string, any>);
     getDataByID(id: string): unknown;
     getSublayout(layoutName: string): SUB_LAYOUT_CLASS;
     addRect(layoutName: string, id: string, left: number, right: number, height: number, data?: Record<string, T>): number | null;

package/util/layouts/MultiLayout.js

@@ -6,12 +6,10 @@ class MultiLayout {
      * basically just a fancier
      * `{ layout1: new GranularRectLayout(), layout2: new GranularRectLayout() ...}`
      */
-    constructor(SubLayoutClass, layoutArgs = {}) {
+    constructor(SubLayoutClass, subLayoutConstructorArgs = {}) {
         this.SubLayoutClass = SubLayoutClass;
+        this.subLayoutConstructorArgs = subLayoutConstructorArgs;
         this.subLayouts = new Map();
-        this.subLayoutConstructorArgs = {};
-        this.subLayouts = new Map();
-        this.subLayoutConstructorArgs = layoutArgs;
     }
     getDataByID(id) {
         for (const layout of this.subLayouts.values()) {
@@ -36,8 +34,8 @@ class MultiLayout {
         return this.getSublayout(layoutName).addRect(id, left, right, height, data);
     }
     discardRange(layoutName, left, right) {
-        const layout = this.subLayouts.get(layoutName);
-        return layout && layout.discardRange(left, right);
+        var _a;
+        return (_a = this.subLayouts.get(layoutName)) === null || _a === void 0 ? void 0 : _a.discardRange(left, right);
     }
     toJSON() {
         const data = {};

package/util/offscreenCanvasPonyfill.d.ts

@@ -1,5 +1,5 @@
-declare type AbstractCanvas = any;
-declare type AbstractImageBitmap = any;
+type AbstractCanvas = any;
+type AbstractImageBitmap = any;
 export declare let createCanvas: (width: number, height: number) => AbstractCanvas;
 export declare let createImageBitmap: (canvas: AbstractCanvas) => Promise<AbstractImageBitmap>;
 /** the JS class (constructor) for offscreen-generated image bitmap data */

package/util/offscreenCanvasUtils.d.ts

@@ -1,5 +1,5 @@
 /// <reference types="react" />
-export declare type RenderReturn = Record<string, unknown>;
+export type RenderReturn = Record<string, unknown>;
 export declare function renderToAbstractCanvas(width: number, height: number, opts: {
     exportSVG?: {
         rasterizeLayers?: boolean;

package/util/simpleFeature.d.ts

@@ -31,6 +31,9 @@ export interface Feature {
      * Get an array of child features, or undefined if none.
      */
     children(): Feature[] | undefined;
+    /**
+     * Convert to JSON
+     */
     toJSON(): SimpleFeatureSerialized;
 }
 export declare function isFeature(thing: unknown): thing is Feature;

package/util/stats.d.ts

@@ -14,8 +14,34 @@ export interface FeatureStats extends UnrectifiedFeatureStats {
     scoreMean: number;
     scoreStdDev: number;
 }
+/**
+ * calculate standard deviation using the 'shortcut method' that accepts
+ * the sum and the sum squares of the elements
+ *
+ * @param sum - sum(i, 1..n)
+ * @param sumSquares - sum(i^2, 1..n)
+ * @param n - number of elements
+ * @param population - boolean: use population instead of sample correction
+ * @returns - the estimated std deviation
+ */
 export declare function calcStdFromSums(sum: number, sumSquares: number, n: number, population?: boolean): number;
+/**
+ * @param stats - a summary stats object with scoreSum, featureCount, scoreSumSquares, and basesCovered
+ * @returns - a summary stats object with scoreMean, scoreStdDev, and featureDensity added
+ */
 export declare function rectifyStats(s: UnrectifiedFeatureStats): FeatureStats;
+/**
+ * calculates per-base scores for variable width features over a region
+ * @param region - object contains start, end
+ * @param features - list of features with start, end, score
+ * @returns array of numeric scores
+ */
 export declare function calcPerBaseStats(region: NoAssemblyRegion, features: Feature[]): number[];
+/**
+ * transform a list of scores to summary statistics
+ * @param region - object with start, end
+ * @param features - array of features which are possibly summary features
+ * @returns - object with scoreMax, scoreMin, scoreSum, scoreSumSquares, etc
+ */
 export declare function scoresToStats(region: NoAssemblyRegion, features: Observable<Feature>): Promise<FeatureStats>;
 export declare function blankStats(): FeatureStats;