@jbrowse/core 2.4.0 → 2.4.2

package/util/layouts/GranularRectLayout.js

@@ -64,7 +64,7 @@ class LayoutRow {
             offset: left - rectWidth,
             min: left,
             max: right,
-            bits: new Array(3 * rectWidth),
+            bits: Array.from({ length: 3 * rectWidth }),
         };
     }
     addRect(rect, data) {
@@ -85,7 +85,10 @@ class LayoutRow {
                 this.rowState = this.initialize(left, right);
             }
             else if (additionalLength > 0) {
-                this.rowState.bits = this.rowState.bits.concat(new Array(additionalLength));
+                this.rowState.bits = [
+                    ...this.rowState.bits,
+                    ...Array.from({ length: additionalLength }),
+                ];
             }
         }
         // expand leftward if necessary
@@ -97,7 +100,10 @@ class LayoutRow {
                 this.rowState = this.initialize(left, right);
             }
             else {
-                this.rowState.bits = new Array(additionalLength).concat(this.rowState.bits);
+                this.rowState.bits = [
+                    ...Array.from({ length: additionalLength }),
+                    ...this.rowState.bits,
+                ];
                 this.rowState.offset -= additionalLength;
             }
         }
@@ -370,7 +376,7 @@ class GranularRectLayout {
         return this.getTotalHeight();
     }
     getRectangles() {
-        return new Map(Array.from(this.rectangles.entries()).map(([id, rect]) => {
+        return new Map([...this.rectangles.entries()].map(([id, rect]) => {
             const { l, r, originalHeight, top } = rect;
             const t = (top || 0) * this.pitchY;
             const b = t + originalHeight;

package/util/layouts/MultiLayout.js

@@ -13,7 +13,7 @@ class MultiLayout {
     }
     getDataByID(id) {
         for (const layout of this.subLayouts.values()) {
-            // @ts-ignore
+            // @ts-expect-error
             const r = layout.getDataByID(id);
             if (r) {
                 return r;

package/util/layouts/SceneGraph.js

@@ -32,13 +32,9 @@ class SceneGraph {
     addChild(nameOrSceneGraph, left, top, width, height, 
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
     data) {
-        let child;
-        if (nameOrSceneGraph instanceof SceneGraph) {
-            child = nameOrSceneGraph;
-        }
-        else {
-            child = new SceneGraph(nameOrSceneGraph, left, top, width, height, data);
-        }
+        const child = nameOrSceneGraph instanceof SceneGraph
+            ? nameOrSceneGraph
+            : new SceneGraph(nameOrSceneGraph, left, top, width, height, data);
         if (!(child instanceof SceneGraph)) {
             throw new TypeError('argument to addChild must be an array or a SceneGraph');
         }

package/util/mst-reflection.d.ts

@@ -1,29 +1,24 @@
+import { IAnyType, IModelReflectionPropertiesData, IAnyComplexType, ISimpleType, UnionStringArray } from 'mobx-state-tree';
+export interface ILiteralType<T> extends ISimpleType<T> {
+    value: T;
+}
 /**
  * get the inner type of an MST optional, array, or late type object
- *
- * @param {IModelType} type
- * @returns {IModelType}
  */
-export function getSubType(type: IModelType): IModelType;
+export declare function getSubType(type: IAnyType): IAnyType;
 /**
- * get the array of
- * @param {MST Union Type obj} unionType
- * @returns {Array<IModelType>}
+ * get the array of the subtypes in a union
  */
-export function getUnionSubTypes(unionType: any): Array<IModelType>;
+export declare function getUnionSubTypes(unionType: IAnyType): IAnyType[];
 /**
  * get the type of one of the properties of the given MST model type
- *
- * @param {IModelType} type
- * @param {string} propertyName
- * @returns {IModelType}
  */
-export function getPropertyType(type: IModelType, propertyName: string): IModelType;
+export declare function getPropertyType(type: IModelReflectionPropertiesData, propertyName: string): IAnyType;
 /**
  * get the base type from inside an MST optional type
- * @param {*} type
  */
-export function getDefaultValue(type: any): any;
+export declare function getDefaultValue(type: IAnyType): any;
+export type IEnumerationType<T extends string> = ISimpleType<UnionStringArray<T[]>>;
 /** get the string values of an MST enumeration type */
-export function getEnumerationValues(type: any): any[];
-export function resolveLateType(maybeLate: any): any;
+export declare function getEnumerationValues(type: IAnyComplexType): string[];
+export declare function resolveLateType(maybeLate: IAnyType): any;

