@jbrowse/core 2.1.7 → 2.2.1

package/util/stats.js

@@ -2,7 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.blankStats = exports.scoresToStats = exports.calcPerBaseStats = exports.rectifyStats = exports.calcStdFromSums = void 0;
 const operators_1 = require("rxjs/operators");
-/*
+/**
  * calculate standard deviation using the 'shortcut method' that accepts
  * the sum and the sum squares of the elements
  *
@@ -10,7 +10,7 @@ const operators_1 = require("rxjs/operators");
  * @param sumSquares - sum(i^2, 1..n)
  * @param n - number of elements
  * @param population - boolean: use population instead of sample correction
- * @return the estimated std deviation
+ * @returns - the estimated std deviation
  */
 function calcStdFromSums(sum, sumSquares, n, population = false) {
     if (n === 0) {
@@ -30,9 +30,9 @@ function calcStdFromSums(sum, sumSquares, n, population = false) {
     return variance < 0 ? 0 : Math.sqrt(variance);
 }
 exports.calcStdFromSums = calcStdFromSums;
-/*
+/**
  * @param stats - a summary stats object with scoreSum, featureCount, scoreSumSquares, and basesCovered
- * @return - a summary stats object with scoreMean, scoreStdDev, and featureDensity added
+ * @returns - a summary stats object with scoreMean, scoreStdDev, and featureDensity added
  */
 function rectifyStats(s) {
     return {
@@ -43,11 +43,11 @@ function rectifyStats(s) {
     };
 }
 exports.rectifyStats = rectifyStats;
-/*
+/**
  * calculates per-base scores for variable width features over a region
  * @param region - object contains start, end
  * @param features - list of features with start, end, score
- * @return array of numeric scores
+ * @returns array of numeric scores
  */
 function calcPerBaseStats(region, features) {
     const { start, end } = region;
@@ -76,11 +76,11 @@ function calcPerBaseStats(region, features) {
     return scores;
 }
 exports.calcPerBaseStats = calcPerBaseStats;
-/*
+/**
  * transform a list of scores to summary statistics
  * @param region - object with start, end
- * @param feats - array of features which are possibly summary features
- * @return - object with scoreMax, scoreMin, scoreSum, scoreSumSquares, etc
+ * @param features - array of features which are possibly summary features
+ * @returns - object with scoreMax, scoreMin, scoreSum, scoreSumSquares, etc
  */
 async function scoresToStats(region, features) {
     const { start, end } = region;

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>>;