@jbrowse/core 4.3.0 → 5.0.0-beta.10

package/esm/util/htmlText.d.ts

@@ -0,0 +1,13 @@
+/**
+ * Whether a string is markup to RENDER rather than text that merely contains
+ * angle brackets — a VCF symbolic allele (`<DEL>`), an email in brackets, `a<b`.
+ *
+ * The one place that question is answered, because two callers answer it about
+ * the same string and a disagreement is silent: `SanitizedHTML` escapes what
+ * this rejects (so `<DEL>` reaches the screen intact), and anything extracting
+ * that string's words for the clipboard has to make the same call or a parser
+ * eats the allele the tooltip displayed.
+ */
+export declare function looksLikeHTML(str: string): boolean;
+/** Angle brackets and friends as entities, so text renders as itself. */
+export declare function escapeHTML(str: string): string;

package/esm/util/htmlText.js

@@ -0,0 +1,66 @@
+// source https://github.com/sindresorhus/html-tags/blob/master/html-tags.json
+// with some random uncommon ones removed. note: we just use this to run the
+// content through dompurify without escaping if we see an htmlTag from this
+// list otherwise we escape angle brackets and things prematurely because it
+// might be something like <TRA> in VCF. Ref #657
+const htmlTags = [
+    'a',
+    'b',
+    'br',
+    'code',
+    'div',
+    'em',
+    'h1',
+    'h2',
+    'h3',
+    'h4',
+    'h5',
+    'h6',
+    'i',
+    'img',
+    'li',
+    'mark',
+    'p',
+    'pre',
+    'span',
+    'small',
+    'strong',
+    'table',
+    'tbody',
+    'sup',
+    'sub',
+    'td',
+    'tfoot',
+    'th',
+    'thead',
+    'tr',
+    'u',
+    'ul',
+];
+// adapted from is-html
+// https://github.com/sindresorhus/is-html/blob/master/index.js
+const full = new RegExp(htmlTags.map(tag => String.raw `<${tag}\b[^>]*>`).join('|'), 'i');
+/**
+ * Whether a string is markup to RENDER rather than text that merely contains
+ * angle brackets — a VCF symbolic allele (`<DEL>`), an email in brackets, `a<b`.
+ *
+ * The one place that question is answered, because two callers answer it about
+ * the same string and a disagreement is silent: `SanitizedHTML` escapes what
+ * this rejects (so `<DEL>` reaches the screen intact), and anything extracting
+ * that string's words for the clipboard has to make the same call or a parser
+ * eats the allele the tooltip displayed.
+ */
+export function looksLikeHTML(str) {
+    return full.test(str);
+}
+const htmlEscapes = {
+    '&': '&amp;',
+    '<': '&lt;',
+    '>': '&gt;',
+    '"': '&quot;',
+    "'": '&#39;',
+};
+/** Angle brackets and friends as entities, so text renders as itself. */
+export function escapeHTML(str) {
+    return str.replaceAll(/[&<>"']/g, c => htmlEscapes[c]);
+}

package/esm/util/idMaker.d.ts

@@ -1 +1 @@
-export default function idMaker(args: Record<string, unknown>, id?: string, len?: number): string | number;
+export default function idMaker(args: Record<string, unknown>): string;

package/esm/util/idMaker.js

@@ -1,29 +1,42 @@
-import { hashCode } from "./index.js";
-export default function idMaker(args, id = '', len = 5000) {
+// generates a short "id fingerprint" from the config passed to the base
+// feature adapter. hashes incrementally during traversal so no large
+// intermediate string is ever allocated — important for FromConfigAdapter
+// which can contain thousands of inline features. exits early once enough
+// data has been hashed (equivalent to the old 5000 char budget)
+export default function idMaker(args) {
+    let hash = 0;
+    let count = 0;
     const stack = [args];
-    while (stack.length) {
+    outer: while (stack.length) {
         const obj = stack.pop();
-        for (const [key, val] of Object.entries(obj)) {
-            if (id.length > len) {
-                return hashCode(id);
+        for (const key in obj) {
+            if (count > 5000) {
+                break outer;
+            }
+            const val = obj[key];
+            if (typeof val === 'object' && val !== null) {
+                stack.push(val);
             }
             else {
-                if (typeof val === 'object' && val !== null) {
-                    stack.push(val);
+                // normalize FileHandleLocation for consistent hashing across
+                // rpcSessionId and adapter cache key