package/util/mst-reflection.js

@@ -5,19 +5,20 @@ exports.resolveLateType = exports.getEnumerationValues = exports.getDefaultValue
 const mobx_state_tree_1 = require("mobx-state-tree");
 /**
  * get the inner type of an MST optional, array, or late type object
- *
- * @param {IModelType} type
- * @returns {IModelType}
  */
 function getSubType(type) {
     let t;
     if ((0, mobx_state_tree_1.isOptionalType)(type)) {
+        // @ts-expect-error
         t = type._subtype || type.type;
     }
     else if ((0, mobx_state_tree_1.isArrayType)(type) || (0, mobx_state_tree_1.isMapType)(type)) {
+        // @ts-expect-error
         t = type._subtype || type._subType || type.subType;
+        // @ts-expect-error
     }
     else if (typeof type.getSubType === 'function') {
+        // @ts-expect-error
         return type.getSubType();
     }
     else {
@@ -31,17 +32,20 @@ function getSubType(type) {
 }
 exports.getSubType = getSubType;
 /**
- * get the array of
- * @param {MST Union Type obj} unionType
- * @returns {Array<IModelType>}
+ * get the array of the subtypes in a union
  */
 function getUnionSubTypes(unionType) {
     if (!(0, mobx_state_tree_1.isUnionType)(unionType)) {
         throw new TypeError('not an MST union type');
     }
-    const t = unionType._types ||
+    const t = 
+    // @ts-expect-error
+    unionType._types ||
+        // @ts-expect-error
         unionType.types ||
+        // @ts-expect-error
         getSubType(unionType)._types ||
+        // @ts-expect-error
         getSubType(unionType).types;
     if (!t) {
         // debugger
@@ -52,10 +56,6 @@ function getUnionSubTypes(unionType) {
 exports.getUnionSubTypes = getUnionSubTypes;
 /**
  * get the type of one of the properties of the given MST model type
- *
- * @param {IModelType} type
- * @param {string} propertyName
- * @returns {IModelType}
  */
 function getPropertyType(type, propertyName) {
     const propertyType = type.properties[propertyName];
@@ -64,12 +64,12 @@ function getPropertyType(type, propertyName) {
 exports.getPropertyType = getPropertyType;
 /**
  * get the base type from inside an MST optional type
- * @param {*} type
  */
 function getDefaultValue(type) {
     if (!(0, mobx_state_tree_1.isOptionalType)(type)) {
         throw new TypeError('type must be an optional type');
     }
+    // @ts-expect-error
     return type._defaultValue || type.defaultValue;
 }
 exports.getDefaultValue = getDefaultValue;
@@ -84,6 +84,7 @@ function resolveLateType(maybeLate) {
     if (!(0, mobx_state_tree_1.isUnionType)(maybeLate) &&
         !(0, mobx_state_tree_1.isArrayType)(maybeLate) &&
         (0, mobx_state_tree_1.isLateType)(maybeLate)) {
+        // @ts-expect-error
         return maybeLate.getSubType();
     }
     return maybeLate;

package/util/offscreenCanvasPonyfill.js

@@ -33,19 +33,20 @@ if (weHave.realOffscreenCanvas) {
 else if (weHave.node) {
     // use node-canvas if we are running in node (i.e. automated tests)
     exports.createCanvas = (...args) => {
-        // @ts-ignore
+        // @ts-expect-error
         // eslint-disable-next-line no-undef
         return nodeCreateCanvas(...args);
     };
     exports.createImageBitmap = async (canvas, ...otherargs) => {
-        if (otherargs.length) {
+        if (otherargs.length > 0) {
             throw new Error('only one-argument uses of createImageBitmap are supported by the node offscreencanvas ponyfill');
         }
         const dataUri = canvas.toDataURL();
-        // @ts-ignore
+        // @ts-expect-error
         // eslint-disable-next-line no-undef
         const img = new nodeImage();
         return new Promise((resolve, reject) => {
+            // need onload for jest
             img.onload = () => resolve(img);
             img.onerror = reject;
             img.src = dataUri;

package/util/offscreenCanvasUtils.js

@@ -79,6 +79,7 @@ async function renderToAbstractCanvas(width, height, opts, cb) {
 exports.renderToAbstractCanvas = renderToAbstractCanvas;
 async function getSerializedSvg(results) {
     const { width, height, canvasRecordedData } = results;
+    // @ts-ignore needs to be ignore not expect error, produces error in build step
     const C2S = await Promise.resolve().then(() => __importStar(require('canvas2svg')));
     const ctx = new C2S.default(width, height);
     const seq = new canvas_sequencer_1.CanvasSequence(canvasRecordedData);

package/util/tracks.d.ts

@@ -75,4 +75,4 @@ export declare function generateUnknownTrackConf(trackName: string, trackUrl: st
 };
 export declare function getTrackName(conf: AnyConfigurationModel, session: {
     assemblies: AnyConfigurationModel[];
-}): any;
+}): string;

