@jbrowse/core 2.1.4 → 2.1.6

package/ui/theme.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createJBrowseTheme = exports.jbrowseBaseTheme = exports.createJBrowseDefaultOverrides = exports.createJBrowseDefaultProps = exports.jbrowseDefaultPalette = void 0;
+exports.createJBrowseTheme = exports.createJBrowseBaseTheme = exports.createJBrowseDefaultOverrides = exports.createJBrowseDefaultProps = exports.jbrowseDefaultPalette = void 0;
 const colors_1 = require("@mui/material/colors");
 const styles_1 = require("@mui/material/styles");
 const deepmerge_1 = __importDefault(require("deepmerge"));
@@ -168,38 +168,35 @@ function createJBrowseDefaultOverrides(palette = {}) {
     };
 }
 exports.createJBrowseDefaultOverrides = createJBrowseDefaultOverrides;
-exports.jbrowseBaseTheme = {
-    palette: exports.jbrowseDefaultPalette,
-    typography: { fontSize: 12 },
-    spacing: 4,
-    ...(0, deepmerge_1.default)(createJBrowseDefaultProps(), createJBrowseDefaultOverrides()),
-};
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
+function createJBrowseBaseTheme(palette) {
+    return {
+        palette: exports.jbrowseDefaultPalette,
+        typography: { fontSize: 12 },
+        spacing: 4,
+        ...(0, deepmerge_1.default)(createJBrowseDefaultProps(), createJBrowseDefaultOverrides(palette)),
+    };
+}
+exports.createJBrowseBaseTheme = createJBrowseBaseTheme;
 function createJBrowseTheme(theme) {
-    var _a, _b, _c, _d;
+    var _a, _b;
     if ((_a = theme === null || theme === void 0 ? void 0 : theme.palette) === null || _a === void 0 ? void 0 : _a.tertiary) {
         theme = (0, deepmerge_1.default)(theme, {
             palette: {
-                tertiary: refTheme.palette.augmentColor(((_b = theme.palette.tertiary) === null || _b === void 0 ? void 0 : _b.color)
+                tertiary: refTheme.palette.augmentColor('color' in theme.palette.tertiary
                     ? theme.palette.tertiary
-                    : {
-                        color: theme.palette.tertiary,
-                    }),
+                    : { color: theme.palette.tertiary }),
             },
         });
     }
-    if ((_c = theme === null || theme === void 0 ? void 0 : theme.palette) === null || _c === void 0 ? void 0 : _c.quaternary) {
+    if ((_b = theme === null || theme === void 0 ? void 0 : theme.palette) === null || _b === void 0 ? void 0 : _b.quaternary) {
         theme = (0, deepmerge_1.default)(theme, {
             palette: {
-                quaternary: refTheme.palette.augmentColor(((_d = theme.palette.quaternary) === null || _d === void 0 ? void 0 : _d.color)
+                quaternary: refTheme.palette.augmentColor('color' in theme.palette.quaternary
                     ? theme.palette.quaternary
-                    : {
-                        color: theme.palette.quaternary,
-                    }),
+                    : { color: theme.palette.quaternary }),
             },
         });
     }
-    // @ts-ignore
-    return (0, styles_1.createTheme)((0, deepmerge_1.default)(exports.jbrowseBaseTheme, theme || {}));
+    return (0, styles_1.createTheme)((0, deepmerge_1.default)(createJBrowseBaseTheme(theme === null || theme === void 0 ? void 0 : theme.palette), theme || {}));
 }
 exports.createJBrowseTheme = createJBrowseTheme;

package/util/calculateStaticBlocks.js

@@ -3,15 +3,10 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const mobx_state_tree_1 = require("mobx-state-tree");
 const _1 = require(".");
 const blockTypes_1 = require("./blockTypes");
-function calculateStaticBlocks(model, padding = true, elision = true, extra = 0, 
-// on the main thread, window.innerWidth is used because this reduces
-// recalculating the blocks, otherwise, model.width for cases such as
-// off-main-thread. also this is not a ternary because our window.innerWidth
-// might be undefined on off-main-thread, so instead use || model.width
-width = (typeof window !== 'undefined' && window.innerWidth) || model.width) {
-    const { offsetPx, displayedRegions, bpPerPx, minimumBlockWidth, interRegionPaddingWidth, } = model;
+function calculateStaticBlocks(model, padding = true, elision = true, extra = 0, width = 800) {
+    const { offsetPx, displayedRegions, bpPerPx, minimumBlockWidth, interRegionPaddingWidth, width: modelWidth, } = model;
     const windowLeftBp = offsetPx * bpPerPx;
-    const windowRightBp = (offsetPx + width) * bpPerPx;
+    const windowRightBp = (offsetPx + modelWidth) * bpPerPx;
     const blockSizePx = width;
     const blockSizeBp = Math.ceil(blockSizePx * bpPerPx);
     // for each displayed region

