@jbrowse/core 2.6.2 → 2.7.0

package/util/blockTypes.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.InterRegionPaddingBlock = exports.ElidedBlock = exports.ContentBlock = exports.BaseBlock = exports.BlockSet = void 0;
+const _1 = require(".");
 class BlockSet {
     constructor(blocks = []) {
         this.blocks = blocks;
@@ -34,15 +35,14 @@ class BlockSet {
     }
     get totalWidthPx() {
         return this.blocks.length > 0
-            ? this.blocks.map(blocks => blocks.widthPx).reduce((a, b) => a + b)
+            ? (0, _1.sum)(this.blocks.map(blocks => blocks.widthPx))
             : 0;
     }
     get totalWidthPxWithoutBorders() {
         return this.blocks.length > 0
-            ? this.blocks
+            ? (0, _1.sum)(this.blocks
                 .filter(block => block.variant !== 'boundary')
-                .map(blocks => blocks.widthPx)
-                .reduce((a, b) => a + b)
+                .map(blocks => blocks.widthPx))
             : 0;
     }
     get offsetPx() {
@@ -52,9 +52,7 @@ class BlockSet {
         return this.blocks.filter(block => block instanceof ContentBlock);
     }
     get totalBp() {
-        return this.contentBlocks
-            .map(block => block.end - block.start)
-            .reduce((a, b) => a + b, 0);
+        return (0, _1.sum)(this.contentBlocks.map(block => block.end - block.start));
     }
 }
 exports.BlockSet = BlockSet;
@@ -73,20 +71,6 @@ class BaseBlock {
         this.key = data.key;
         this.offsetPx = data.offsetPx;
     }
-    /**
-     * rename the reference sequence of this block and return a new one
-     *
-     * @param refName -
-     * @returns either a new block with a renamed reference sequence,
-     * or the same block, if the ref name is not actually different
-     */
-    renameReference(refName) {
-        if (this.refName && refName !== this.refName) {
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            return new this.constructor({ ...this, refName });
-        }
-        return this;
-    }
     toRegion() {
         return {
             refName: this.refName,

package/util/calculateDynamicBlocks.js

@@ -32,7 +32,8 @@ function calculateDynamicBlocks(model, padding = true, elision = true) {
     let displayedRegionLeftPx = 0;
     const windowLeftPx = offsetPx;
     const windowRightPx = windowLeftPx + width;
-    displayedRegions.forEach((region, regionNumber) => {
+    for (let regionNumber = 0; regionNumber < displayedRegions.length; regionNumber++) {
+        const region = displayedRegions[regionNumber];
         const { assemblyName, refName, start: regionStart, end: regionEnd, reversed, } = region;
         const displayedRegionRightPx = displayedRegionLeftPx + (regionEnd - regionStart) / bpPerPx;
         const regionWidthPx = (regionEnd - regionStart) / bpPerPx;
@@ -115,7 +116,7 @@ function calculateDynamicBlocks(model, padding = true, elision = true) {
             }
         }
         displayedRegionLeftPx += (regionEnd - regionStart) / bpPerPx;
-    });
+    }
     return blocks;
 }
 exports.default = calculateDynamicBlocks;

package/util/calculateStaticBlocks.js

@@ -12,9 +12,8 @@ function calculateStaticBlocks(model, padding = true, elision = true, extra = 0,
     // for each displayed region
     let regionBpOffset = 0;
     const blocks = new blockTypes_1.BlockSet();
-    displayedRegions.forEach((region, regionNumber) => {
-        // find the block numbers of the left and right window sides,
-        // clamp those to the region range, and then make blocks for that range
+    for (let regionNumber = 0; regionNumber < displayedRegions.length; regionNumber++) {
+        const region = displayedRegions[regionNumber];
         const { assemblyName, refName, start: regionStart, end: regionEnd, reversed, } = region;
         const regionBlockCount = Math.ceil((regionEnd - regionStart) / blockSizeBp);
         const parentRegion = (0, mobx_state_tree_1.isStateTreeNode)(region) ? (0, mobx_state_tree_1.getSnapshot)(region) : region;
@@ -99,7 +98,7 @@ function calculateStaticBlocks(model, padding = true, elision = true, extra = 0,
             }
         }
         regionBpOffset += regionEnd - regionStart;
-    });
+    }
     return blocks;
 }
 exports.default = calculateStaticBlocks;