+                let s;
+                if (key === 'locationType' && val === 'FileHandleLocation') {
+                    s = `${key}-BlobLocation`;
+                }
+                else if (key === 'handleId') {
+                    s = `blobId-fh-blob-${val}`;
                 }
                 else {
-                    if (key === 'locationType' && val === 'FileHandleLocation') {
-                        id += `${key}-BlobLocation`;
-                    }
-                    else if (key === 'handleId') {
-                        id += `blobId-fh-blob-${val}`;
-                    }
-                    else {
-                        id += `${key}-${val}`;
-                    }
+                    s = `${key}-${val}`;
+                }
+                for (let i = 0; i < s.length; i++) {
+                    hash = (hash << 5) - hash + s.charCodeAt(i);
+                    hash |= 0;
                 }
+                count += s.length;
             }
         }
     }
-    return `adp-${hashCode(id)}`;
+    return `adp-${hash}`;
 }

package/esm/util/index.d.ts

@@ -1,274 +1,88 @@
-import type React from 'react';
-import type { ParsedLocString } from './locString.ts';
-import type PluginManager from '../PluginManager.ts';
-import type { BaseBlock } from './blockTypes.ts';
-import type { Feature } from './simpleFeature.ts';
-import type { StopToken } from './stopToken.ts';
-import type { AbstractDisplayModel, AbstractSessionModel, AbstractTrackModel, AbstractViewModel, AssemblyManager, Region, TypeTestedByPredicate } from './types/index.ts';
-import type { Region as MUIRegion } from './types/mst.ts';
-import type { BaseOptions } from '../data_adapters/BaseAdapter/index.ts';
-import type { IAnyStateTreeNode, IStateTreeNode, Instance } from '@jbrowse/mobx-state-tree';
-import type { GenericFilehandle } from 'generic-filehandle2';
-export * from './types/index.ts';
-export * from './when.ts';
-export * from './range.ts';
-export * from './dedupe.ts';
-export * from './coarseStripHTML.ts';
-export * from './offscreenCanvasPonyfill.tsx';
-export * from './offscreenCanvasUtils.tsx';
-export * from './rpc.ts';
-export * from './crypto.ts';
-export declare function useDebounce<T>(value: T, delay: number): T;
-export declare function useWidthSetter(view: {
-    setWidth: (arg: number) => void;
-}, padding: string): React.RefObject<HTMLDivElement | null>;
-export declare function useDebouncedCallback<T>(callback: (...args: T[]) => void, wait?: number): (...args: T[]) => void;
-export declare function findParentThat(node: IAnyStateTreeNode, predicate: (thing: IAnyStateTreeNode) => boolean): (object & IStateTreeNode<import("@jbrowse/mobx-state-tree").IAnyComplexType>) | IStateTreeNode<IAnyStateTreeNode>;
-export declare function springAnimate(fromValue: number, toValue: number, setValue: (value: number) => void, onFinish?: () => void, precision?: number, tension?: number, friction?: number, clamp?: boolean): (() => void)[];
-export declare function findParentThatIs<T extends (a: IAnyStateTreeNode) => boolean>(node: IAnyStateTreeNode, predicate: T): TypeTestedByPredicate<T>;
-export declare function getSession(node: IAnyStateTreeNode): AbstractSessionModel;
-export declare function getContainingView(node: IAnyStateTreeNode): AbstractViewModel;
-export declare function getContainingTrack(node: IAnyStateTreeNode): AbstractTrackModel;
-export declare function getContainingDisplay(node: IAnyStateTreeNode): AbstractDisplayModel;
-export declare function assembleLocString(region: ParsedLocString): string;
-export declare function assembleLocStringFast(region: ParsedLocString, cb?: (n: number) => string | number): string;
-export declare function compareLocs(locA: ParsedLocString, locB: ParsedLocString): number;
-export declare function compareLocStrings(a: string, b: string, isValidRefName: (refName: string, assemblyName?: string) => boolean): number;
-export declare function clamp(num: number, min: number, max: number): number;
-export declare function bpToPx(bp: number, { reversed, end, start, }: {
-    start?: number;
-    end?: number;
-    reversed?: boolean;
-}, bpPerPx: number): number;
-export declare function radToDeg(radians: number): number;
-export declare function degToRad(degrees: number): number;