package/util/tracks.js

@@ -141,7 +141,6 @@ function guessAdapter(file, index, adapterHint, model) {
 exports.guessAdapter = guessAdapter;
 function guessTrackType(adapterType, model) {
     if (model) {
-        // @ts-ignore
         const session = (0, index_1.getSession)(model);
         const trackTypeGuesser = (0, index_1.getEnv)(session).pluginManager.evaluateExtensionPoint('Core-guessTrackTypeForLocation', (_adapterName) => {
             return undefined;

package/util/types/index.d.ts

@@ -22,7 +22,6 @@ export interface SnackAction {
     onClick: () => void;
 }
 export type AssemblyManager = Instance<ReturnType<typeof assemblyManager>>;
-export type { TextSearchManager };
 export interface BasePlugin {
     version?: string;
     name: string;
@@ -195,6 +194,7 @@ export interface AbstractMenuManager {
 export declare function isAbstractMenuManager(thing: unknown): thing is AbstractMenuManager;
 export interface NoAssemblyRegion extends SnapshotIn<typeof MUNoAssemblyRegion> {
 }
+/** a description of a specific genomic region. assemblyName, refName, start, end, and reversed */
 export interface Region extends SnapshotIn<typeof MUIRegion> {
 }
 export interface AugmentedRegion extends Region {
@@ -230,3 +230,4 @@ export type PreBlobLocation = {
     blob: File;
 };
 export type PreFileLocation = PreUriLocation | PreLocalPathLocation | PreBlobLocation;
+export { type default as TextSearchManager } from '../../TextSearch/TextSearchManager';

package/util/types/index.js

@@ -37,7 +37,7 @@ function isSessionModelWithConfigEditing(thing) {
 exports.isSessionModelWithConfigEditing = isSessionModelWithConfigEditing;
 function isSessionWithAddTracks(thing) {
     return (
-    // @ts-ignore
+    // @ts-expect-error
     isSessionModel(thing) && 'addTrackConf' in thing && !thing.disableAddTracks);
 }
 exports.isSessionWithAddTracks = isSessionWithAddTracks;
@@ -71,7 +71,7 @@ function isTrackModel(thing) {
     return (typeof thing === 'object' &&
         thing !== null &&
         'configuration' in thing &&
-        // @ts-ignore
+        // @ts-expect-error
         thing.configuration.trackId);
 }
 exports.isTrackModel = isTrackModel;
@@ -79,7 +79,7 @@ function isDisplayModel(thing) {
     return (typeof thing === 'object' &&
         thing !== null &&
         'configuration' in thing &&
-        // @ts-ignore
+        // @ts-expect-error
         thing.configuration.displayId);
 }
 exports.isDisplayModel = isDisplayModel;

package/util/types/mst.js

@@ -70,16 +70,16 @@ exports.UriLocation = mobx_state_tree_1.types.snapshotProcessor(exports.UriLocat
     },
 });
 exports.FileLocation = mobx_state_tree_1.types.snapshotProcessor(mobx_state_tree_1.types.union(exports.LocalPathLocation, exports.UriLocation, exports.BlobLocation), {
-    // @ts-ignore
+    // @ts-expect-error
     preProcessor(snap) {
         if (!snap) {
             return undefined;
         }
-        // @ts-ignore
+        // @ts-expect-error
         // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
         const { locationType, ...rest } = snap;
         if (!locationType) {
-            // @ts-ignore
+            // @ts-expect-error
             const { uri, localPath, blob } = rest;
             let locationType = '';
             if (uri !== undefined) {

package/util/useMeasure.d.ts

@@ -0,0 +1,5 @@
+/// <reference types="react" />
+export default function useMeasure(): readonly [import("react").RefObject<HTMLDivElement>, {
+    width?: number | undefined;
+    height?: number | undefined;
+}];

package/util/useMeasure.js

@@ -0,0 +1,34 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = require("react");
+function useMeasure() {
+    const ref = (0, react_1.useRef)(null);
+    const [dims, setDims] = (0, react_1.useState)({
+        width: undefined,
+        height: undefined,
+    });
+    (0, react_1.useEffect)(() => {
+        if (!ref.current) {
+            return;
+        }
+        const RS = typeof window !== 'undefined' && 'ResizeObserver' in window
+            ? window.ResizeObserver
+            : undefined;
+        if (!RS) {
+            return;
+        }
+        const observer = new RS(entries => {
+            setDims({
+                width: entries[0].contentRect.width,
+                height: entries[0].contentRect.height,
+            });
+        });
+        observer.observe(ref.current);
+        // Callback fired when component is unmounted
+        return () => {
+            observer.disconnect();
+        };
+    }, []);
+    return [ref, dims];
+}
+exports.default = useMeasure;