package/util/colord.d.ts

@@ -0,0 +1 @@
+export { Colord, colord } from 'colord';

package/util/colord.js

@@ -0,0 +1,13 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.colord = exports.Colord = void 0;
+const colord_1 = require("colord");
+const mix_1 = __importDefault(require("colord/plugins/mix"));
+const names_1 = __importDefault(require("colord/plugins/names"));
+(0, colord_1.extend)([mix_1.default, names_1.default]);
+var colord_2 = require("colord");
+Object.defineProperty(exports, "Colord", { enumerable: true, get: function () { return colord_2.Colord; } });
+Object.defineProperty(exports, "colord", { enumerable: true, get: function () { return colord_2.colord; } });

package/util/dedupe.js

@@ -5,8 +5,7 @@ exports.dedupe = void 0;
 function dedupe(list, hasher = JSON.stringify) {
     const clone = [];
     const lookup = new Set();
-    for (let i = 0; i < list.length; i++) {
-        const entry = list[i];
+    for (const entry of list) {
         const hashed = hasher(entry);
         if (!lookup.has(hashed)) {
             clone.push(entry);

package/util/index.d.ts

@@ -23,14 +23,14 @@ export declare function useDebouncedCallback<T>(callback: (...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)[];
-export declare function findParentThatIs<T extends (a: IAnyStateTreeNode) => boolean>(node: IAnyStateTreeNode, predicate: T): TypeTestedByPredicate<T> & IAnyStateTreeNode;
+export declare function findParentThatIs<T extends (a: IAnyStateTreeNode) => boolean>(node: IAnyStateTreeNode, predicate: T): TypeTestedByPredicate<T>;
 /** get the current JBrowse session model, starting at any node in the state tree */
-export declare function getSession(node: IAnyStateTreeNode): import("./types").AbstractSessionModel & IAnyStateTreeNode;
+export declare function getSession(node: IAnyStateTreeNode): import("./types").AbstractSessionModel;
 /** get the state model of the view in the state tree that contains the given node */
-export declare function getContainingView(node: IAnyStateTreeNode): import("./types").AbstractViewModel & IAnyStateTreeNode;
+export declare function getContainingView(node: IAnyStateTreeNode): import("./types").AbstractViewModel;
 /** get the state model of the view in the state tree that contains the given node */
-export declare function getContainingTrack(node: IAnyStateTreeNode): import("./types").AbstractTrackModel & IAnyStateTreeNode;
-export declare function getContainingDisplay(node: IAnyStateTreeNode): import("./types").AbstractDisplayModel & IAnyStateTreeNode;
+export declare function getContainingTrack(node: IAnyStateTreeNode): import("./types").AbstractTrackModel;
+export declare function getContainingDisplay(node: IAnyStateTreeNode): import("./types").AbstractDisplayModel;
 /**
  * Assemble a 1-based "locString" from an interbase genomic location
  * @param region - Region
@@ -165,8 +165,8 @@ export declare function iterMap<T, U>(iter: Iterable<T>, func: (arg: T) => U, si
  * element is found, findLastIndex immediately returns that element index.
  * Otherwise, findLastIndex returns -1.
  */
-export declare function findLastIndex<T>(array: Array<T>, predicate: (value: T, index: number, obj: T[]) => boolean): number;
-export declare function findLast<T>(array: Array<T>, predicate: (value: T, index: number, obj: T[]) => boolean): T | undefined;
+export declare function findLastIndex<T>(array: T[], predicate: (value: T, index: number, obj: T[]) => boolean): number;
+export declare function findLast<T>(array: T[], predicate: (value: T, index: number, obj: T[]) => boolean): T | undefined;
 /**
  * makes a mobx reaction with the given functions, that calls actions on the
  * model for each stage of execution, and to abort the reaction function when
@@ -287,9 +287,7 @@ export declare const defaultCodonTable: {
  * take CodonTable above and generate larger codon table that includes all
  * permutations of upper and lower case nucleotides
  */
-export declare function generateCodonTable(table: any): {
-    [key: string]: string;
-};
+export declare function generateCodonTable(table: any): Record<string, string>;
 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;
@@ -303,7 +301,7 @@ interface Block {
 export declare function bytesForRegions(regions: Region[], index: {
     blocksForRange: (ref: string, start: number, end: number) => Promise<Block[]>;
 }): Promise<number>;
-export type ViewSnap = {
+export interface ViewSnap {
     bpPerPx: number;
     interRegionPaddingWidth: number;
     minimumBlockWidth: number;
@@ -320,8 +318,8 @@ export type ViewSnap = {
         reversed: boolean;
         assemblyName: string;
     })[];
-};
-export declare function supportedIndexingAdapters(type: string): boolean;
+}
+export declare function isSupportedIndexingAdapter(type: string): boolean;
 export declare function getBpDisplayStr(totalBp: number): string;
 export declare function toLocale(n: number): string;
 export declare function getTickDisplayStr(totalBp: number, bpPerPx: number): string;
@@ -357,9 +355,7 @@ 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 declare function groupBy<T>(array: T[], predicate: (v: T) => string): {
-    [key: string]: T[];
-};
+export declare function groupBy<T>(array: T[], predicate: (v: T) => string): Record<string, T[]>;
 export declare function notEmpty<T>(value: T | null | undefined): value is T;
 export declare function mergeIntervals<T extends {
     start: number;
@@ -372,3 +368,4 @@ interface BasicFeature {
 }
 export declare function gatherOverlaps(regions: BasicFeature[]): BasicFeature[];
 export { default as SimpleFeature, type Feature, type SimpleFeatureSerialized, isFeature, } from './simpleFeature';
+export declare function stripAlpha(str: string): string;