-export declare function polarToCartesian(rho: number, theta: number): [number, number];
-export declare function cartesianToPolar(x: number, y: number): [number, number];
-interface MinimalRegion {
-    start: number;
-    end: number;
-    reversed?: boolean;
-}
-export declare function featureSpanPx(feature: Feature, region: MinimalRegion, bpPerPx: number): readonly [number, number];
-export declare function bpSpanPx(leftBp: number, rightBp: number, region: MinimalRegion, bpPerPx: number): readonly [number, number];
-export declare function calculateLayoutBounds(featureStart: number, featureEnd: number, layoutWidthBp: number, reversed?: boolean): [number, number];
-export declare function iterMap<T, U>(iter: Iterable<T>, func: (arg: T) => U, sizeHint?: number): U[];
-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;
-export declare function renameRegionIfNeeded(refNameMap: Record<string, string> | undefined, region: Region | Instance<typeof MUIRegion>, getSeqAdapterRefName?: (refName: string) => string): Region & {
-    originalRefName?: string;
-};
-export declare function renameRegionsIfNeeded<ARGTYPE extends {
-    assemblyName?: string;
-    regions?: Region[];
-    stopToken?: string;
-    adapterConfig: Record<string, unknown>;
-    sessionId: string;
-    statusCallback?: (arg: string) => void;
-}>(assemblyManager: AssemblyManager, args: ARGTYPE): Promise<ARGTYPE & {
-    regions: (Region & {
-        originalRefName?: string;
-    })[];
-}>;
-export declare function minmax(a: number, b: number): readonly [number, number];
-export declare function shorten(name: string, max?: number, short?: number): string;
-export declare function shorten2(name: string, max?: number): string;
-export declare function stringify({ refName, coord, assemblyName, oob, }: {
-    assemblyName?: string;
-    coord: number;
-    refName?: string;
-    oob?: boolean;
-}, useAssemblyName?: boolean): string;
-export declare const isElectron: boolean;
-export declare const complementTable: Record<string, string>;
-export declare function revcom(str: string): string;
-export declare function reverse(str: string): string;
-export declare function complement(str: string): string;
-export declare const rIC: (((callback: IdleRequestCallback, options?: IdleRequestOptions) => number) & typeof requestIdleCallback) | ((cb: () => void) => void);
-export declare function measureText(str: unknown, fontSize?: number): number;
-export type Frame = 1 | 2 | 3 | -1 | -2 | -3;
-export declare function getFrame(start: number, end: number, strand: 1 | -1, phase: 0 | 1 | 2): Frame;
-export declare const defaultStarts: string[];
-export declare const defaultStops: string[];
-export declare const defaultCodonTable: {
-    TCA: string;
-    TCC: string;
-    TCG: string;
-    TCT: string;
-    TTC: string;
-    TTT: string;
-    TTA: string;
-    TTG: string;
-    TAC: string;
-    TAT: string;
-    TAA: string;
-    TAG: string;
-    TGC: string;
-    TGT: string;
-    TGA: string;
-    TGG: string;
-    CTA: string;
-    CTC: string;
-    CTG: string;
-    CTT: string;
-    CCA: string;
-    CCC: string;
-    CCG: string;
-    CCT: string;
-    CAC: string;
-    CAT: string;
-    CAA: string;
-    CAG: string;
-    CGA: string;
-    CGC: string;
-    CGG: string;
-    CGT: string;
-    ATA: string;
-    ATC: string;
-    ATT: string;
-    ATG: string;
-    ACA: string;
-    ACC: string;
-    ACG: string;
-    ACT: string;
-    AAC: string;
-    AAT: string;
-    AAA: string;
-    AAG: string;
-    AGC: string;
-    AGT: string;
-    AGA: string;
-    AGG: string;
-    GTA: string;
-    GTC: string;
-    GTG: string;
-    GTT: string;
-    GCA: string;
-    GCC: string;
-    GCG: string;
-    GCT: string;
-    GAC: string;
-    GAT: string;
-    GAA: string;
-    GAG: string;
-    GGA: string;
-    GGC: string;
-    GGG: string;
-    GGT: string;
-};
-export declare function generateCodonTable(table: any): Record<string, string>;
-export declare function updateStatus<U>(msg: string, cb: ((arg: string) => void) | undefined, fn: () => U | Promise<U>): Promise<U>;
-export declare function updateStatus2<U>(msg: string, cb: (arg: string) => void, stopToken: StopToken | undefined, fn: () => U | Promise<U>): Promise<U>;
-export declare function hashCode(str: string): number;