package/util/index.d.ts

@@ -1,3 +1,4 @@
+import PluginManager from '../PluginManager';
 import { IAnyStateTreeNode, IStateTreeNode } from 'mobx-state-tree';
 import { IReactionPublic, IReactionOptions } from 'mobx';
 import SimpleFeature, { Feature, isFeature } from './simpleFeature';
@@ -327,10 +328,13 @@ export declare function getLayoutId({ sessionId, layoutId, }: {
     sessionId: string;
     layoutId: string;
 }): string;
-export declare const useLocalStorage: (key: string, defaultValue?: string) => [string, (arg: string) => void];
+export declare function useLocalStorage<T>(key: string, initialValue: T): 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 measureGridWidth(elements: string[]): number;
+export declare function getEnv(obj: any): {
+    pluginManager: PluginManager;
+};

package/util/index.js

@@ -30,7 +30,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getBpDisplayStr = 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.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.measureGridWidth = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = exports.toLocale = void 0;
+exports.getEnv = exports.measureGridWidth = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = exports.toLocale = void 0;
 /* eslint-disable @typescript-eslint/no-explicit-any */
 const react_1 = require("react");
 const is_object_1 = __importDefault(require("is-object"));
@@ -941,16 +941,35 @@ function getLayoutId({ sessionId, layoutId, }) {
     return sessionId + '-' + layoutId;
 }
 exports.getLayoutId = getLayoutId;
-// similar to https://blog.logrocket.com/using-localstorage-react-hooks/
-const useLocalStorage = (key, defaultValue = '') => {
-    const [value, setValue] = (0, react_1.useState)(() => localStorage.getItem(key) || defaultValue);
-    (0, react_1.useEffect)(() => {
-        localStorage.setItem(key, value);
-    }, [key, value]);
-    // without this cast, tsc complained that the type of setValue could be a
-    // string or a callback
-    return [value, setValue];
-};
+// Hook from https://usehooks.com/useLocalStorage/
+function useLocalStorage(key, initialValue) {
+    const [storedValue, setStoredValue] = (0, react_1.useState)(() => {
+        if (typeof window === 'undefined') {
+            return initialValue;
+        }
+        try {
+            const item = window.localStorage.getItem(key);
+            return item ? JSON.parse(item) : initialValue;
+        }
+        catch (error) {
+            console.error(error);
+            return initialValue;
+        }
+    });
+    const setValue = (value) => {
+        try {
+            const valueToStore = value instanceof Function ? value(storedValue) : value;
+            setStoredValue(valueToStore);
+            if (typeof window !== 'undefined') {
+                window.localStorage.setItem(key, JSON.stringify(valueToStore));
+            }
+        }
+        catch (error) {
+            console.error(error);
+        }
+    };
+    return [storedValue, setValue];
+}
 exports.useLocalStorage = useLocalStorage;
 function getUriLink(value) {
     const { uri, baseUri = '' } = value;
@@ -977,3 +996,7 @@ function measureGridWidth(elements) {
     return Math.max(...elements.map(element => Math.min(Math.max(measureText(getStr(element), 14) + 50, 80), 1000)));
 }
 exports.measureGridWidth = measureGridWidth;
+function getEnv(obj) {
+    return (0, mobx_state_tree_1.getEnv)(obj);
+}
+exports.getEnv = getEnv;

package/util/simpleFeature.d.ts

@@ -42,7 +42,7 @@ export interface SimpleFeatureArgs {
     /** unique identifier. can also be in data.uniqueId */
     id: string | number;
 }
-interface SimpleFeatureSerializedNoId {
+export interface SimpleFeatureSerializedNoId {
     [key: string]: unknown;
     parentId?: string;
     subfeatures?: SimpleFeatureSerializedNoId[];
@@ -94,4 +94,3 @@ export default class SimpleFeature implements Feature {
     toJSON(): SimpleFeatureSerialized;
     static fromJSON(json: SimpleFeatureSerialized): SimpleFeature;
 }
-export {};