package/util/index.js

@@ -18,7 +18,7 @@ var __importDefault = (this && this.__importDefault) || function (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.findLast = exports.findLastIndex = exports.iterMap = exports.bpSpanPx = exports.featureSpanPx = exports.cartesianToPolar = exports.polarToCartesian = exports.degToRad = exports.radToDeg = exports.bpToPx = exports.clamp = exports.compareLocStrings = exports.compareLocs = exports.parseLocString = exports.parseLocStringOneBased = exports.assembleLocStringFast = exports.assembleLocString = exports.getContainingDisplay = exports.getContainingTrack = exports.getContainingView = exports.getSession = exports.findParentThatIs = exports.springAnimate = exports.findParentThat = exports.useDebouncedCallback = exports.useWidthSetter = exports.useDebounce = exports.inProduction = exports.inDevelopment = void 0;
-exports.isFeature = exports.SimpleFeature = exports.gatherOverlaps = exports.mergeIntervals = exports.notEmpty = exports.groupBy = exports.avg = exports.sum = exports.min = exports.max = exports.localStorageSetItem = exports.localStorageGetItem = exports.getEnv = exports.measureGridWidth = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = exports.toLocale = exports.getBpDisplayStr = exports.supportedIndexingAdapters = void 0;
+exports.stripAlpha = exports.isFeature = exports.SimpleFeature = exports.gatherOverlaps = exports.mergeIntervals = exports.notEmpty = exports.groupBy = exports.avg = exports.sum = exports.min = exports.max = exports.localStorageSetItem = exports.localStorageGetItem = exports.getEnv = exports.measureGridWidth = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = exports.toLocale = exports.getBpDisplayStr = exports.isSupportedIndexingAdapter = void 0;
 /* eslint-disable @typescript-eslint/no-explicit-any */
 const react_1 = require("react");
 const is_object_1 = __importDefault(require("is-object"));
@@ -27,7 +27,9 @@ const mobx_1 = require("mobx");
 const types_1 = require("./types");
 const aborting_1 = require("./aborting");
 const types_2 = require("./types");
+// has to be the full path and not the relative path to get the jest mock
 const useMeasure_1 = __importDefault(require("@jbrowse/core/util/useMeasure"));
+const colord_1 = require("./colord");
 __exportStar(require("./types"), exports);
 __exportStar(require("./aborting"), exports);
 __exportStar(require("./when"), exports);
@@ -905,7 +907,7 @@ async function bytesForRegions(regions, index) {
 exports.bytesForRegions = bytesForRegions;
 // supported adapter types by text indexer
 //  ensure that this matches the method found in @jbrowse/text-indexing/util
-function supportedIndexingAdapters(type) {
+function isSupportedIndexingAdapter(type) {
     return [
         'Gff3TabixAdapter',
         'VcfTabixAdapter',
@@ -913,7 +915,7 @@ function supportedIndexingAdapters(type) {
         'VcfAdapter',
     ].includes(type);
 }
-exports.supportedIndexingAdapters = supportedIndexingAdapters;
+exports.isSupportedIndexingAdapter = isSupportedIndexingAdapter;
 function getBpDisplayStr(totalBp) {
     let str;