-export declare function objectHash(obj: Record<string, any>): string;
-interface VirtualOffset {
-    blockPosition: number;
-}
-interface Block {
-    minv: VirtualOffset;
-    maxv: VirtualOffset;
-}
-export declare function bytesForRegions(regions: Region[], index: {
-    blocksForRange: (ref: string, start: number, end: number) => Promise<Block[]>;
-}): Promise<number>;
-export interface ViewSnap {
-    bpPerPx: number;
-    interRegionPaddingWidth: number;
-    minimumBlockWidth: number;
-    width: number;
-    offsetPx: number;
-    staticBlocks: {
-        contentBlocks: BaseBlock[];
-        blocks: BaseBlock[];
-    };
-    displayedRegions: (IStateTreeNode & {
-        start: number;
-        end: number;
-        refName: string;
-        reversed?: boolean;
-        assemblyName: string;
-    })[];
-}
+import type { FileLocation } from './types/data.ts';
+export { capitalizeFirst, pluralize, shorten, shorten2, truncateMiddle, } from './stringUtils.ts';
+export { formatBytes } from './formatBytes.ts';
+export { getFillProps, getStrokeProps, stripAlpha } from './svgColorProps.ts';
+export { fetchAndMaybeUnzip, fetchAndMaybeUnzipText, isGzip, } from './fetchAndMaybeUnzip.ts';
+export { type AbstractDisplayModel, type AbstractMenuManager, type AbstractRootModel, type AbstractSessionModel, type AbstractTrackModel, type AbstractViewContainer, type AbstractViewModel, type AnimationMode, type AnyReactComponentType, type AppRootModel, type AssemblyHost, type AssemblyManager, type AugmentedRegion, AuthNeededError, type BasePlugin, type BlobLocation, type ClassReturnedBy, type ConnectionInstance, type DialogComponentType, type DialogHost, type DrawerPosition, type FileHandleLocation, type FileLocation, type InstanceTypeRestrictive, type JBrowsePlugin, type JBrowsePluginVersion, type LocalPathLocation, type NoAssemblyRegion, type NotificationLevel, type NotificationSink, type PaletteHost, type PreBlobLocation, type PreFileHandleLocation, type PreFileLocation, type PreLocalPathLocation, type PreUriLocation, type Region, type RenderingServices, type RpcCaller, type RpcHost, type RootModelWithInternetAccounts, type SelectionContainer, type SessionServices, type SessionWithAddAssembly, type SessionWithAddSessionTrack, type SessionWithPublishTrackConf, type SessionWithConfigEditing, type SessionWithConnectionEditing, type SessionWithConnections, type SessionWithDeleteTrackConf, type SessionWithDrawerWidgets, type SessionWithFocusedViewAndDrawerWidgets, type SessionWithPermanentPlugins, type SessionWithSessionPlugins, type SessionWithShareURL, type SessionWithViewReplacement, type SessionWithWidgets, type SnackAction, type TrackActionView, type TrackCatalog, type TrackContainer, type TrackViewModel, type TypeTestedByPredicate, type UriLocation, type Widget, type WidgetMap, addOrReplaceView, canReplaceView, isAbstractMenuManager, isAppRootModel, isAuthNeededException, isBlobLocation, isDisplayModel, isFileHandleLocation, isLocalPathLocation, isRootModelWithInternetAccounts, isSelectionContainer, isSessionModel, isSessionServices, isSessionModelWithConfigEditing, isSessionModelWithConnectionEditing, isSessionModelWithConnections, isSessionModelWithWidgets, isSessionWithAddAssembly, isSessionWithAddSessionTrack, isSessionWithAddTracks, isSessionWithPublishTrackConf, isSessionWithDeleteTrackConf, isSessionWithMultipleViews, isSessionWithPermanentPlugins, isSessionWithSessionPlugins, isSessionWithSessionTracks, isSessionWithShareURL, isSessionWithViewReplacement, isTrackModel, isTrackViewModel, isUriLocation, isViewContainer, isViewModel, } from './types/index.ts';
+export { type PluginUpdate, type ResolvedPlugin, type StorePluginFailure, type StorePluginResolution, getPluginUpdate, installablePlugins, installedVersionFromUrl, isPluginInstalled, resolvePlugin, resolveStorePluginRefs, resolveStoreRefs, } from './pluginStore.ts';
+export { type PhaseFailure, type ProgressReporter, type RpcStatus, type StatusCallback, type StatusPhase, type StatusStream, type StatusWindow, type StatusWithProgress, createProgressReporter, createStatusFanOut, createStatusWindow, downloadStatus, progressLabel, statusFraction, statusMessageText, statusProgressLabel, statusReading, statusSource, throttleStatusEmits, updateStatus, withProgress, } from './progress.ts';
