@jbrowse/core 3.7.0 → 4.0.0

package/esm/util/index.d.ts

@@ -0,0 +1,271 @@
+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 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): 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>): 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;
+    })[];
+}
+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';