     if (Math.floor(totalBp / 1000000) > 0) {
@@ -939,6 +941,7 @@ function getTickDisplayStr(totalBp, bpPerPx) {
 }
 exports.getTickDisplayStr = getTickDisplayStr;
 function getViewParams(model, exportSVG) {
+    // @ts-expect-error
     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]) || {};
@@ -1037,24 +1040,24 @@ function localStorageSetItem(str, item) {
 exports.localStorageSetItem = localStorageSetItem;
 function max(arr, init = -Infinity) {
     let max = init;
-    for (let i = 0; i < arr.length; i++) {
-        max = arr[i] > max ? arr[i] : max;
+    for (const entry of arr) {
+        max = entry > max ? entry : max;
     }
     return max;
 }
 exports.max = max;
 function min(arr, init = Infinity) {
     let min = init;
-    for (let i = 0; i < arr.length; i++) {
-        min = arr[i] < min ? arr[i] : min;
+    for (const entry of arr) {
+        min = entry < min ? entry : min;
     }
     return min;
 }
 exports.min = min;
 function sum(arr) {
     let sum = 0;
-    for (let i = 0; i < arr.length; i++) {
-        sum += arr[i];
+    for (const entry of arr) {
+        sum += entry;
     }
     return sum;
 }
@@ -1091,7 +1094,6 @@ function mergeIntervals(intervals, w = 5000) {
     // start from the next interval and merge if needed
     for (let i = 1; i < intervals.length; i++) {
         // get the top element
-        // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
         top = stack.at(-1);
         // if the current interval doesn't overlap with the
         // stack top element, push it to the stack
@@ -1123,3 +1125,8 @@ exports.gatherOverlaps = gatherOverlaps;
 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; } });
+function stripAlpha(str) {
+    const c = (0, colord_1.colord)(str);
+    return c.alpha(1).toHex();
+}
+exports.stripAlpha = stripAlpha;

package/util/io/RemoteFileWithRangeCache.js

@@ -15,7 +15,7 @@ function binaryRangeFetch(url, start, end, options = {}) {
 const globalRangeCache = new http_range_fetcher_1.HttpRangeFetcher({
     fetch: binaryRangeFetch,
     size: 500 * 1024 ** 2,
-    chunkSize: 128 * 124,
+    chunkSize: 128 * 1024,
     maxFetchSize: 100 * 1024 ** 2,
     minimumTTL: 24 * 60 * 60 * 1000, // 1 day
 });
@@ -29,7 +29,7 @@ class RemoteFileWithRangeCache extends generic_filehandle_1.RemoteFile {
             fetchers[String(url)] = this.fetchBinaryRange.bind(this);
         }
         // if it is a range request, route it through the range cache
-        const requestHeaders = init && init.headers;
+        const requestHeaders = init === null || init === void 0 ? void 0 : init.headers;
         let range;
         if (requestHeaders) {
             if (requestHeaders instanceof Headers) {
@@ -53,7 +53,7 @@ class RemoteFileWithRangeCache extends generic_filehandle_1.RemoteFile {
                 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,
+                    signal: init === null || init === void 0 ? void 0 : init.signal,
                 }));
                 const { headers } = response;
                 return new Response(response.buffer, { status: 206, headers });