+export { calculateRedispatchRange, doesIntersect2, intersection2, } from './range.ts';
+export { dedupe } from './dedupe.ts';
+export { MAX_GLOB_REGIONS, matchRefNames, parseRegionNames, resolveNamedRegions, selectNamedRegions, } from './selectNamedRegions.ts';
+export type { RefNameMatchSource } from './selectNamedRegions.ts';
+export { isValidTag, tagRegex } from './tags.ts';
+export { formatRelativeTime } from './formatRelativeTime.ts';
+export { fetchJson } from './fetchJson.ts';
+export { type EncodedSessionParam, type SessionShareMode, ENCODED_PREFIX, JSON_PREFIX, SHARE_PREFIX, b64PadSuffix, encodeSessionParam, fromUrlSafeB64, readSessionFromDynamo, shareEndpoint, toUrlSafeB64, } from './sessionSharing.ts';
+export { coarseStripHTML } from './coarseStripHTML.ts';
+export { measureText, measuredFont } from './measureText.ts';
+export type { MeasuredFont } from './measureText.ts';
+export { createScrollLatch } from './scrollLatch.ts';
+export { MAX_ZOOM_RATE_PER_MS, SCROLL_ZOOM_FACTOR_DIVISOR, ZOOM_ACTIVE_WINDOW_MS, accumulateScroll, applyZoomAccum, getZoomNormalizer, isActivelyZooming, normalizeWheelDelta, wheelFrameElapsedMs, wheelZoomAccum, } from './wheelZoom.ts';
+export { avg, clamp, getDisplayStr, getNumberGrouping, max, maxFinite, min, minmax, polarToCartesian, radToDeg, reducePrecision, setNumberGrouping, sum, toLocale, } from './numericUtils.ts';
+export { type MinimalRegion, bpSpanPx, bpToPx, bytesForRegions, featureSpanPx, getBpDisplayStr, getTickDisplayStr, parseBpString, } from './bpUtils.ts';
+export { type BasicFeature, gatherOverlaps, mergeIntervals, } from './intervals.ts';
+export { clampToContig, clampToListedContig } from './clampToContig.ts';
+export { MORPH_DURATION_MS, animationAllowed, easeInOutCubic, morphClockMs, } from './animationAllowed.ts';
+export { springAnimate } from './springAnimate.ts';
+export { localStorageAvailable, localStorageGetBoolean, localStorageGetItem, localStorageGetJSON, localStorageGetNumber, localStorageGetStringArray, localStorageRemoveItem, localStorageSetBoolean, localStorageSetItem, localStorageSetJSON, localStorageSetNumber, notifyLocalStorageKey, subscribeToLocalStorageKey, } from './localStorage.ts';
+export { renameComparativeRegions, renameRegionIfNeeded, renameRegionsIfNeeded, } from './renameRegions.ts';
+export { addAndShowTrack } from './addAndShowTrack.ts';
+export { addTrackFromWidget, containerDisplaysAssembly, finishAddTrack, type AddTrackWidgetSelf, type AddTrackWorkflowModel, } from './addTrackFromWidget.ts';
+export { namesTemporaryAssembly } from './temporaryAssembly.ts';
+export { makeTrackId } from './makeTrackId.ts';
+export { matchTrackId } from './matchTrackId.ts';
+export { drawImageOntoCanvasContext } from './offscreenCanvasPonyfill.ts';
+export { indexedDBAvailable, isElectron, isNode, rIC } from './environment.ts';
+export { isWebWorker } from './isWebWorker.ts';
+export { sessionStorageAvailable, sessionStorageGetItem, sessionStorageRemoveItem, sessionStorageSetItem, } from './sessionStorage.ts';
+export { isObject } from './objectUtils.ts';
+export { type ReorderDirection, applyOrderWithin, reorder, reorderWithin, } from './reorder.ts';
+export { getStr } from './getStr.ts';
+export { downloadPhase, getLocationUri, resolveUri } from './getLocationUri.ts';
+export { measureGridWidth, resolveSelectedIds } from './dataGridUtils.ts';
+export { isRpcResult } from './rpc.ts';
+export { aesDecrypt, aesEncrypt, sha256, sha256Base64, sha256Base64Url, toBase64, toBase64Url, } from './crypto.ts';
+export { type FeatureWidgetTypeRef, type ParentFeatureSummary, notifyFeatureDetailsMiss, openFeatureWidget, } from './openFeatureWidget.ts';
+export { withFeatureDetails } from './withFeatureDetails.ts';
+export { canonicalizeViewRefName, findParentThat, findParentThatIs, getAssemblyHost, getContainingDisplay, getContainingTrack, getContainingView, getEnv, getRenderingServices, launchOrReplaceView, getSession, hashCode, objectHash, } from './mstUtils.ts';
+export { getDialogHost, getNotificationSink, getPaletteHost, getRpcHost, getSessionServices, } from './sessionServices.ts';
+/**
+ * Convert a browser File (from a drop zone or file input) into a FileLocation:
+ * a native local path under electron, or an in-memory blob location otherwise.
