@jbrowse/core 2.2.0 → 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/index.d.ts

@@ -197,6 +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;
@@ -297,7 +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.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.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 = 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"));
@@ -651,9 +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
-        ? `${refName}:${toLocale(coord)}${oob ? ' (out of bounds)' : ''}`
+        ? `${shorten(refName)}:${toLocale(coord)}${oob ? ' (out of bounds)' : ''}`
         : '';
 }
 exports.stringify = stringify;

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/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/tracks.d.ts

@@ -54,8 +54,8 @@ export interface AdapterConfig {
     type: string;
     [key: string]: unknown;
 }
-export declare type AdapterGuesser = (file: FileLocation, index?: FileLocation, adapterHint?: string) => AdapterConfig | undefined;
-export declare type TrackTypeGuesser = (adapterName: string) => string | undefined;
+export type AdapterGuesser = (file: FileLocation, index?: FileLocation, adapterHint?: string) => AdapterConfig | undefined;
+export type TrackTypeGuesser = (adapterName: string) => string | undefined;
 export declare function getFileName(track: FileLocation): string;
 export declare function guessAdapter(file: FileLocation, index: FileLocation | undefined, adapterHint?: string, model?: IAnyStateTreeNode): AdapterConfig;
 export declare function guessTrackType(adapterType: string, model?: IAnyStateTreeNode): string;

package/util/types/index.d.ts

@@ -16,12 +16,12 @@ export interface AbstractViewContainer extends IStateTreeNode<IType<any, unknown
     addView(typeName: string, initialState?: Record<string, unknown>): AbstractViewModel;
 }
 export declare function isViewContainer(thing: unknown): thing is AbstractViewContainer;
-export declare type NotificationLevel = 'error' | 'info' | 'warning' | 'success';
+export type NotificationLevel = 'error' | 'info' | 'warning' | 'success';
 export interface SnackAction {
     name: string;
     onClick: () => void;
 }
-export declare type AssemblyManager = Instance<ReturnType<typeof assemblyManager>>;
+export type AssemblyManager = Instance<ReturnType<typeof assemblyManager>>;
 export type { TextSearchManager };
 export interface BasePlugin {
     version?: string;
@@ -40,7 +40,7 @@ export interface JBrowsePlugin {
     license: string;
     image?: string;
 }
-export declare type DialogComponentType = React.LazyExoticComponent<React.FC<any>> | React.FC<any>;
+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 {
     drawerPosition?: string;
@@ -135,7 +135,9 @@ export interface AbstractViewModel {
     id: string;
     type: string;
     width: number;
+    minimized: boolean;
     setWidth(width: number): void;
+    setMinimized(flag: boolean): void;
     displayName: string | undefined;
     setDisplayName: (arg: string) => void;
     menuItems: () => MenuItem[];
@@ -176,6 +178,11 @@ export interface AppRootModel extends AbstractRootModel {
     findAppropriateInternetAccount(location: UriLocation): BaseInternetAccountModel | undefined;
 }
 export declare function isAppRootModel(thing: unknown): thing is AppRootModel;
+export interface RootModelWithInternetAccounts extends AbstractRootModel {
+    internetAccounts: BaseInternetAccountModel[];
+    findAppropriateInternetAccount(location: UriLocation): BaseInternetAccountModel | undefined;
+}
+export declare function isRootModelWithInternetAccounts(thing: unknown): thing is RootModelWithInternetAccounts;
 /** a root model that manages global menus */
 export interface AbstractMenuManager {
     appendMenu(menuName: string): void;
@@ -212,14 +219,14 @@ export declare function isAuthNeededException(exception: unknown): exception is
 export declare function isRetryException(exception: Error): boolean;
 export interface BlobLocation extends SnapshotIn<typeof MUBlobLocation> {
 }
-export declare type FileLocation = LocalPathLocation | UriLocation | BlobLocation;
-export declare type PreUriLocation = {
+export type FileLocation = LocalPathLocation | UriLocation | BlobLocation;
+export type PreUriLocation = {
     uri: string;
 };
-export declare type PreLocalPathLocation = {
+export type PreLocalPathLocation = {
     localPath: string;
 };
-export declare type PreBlobLocation = {
+export type PreBlobLocation = {
     blob: File;
 };
-export declare type PreFileLocation = PreUriLocation | PreLocalPathLocation | PreBlobLocation;
+export type PreFileLocation = PreUriLocation | PreLocalPathLocation | PreBlobLocation;

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.isAppRootModel = exports.isTrackViewModel = exports.isDisplayModel = exports.isTrackModel = exports.isViewModel = exports.isSelectionContainer = exports.isSessionWithSessionPlugins = exports.isSessionModelWithConnections = exports.isSessionModelWithWidgets = exports.isSessionWithAddTracks = exports.isSessionModelWithConfigEditing = exports.isSessionModel = exports.isViewContainer = void 0;
+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.isSessionModelWithConnections = exports.isSessionModelWithWidgets = 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) {
@@ -97,6 +97,13 @@ function isAppRootModel(thing) {
         'findAppropriateInternetAccount' in thing);
 }
 exports.isAppRootModel = isAppRootModel;
+function isRootModelWithInternetAccounts(thing) {
+    return (typeof thing === 'object' &&
+        thing !== null &&
+        'internetAccounts' in thing &&
+        'findAppropriateInternetAccount' in thing);
+}
+exports.isRootModelWithInternetAccounts = isRootModelWithInternetAccounts;
 function isAbstractMenuManager(thing) {
     return (typeof thing === 'object' &&
         thing !== null &&

package/util/types/util.d.ts

@@ -5,12 +5,12 @@ import PluginManager from '../../PluginManager';
  * Obtain the return type of a constructor function type.
  * Differs from core Typescript InstanceType in that it returns never if not matched.
  */
-export declare type InstanceTypeRestrictive<CONSTRUCTOR extends new (...args: any[]) => any> = CONSTRUCTOR extends new (...args: any[]) => infer CLASS ? CLASS : never;
+export type InstanceTypeRestrictive<CONSTRUCTOR extends new (...args: any[]) => any> = CONSTRUCTOR extends new (...args: any[]) => infer CLASS ? CLASS : never;
 /** extracts the class type from a factory function that returns a constructor */
-export declare type ClassReturnedBy<FACT extends (pm: PluginManager) => any> = InstanceTypeRestrictive<ReturnType<FACT>>;
+export type ClassReturnedBy<FACT extends (pm: PluginManager) => any> = InstanceTypeRestrictive<ReturnType<FACT>>;
 /** A react component with any props. Consider using something more specific if possible */
-export declare type AnyReactComponentType = React.ComponentType<any>;
+export type AnyReactComponentType = React.ComponentType<any>;
 /** get the type that a predicate asserts */
-export declare type TypeTestedByPredicate<PREDICATE extends (thing: any) => boolean> = PREDICATE extends (thing: any) => thing is infer TYPE ? TYPE : never;
+export type TypeTestedByPredicate<PREDICATE extends (thing: any) => boolean> = PREDICATE extends (thing: any) => thing is infer TYPE ? TYPE : never;
 /** get the type for an instance of an MST model in a PM factory function */
-export declare type InstanceOfModelReturnedBy<FACTORY extends (pm: PluginManager) => IAnyModelType> = Instance<ReturnType<FACTORY>>;
+export type InstanceOfModelReturnedBy<FACTORY extends (pm: PluginManager) => IAnyModelType> = Instance<ReturnType<FACTORY>>;