package/util/layouts/GranularRectLayout.js

@@ -332,8 +332,7 @@ class GranularRectLayout {
         const pLeft = Math.floor(left / this.pitchX);
         const pRight = Math.floor(right / this.pitchX);
         const { bitmap } = this;
-        for (let y = 0; y < bitmap.length; y += 1) {
-            const row = bitmap[y];
+        for (const row of bitmap) {
             if (row) {
                 row.discardRange(pLeft, pRight);
             }

package/util/map-obj.d.ts

@@ -1,3 +1,3 @@
 type Obj = Record<string, unknown>;
-export default function map(object: Obj, mapper: (val: unknown) => void, isSeen?: WeakSet<object>): void;
+export default function map(object: Obj, mapper: (val: unknown) => void, isSeen?: WeakSet<WeakKey>): void;
 export {};

package/util/nanoid.d.ts

@@ -0,0 +1,5 @@
+export const urlAlphabet: "useandom-26T198340PX75pxJACKVERYMINDBUSHWOLF_GQZbfghjklqvwyzrict";
+export function random(bytes: any): Uint8Array;
+export function customRandom(alphabet: any, defaultSize: any, getRandom: any): (size?: any) => string;
+export function customAlphabet(alphabet: any, size?: number): (size?: any) => string;
+export function nanoid(size?: number): string;

package/util/nanoid.js

@@ -0,0 +1,73 @@
+"use strict";
+// This file replaces `index.js` in bundlers like webpack or Rollup,
+// according to `browser` config in `package.json`.
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.nanoid = exports.customAlphabet = exports.customRandom = exports.random = exports.urlAlphabet = void 0;
+// This alphabet uses `A-Za-z0-9_-` symbols.
+// The order of characters is optimized for better gzip and brotli compression.
+// Same as in non-secure/index.js
+exports.urlAlphabet = 'useandom-26T198340PX75pxJACKVERYMINDBUSHWOLF_GQZbfghjklqvwyzrict';
+let random = bytes => crypto.getRandomValues(new Uint8Array(bytes));
+exports.random = random;
+let customRandom = (alphabet, defaultSize, getRandom) => {
+    // First, a bitmask is necessary to generate the ID. The bitmask makes bytes
+    // values closer to the alphabet size. The bitmask calculates the closest
+    // `2^31 - 1` number, which exceeds the alphabet size.
+    // For example, the bitmask for the alphabet size 30 is 31 (00011111).
+    // `Math.clz32` is not used, because it is not available in browsers.
+    let mask = (2 << (Math.log(alphabet.length - 1) / Math.LN2)) - 1;
+    // Though, the bitmask solution is not perfect since the bytes exceeding
+    // the alphabet size are refused. Therefore, to reliably generate the ID,
+    // the random bytes redundancy has to be satisfied.
+    // Note: every hardware random generator call is performance expensive,
+    // because the system call for entropy collection takes a lot of time.
+    // So, to avoid additional system calls, extra bytes are requested in advance.
+    // Next, a step determines how many random bytes to generate.
+    // The number of random bytes gets decided upon the ID size, mask,
+    // alphabet size, and magic number 1.6 (using 1.6 peaks at performance
+    // according to benchmarks).
+    // `-~f => Math.ceil(f)` if f is a float
+    // `-~i => i + 1` if i is an integer
+    let step = -~((1.6 * mask * defaultSize) / alphabet.length);
+    return (size = defaultSize) => {
+        let id = '';
+        while (true) {
+            let bytes = getRandom(step);
+            // A compact alternative for `for (var i = 0; i < step; i++)`.
+            let j = step;
+            while (j--) {
+                // Adding `|| ''` refuses a random byte that exceeds the alphabet size.
+                id += alphabet[bytes[j] & mask] || '';
+                if (id.length === size)
+                    return id;
+            }
+        }
+    };
+};
+exports.customRandom = customRandom;
+let customAlphabet = (alphabet, size = 21) => (0, exports.customRandom)(alphabet, size, exports.random);
+exports.customAlphabet = customAlphabet;
+let nanoid = (size = 21) => crypto.getRandomValues(new Uint8Array(size)).reduce((id, byte) => {
+    // It is incorrect to use bytes exceeding the alphabet size.
+    // The following mask reduces the random byte in the 0-255 value
+    // range to the 0-63 value range. Therefore, adding hacks, such
+    // as empty string fallback or magic numbers, is unnecessary because
+    // the bitmask trims bytes down to the alphabet size.
+    byte &= 63;
+    if (byte < 36) {
+        // `0-9a-z`
+        id += byte.toString(36);
+    }
+    else if (byte < 62) {
+        // `A-Z`
+        id += (byte - 26).toString(36).toUpperCase();
+    }
+    else if (byte > 62) {
+        id += '-';
+    }
+    else {
+        id += '_';
+    }
+    return id;
+}, '');
+exports.nanoid = nanoid;