+ */
+export declare function fileToLocation(file: File): FileLocation;
+export { type Frame, complement, complementTable, defaultStarts, getFrame, revcom, reverse, stitch, } from './seqUtils.ts';
+export { revlist } from './revlist.ts';
+export { useCreateOnce, useDebounce, useFinalUnmount, useLocalStorage, useWidthSetter, } from './hooks.ts';
+export { codonTable, defaultCodonTable, generateCodonTable, } from './geneticCodes.ts';
+export { IUPAC_MOTIF_REGEX, isPalindromic, iupacToRegex, reverseComplementIupac, } from './iupac.ts';
+export { type MotifListParse, type MotifParseError, type ParsedMotif, parseMotifList, } from './parseMotifList.ts';
 export declare function isSupportedIndexingAdapter(type?: string): boolean;
-export declare function getBpDisplayStr(total: number): string;
-export declare function reducePrecision(s: number, n?: number): string;
-export declare function getProgressDisplayStr(current: number, total: number): string;
-export declare function toLocale(n: number): string;
-export declare function getTickDisplayStr(totalBp: number, bpPerPx: number): string;
-export declare function getLayoutId({ sessionId, trackInstanceId, }: {
-    sessionId: string;
-    trackInstanceId: string;
-}): string;
-export declare function getStatsId({ sessionId, trackInstanceId, }: {
-    sessionId: string;
-    trackInstanceId: string;
-}): string;
-export declare function useLocalStorage<T>(key: string, initialValue: T, enabled?: boolean): readonly [T, (value: T | ((val: T) => T)) => void];
-export declare function getUriLink(value: {
-    uri: string;
-    baseUri?: string;
-}): string;
-export declare function getStr(obj: unknown): string;
-export declare function linkify(s: string): string;
-export declare function measureGridWidth(elements: unknown[], args?: {
-    minWidth?: number;
-    fontSize?: number;
-    maxWidth?: number;
-    padding?: number;
-    stripHTML?: boolean;
-}): number;
-export declare function getEnv(obj: any): {
-    pluginManager: PluginManager;
-};
-export declare function localStorageGetItem(item: string): string | null | undefined;
-export declare function localStorageSetItem(str: string, item: string): void;
-export declare function max(arr: Iterable<number>, init?: number): number;
-export declare function min(arr: Iterable<number>, init?: number): number;
-export declare function sum(arr: Iterable<number>): number;
-export declare function avg(arr: number[]): number;
 export declare function groupBy<T>(array: Iterable<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;
-    end: number;
-}>(intervals: T[], w?: number): T[];
-export interface BasicFeature {
-    end: number;
-    start: number;
-    refName: string;
-}
-export declare function gatherOverlaps<T extends BasicFeature>(regions: T[], w?: number): T[];
-export declare function stripAlpha(str: string): string;
-export declare function getStrokeProps(str: string): {
-    strokeOpacity: number;
-    stroke: string;
-} | {
-    strokeOpacity?: undefined;
-    stroke?: undefined;
-};
-export declare function getFillProps(str: string): {
-    fillOpacity: number;
-    fill: string;
-} | {
-    fillOpacity?: undefined;
-    fill?: undefined;
-};
-export declare function renderToStaticMarkup(node: React.ReactElement): string;
-export declare function isGzip(buf: Uint8Array): boolean;
-export declare function fetchAndMaybeUnzip(loc: GenericFilehandle, opts?: BaseOptions): Promise<any>;
-export declare function fetchAndMaybeUnzipText(loc: GenericFilehandle, opts?: BaseOptions): Promise<string>;
-export declare function isObject(x: unknown): x is Record<string | symbol | number, unknown>;