package/util/offscreenCanvasPonyfill.js

@@ -1,4 +1,5 @@
 "use strict";
+/* eslint-disable react-refresh/only-export-components */
 // This file is a ponyfill for the HTML5 OffscreenCanvas API.
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
@@ -25,9 +26,7 @@ const weHave = {
 };
 if (weHave.realOffscreenCanvas) {
     exports.createCanvas = (width, height) => new OffscreenCanvas(width, height);
-    // eslint-disable-next-line no-restricted-globals
     exports.createImageBitmap = window.createImageBitmap || self.createImageBitmap;
-    // eslint-disable-next-line no-restricted-globals
     exports.ImageBitmapType = window.ImageBitmap || self.ImageBitmap;
 }
 else if (weHave.node) {

package/util/offscreenCanvasUtils.js

@@ -27,6 +27,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.ReactRendering = exports.getSerializedSvg = exports.renderToAbstractCanvas = void 0;
+/* eslint-disable react-refresh/only-export-components */
 const react_1 = __importDefault(require("react"));
 const canvas_sequencer_1 = require("canvas-sequencer");
 // locals

package/util/tracks.d.ts

@@ -16,12 +16,8 @@ export declare function getParentRenderProps(node: IAnyStateTreeNode): any;
 export declare const UNKNOWN = "UNKNOWN";
 export declare const UNSUPPORTED = "UNSUPPORTED";
 export declare function getBlob(id: string): File;
-export declare function getBlobMap(): {
-    [key: string]: File;
-};
-export declare function setBlobMap(map: {
-    [key: string]: File;
-}): void;
+export declare function getBlobMap(): Record<string, File>;
+export declare function setBlobMap(map: Record<string, File>): void;
 export declare function storeBlobLocation(location: PreFileLocation): import("./types").PreUriLocation | import("./types").PreLocalPathLocation | {
     name: string;
     blobId: string;

package/util/types/index.d.ts

@@ -8,6 +8,7 @@ import { NoAssemblyRegion as MUNoAssemblyRegion, Region as MUIRegion, LocalPathL
 import RpcManager from '../../rpc/RpcManager';
 import { Feature } from '../simpleFeature';
 import { BaseInternetAccountModel } from '../../pluggableElementTypes/models';
+import { ThemeOptions } from '@mui/material';
 export * from './util';
 /** abstract type for a model that contains multiple views */
 export interface AbstractViewContainer extends IStateTreeNode<IType<any, unknown, any>> {
@@ -42,16 +43,25 @@ export interface JBrowsePlugin {
 export type DialogComponentType = React.LazyExoticComponent<React.FC<any>> | React.FC<any>;
 /** minimum interface that all session state models must implement */
 export interface AbstractSessionModel extends AbstractViewContainer {
+    jbrowse: IAnyStateTreeNode;
     drawerPosition?: string;
-    setSelection(feature: Feature): void;
-    clearSelection(): void;
     configuration: AnyConfigurationModel;
     rpcManager: RpcManager;
     assemblyNames: string[];
     assemblies: AnyConfigurationModel[];
     selection?: unknown;
-    duplicateCurrentSession?(): void;
-    notify(message: string, level?: NotificationLevel, action?: SnackAction): void;
+    focusedViewId?: string;
+    themeName?: string;
+    setFocusedViewId?: (id: string) => void;
+    allThemes?: () => Record<string, ThemeOptions | undefined>;
+    setSelection: (feature: Feature) => void;
+    setSession?: (arg: {
+        name: string;
+        [key: string]: unknown;
+    }) => void;
+    clearSelection: () => void;
+    duplicateCurrentSession?: () => void;
+    notify: (message: string, level?: NotificationLevel, action?: SnackAction) => void;
     assemblyManager: AssemblyManager;
     version: string;
     getTrackActionMenuItems?: Function;
@@ -60,13 +70,19 @@ export interface AbstractSessionModel extends AbstractViewContainer {
     textSearchManager?: TextSearchManager;
     connections: AnyConfigurationModel[];
     deleteConnection?: Function;
+    temporaryAssemblies?: unknown[];
+    addTemporaryAssembly?: (arg: Record<string, unknown>) => void;
+    removeTemporaryAssembly?: (arg: string) => void;
     sessionConnections?: AnyConfigurationModel[];
+    sessionTracks?: AnyConfigurationModel[];
     connectionInstances?: {
         name: string;
         tracks: AnyConfigurationModel[];
         configuration: AnyConfigurationModel;
     }[];
     makeConnection?: Function;
+    breakConnection?: Function;
+    prepareToBreakConnection?: (arg: AnyConfigurationModel) => any;
     adminMode?: boolean;
     showWidget?: Function;
     addWidget?: Function;
@@ -88,6 +104,11 @@ export interface SessionWithConfigEditing extends AbstractSessionModel {
     addTrackConf(configuration: AnyConfigurationModel | SnapshotIn<AnyConfigurationModel>): void;
 }
 export declare function isSessionWithAddTracks(thing: unknown): thing is SessionWithConfigEditing;
+/** abstract interface for a session allows adding tracks */
+export interface SessionWithShareURL extends AbstractSessionModel {
+    shareURL: string;
+}
+export declare function isSessionWithShareURL(thing: unknown): thing is SessionWithShareURL;
 export interface Widget {
     type: string;
     id: string;
@@ -134,6 +155,11 @@ export interface SelectionContainer extends AbstractSessionModel {
     setSelection(thing: unknown): void;
 }
 export declare function isSelectionContainer(thing: unknown): thing is SelectionContainer;
+/** abstract interface for a session allows applying focus to views and widgets */
+export interface SessionWithFocusedViewAndDrawerWidgets extends SessionWithDrawerWidgets {
+    focusedViewId: string | undefined;
+    setFocusedViewId(id: string): void;
+}
 /** minimum interface that all view state models must implement */
 export interface AbstractViewModel {
     id: string;
@@ -211,6 +237,8 @@ export interface LocalPathLocation extends SnapshotIn<typeof MULocalPathLocation
 export interface UriLocation extends SnapshotIn<typeof MUUriLocation> {
 }
 export declare function isUriLocation(location: unknown): location is UriLocation;
+export declare function isLocalPathLocation(location: unknown): location is LocalPathLocation;
+export declare function isBlobLocation(location: unknown): location is BlobLocation;
 export declare class AuthNeededError extends Error {
     message: string;
     url: string;
@@ -226,14 +254,14 @@ export declare function isRetryException(exception: Error): boolean;
 export interface BlobLocation extends SnapshotIn<typeof MUBlobLocation> {
 }
 export type FileLocation = LocalPathLocation | UriLocation | BlobLocation;
-export type PreUriLocation = {
+export interface PreUriLocation {
     uri: string;
-};
-export type PreLocalPathLocation = {
+}
+export interface PreLocalPathLocation {
     localPath: string;
-};
-export type PreBlobLocation = {
+}
+export interface PreBlobLocation {
     blob: File;
-};
+}
 export type PreFileLocation = PreUriLocation | PreLocalPathLocation | PreBlobLocation;
 export { type default as TextSearchManager } from '../../TextSearch/TextSearchManager';