-export declare function localStorageGetNumber(key: string, defaultVal: number): number;
-export declare function localStorageGetBoolean(key: string, defaultVal: boolean): boolean;
-export declare function localStorageSetBoolean(key: string, value: boolean): void;
 export declare function testAdapter(fileName: string, regex: RegExp, adapterHint: string | undefined, expected: string): boolean;
 export { type Feature, type SimpleFeatureSerialized, type SimpleFeatureSerializedNoId, default as SimpleFeature, isFeature, } from './simpleFeature.ts';
-export { blobToDataURL } from './blobToDataURL.ts';
-export { makeAbortableReaction } from './makeAbortableReaction.ts';
-export * from './aborting.ts';
-export * from './linkify.ts';
-export * from './locString.ts';
-export * from './stopToken.ts';
-export * from './tracks.ts';
-export * from './fileHandleStore.ts';
+export { saveAs } from './FileSaver/index.ts';
+export { type SaveSvgAsImageOptions, saveSvgAsImage, svgHtmlToPngBlob, } from '../svg/saveSvgAsImage.ts';
+export { type ActiveFetch, type StatusChannel, type StatusReporter, createStatusChannel, createAbortRotation, } from './createAbortRotation.ts';
+export { createSharedSetup } from './cachedSetup.ts';
+export { scheduleDetachedDestroy } from './scheduleDetachedDestroy.ts';
+export { isDataCurrent } from './isDataCurrent.ts';
+export { handleFetchError, isAbortException, makeAbortError, } from './aborting.ts';
+export { linkify } from './linkify.ts';
+export { isGeneLikeType, isSequenceMatchType } from './featureTypes.ts';
+export { locStringsToRegions } from './locStringsToRegions.ts';
+export type { RefNameSource } from './locStringsToRegions.ts';
+export { type ParsedLocString, UnknownRefNameError, assembleLocString, assembleLocStringRaw, assembleLocStrings, compareLocStrings, compareLocs, parseLocString, parseLocStringOneBased, stringify, } from './locString.ts';
+export { type AbortBreakpoint, checkAbortSignal, createAbortBreakpoint, withAbortCheck, } from './aborting.ts';
+export { type AddTrackComponentModel, type AddTrackComponentProps, adapterNeedsAddTrackComponent, addAddTrackComponent, } from './addTrackComponent.ts';
+export { adapterConfigFromSpec } from './formatGuessers.ts';
+export { type AdapterConfig, type AdapterGuesser, type LooseTrackInput, type TrackTypeGuesser, UNKNOWN, UNSUPPORTED, addAdapterGuesser, addTrackTypeGuesser, clearFileFromCache, ensureFileHandleReady, expandLooseTrackConfig, findFileHandleIds, generateUnknownTrackConf, generateUnsupportedTrackConf, getBlob, getBlobMap, getConfAssemblyNames, getFileFromCache, getFileName, getRpcSessionId, getTrackAssemblyNames, getTrackName, guessAdapter, guessTrackConf, guessTrackType, hasFileHandlesInCache, hideTrackGeneric, isLooseTrackConfig, makeIndex, makeIndexType, restoreFileHandles, restoreFileHandlesFromSnapshot, setBlobMap, setFileInCache, showTrackGeneric, storeBlobLocation, storeFileHandleLocation, stripFileExtension, stripTrackIds, toggleTrackGeneric, } from './tracks.ts';
+export { getFileHandle, isFileSystemAccessSupported, storeFileHandle, verifyPermission, } from './fileHandleStore.ts';
 export { IntervalTree } from './IntervalTree.ts';
+export { cmpStr } from './cmpStr.ts';
+export { diffTrackConfig, flattenTrackConfigDelta, mergeTrackConfig, } from './trackConfigDelta.ts';
+export type { TrackConfigChange } from './trackConfigDelta.ts';
+export { BEZIER_CONNECTOR_MAX_REACH_PX, CUBIC_APEX_RATIO, bezierConnectorPath, } from './bezierConnector.ts';
+export { type AlignmentData, type DiagonalizationResult, diagonalizeRegions, } from './diagonalizeRegions.ts';