package/util/types/index.js

@@ -14,7 +14,7 @@ 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);
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.isRetryException = exports.isAuthNeededException = exports.RetryError = exports.AuthNeededError = exports.isUriLocation = exports.isAbstractMenuManager = exports.isRootModelWithInternetAccounts = exports.isAppRootModel = exports.isTrackViewModel = exports.isDisplayModel = exports.isTrackModel = exports.isViewModel = exports.isSelectionContainer = exports.isSessionWithSessionPlugins = exports.isSessionModelWithConnectionEditing = exports.isSessionModelWithConnections = exports.isSessionModelWithWidgets = exports.isSessionWithAddTracks = exports.isSessionModelWithConfigEditing = exports.isSessionModel = exports.isViewContainer = void 0;
+exports.isRetryException = exports.isAuthNeededException = exports.RetryError = exports.AuthNeededError = exports.isBlobLocation = exports.isLocalPathLocation = exports.isUriLocation = exports.isAbstractMenuManager = exports.isRootModelWithInternetAccounts = exports.isAppRootModel = exports.isTrackViewModel = exports.isDisplayModel = exports.isTrackModel = exports.isViewModel = exports.isSelectionContainer = exports.isSessionWithSessionPlugins = exports.isSessionModelWithConnectionEditing = exports.isSessionModelWithConnections = exports.isSessionModelWithWidgets = exports.isSessionWithShareURL = exports.isSessionWithAddTracks = exports.isSessionModelWithConfigEditing = exports.isSessionModel = exports.isViewContainer = void 0;
 const mobx_state_tree_1 = require("mobx-state-tree");
 __exportStar(require("./util"), exports);
 function isViewContainer(thing) {
@@ -41,6 +41,10 @@ function isSessionWithAddTracks(thing) {
     isSessionModel(thing) && 'addTrackConf' in thing && !thing.disableAddTracks);
 }
 exports.isSessionWithAddTracks = isSessionWithAddTracks;
+function isSessionWithShareURL(thing) {
+    return isSessionModel(thing) && 'shareURL' in thing && !!thing.shareURL;
+}
+exports.isSessionWithShareURL = isSessionWithShareURL;
 function isSessionModelWithWidgets(thing) {
     return isSessionModel(thing) && 'widgets' in thing;
 }
@@ -122,6 +126,20 @@ function isUriLocation(location) {
         !!location.uri);
 }
 exports.isUriLocation = isUriLocation;
+function isLocalPathLocation(location) {
+    return (typeof location === 'object' &&
+        location !== null &&
+        'localPath' in location &&
+        !!location.localPath);
+}
+exports.isLocalPathLocation = isLocalPathLocation;
+function isBlobLocation(location) {
+    return (typeof location === 'object' &&
+        location !== null &&
+        'blobId' in location &&
+        !!location.blobId);
+}
+exports.isBlobLocation = isBlobLocation;
 class AuthNeededError extends Error {
     constructor(message, url) {
         super(message);

package/util/types/mst.js

@@ -4,11 +4,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.FileLocation = exports.UriLocation = exports.UriLocationRaw = exports.BlobLocation = exports.LocalPathLocation = exports.Region = exports.NoAssemblyRegion = exports.PropTypes = exports.ElementId = void 0;
-const shortid_1 = __importDefault(require("shortid"));
 const mobx_state_tree_1 = require("mobx-state-tree");
 const prop_types_1 = __importDefault(require("prop-types"));
 const mobx_react_1 = require("mobx-react");
-exports.ElementId = mobx_state_tree_1.types.optional(mobx_state_tree_1.types.identifier, shortid_1.default.generate);
+const nanoid_1 = require("../nanoid");
+exports.ElementId = mobx_state_tree_1.types.optional(mobx_state_tree_1.types.identifier, () => (0, nanoid_1.nanoid)());
 // PropTypes that are useful when working with instances of these in react components
 exports.PropTypes = {
     Region: prop_types_1.default.shape({