package/util/stats.js

@@ -86,11 +86,13 @@ async function scoresToStats(region, features) {
     const { start, end } = region;
     const { scoreMin, scoreMax, scoreSum, scoreSumSquares, featureCount } = await features
         .pipe((0, operators_1.reduce)((seed, f) => {
-        const score = f.get('score');
-        seed.scoreMax = Math.max(seed.scoreMax, f.get('summary') ? f.get('maxScore') : score);
-        seed.scoreMin = Math.min(seed.scoreMin, f.get('summary') ? f.get('minScore') : score);
-        seed.scoreSum += score;
-        seed.scoreSumSquares += score * score;
+        const s = f.get('score');
+        const summary = f.get('summary');
+        const { scoreMax, scoreMin } = seed;
+        seed.scoreMax = Math.max(scoreMax, summary ? f.get('maxScore') : s);
+        seed.scoreMin = Math.min(scoreMin, summary ? f.get('minScore') : s);
+        seed.scoreSum += s;
+        seed.scoreSumSquares += s * s;
         seed.featureCount += 1;
         return seed;
     }, {

package/util/tracks.d.ts

@@ -1,9 +1,9 @@
 import { IAnyStateTreeNode } from 'mobx-state-tree';
 import { PreFileLocation, FileLocation } from './types';
-import { AnyConfigurationModel } from '../configuration/configurationSchema';
+import { AnyConfigurationModel } from '../configuration';
 export declare function getTrackAssemblyNames(track: IAnyStateTreeNode & {
     configuration: AnyConfigurationModel;
-}): any[];
+}): string[];
 /** return the rpcSessionId of the highest parent node in the tree that has an rpcSessionId */
 export declare function getRpcSessionId(thisNode: IAnyStateTreeNode): string;
 /**
@@ -73,3 +73,6 @@ export declare function generateUnknownTrackConf(trackName: string, trackUrl: st
     category: string[] | undefined;
     trackId: string;
 };
+export declare function getTrackName(conf: AnyConfigurationModel, session: {
+    assemblies: AnyConfigurationModel[];
+}): any;

package/util/tracks.js

@@ -1,13 +1,12 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.generateUnknownTrackConf = exports.generateUnsupportedTrackConf = exports.guessTrackType = exports.guessAdapter = exports.getFileName = exports.makeIndexType = exports.makeIndex = exports.storeBlobLocation = exports.setBlobMap = exports.getBlobMap = exports.getBlob = exports.UNSUPPORTED = exports.UNKNOWN = exports.getParentRenderProps = exports.getRpcSessionId = exports.getTrackAssemblyNames = void 0;
+exports.getTrackName = exports.generateUnknownTrackConf = exports.generateUnsupportedTrackConf = exports.guessTrackType = exports.guessAdapter = exports.getFileName = exports.makeIndexType = exports.makeIndex = exports.storeBlobLocation = exports.setBlobMap = exports.getBlobMap = exports.getBlob = exports.UNSUPPORTED = exports.UNKNOWN = exports.getParentRenderProps = exports.getRpcSessionId = exports.getTrackAssemblyNames = void 0;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const index_1 = require("./index");
 const configuration_1 = require("../configuration");
 /* utility functions for use by track models and so forth */
 function getTrackAssemblyNames(track) {
-    const trackConf = track.configuration;
-    const trackAssemblyNames = (0, configuration_1.readConfObject)(trackConf, 'assemblyNames');
+    const trackAssemblyNames = (0, configuration_1.getConf)(track, 'assemblyNames');
     if (!trackAssemblyNames) {
         // Check if it's an assembly sequence track
         // eslint-disable-next-line @typescript-eslint/no-explicit-any
@@ -126,7 +125,7 @@ function getFileName(track) {
 exports.getFileName = getFileName;
 function guessAdapter(file, index, adapterHint, model) {
     if (model) {
-        const { pluginManager } = (0, mobx_state_tree_1.getEnv)(model);
+        const { pluginManager } = (0, index_1.getEnv)(model);
         const adapterGuesser = pluginManager.evaluateExtensionPoint('Core-guessAdapterForLocation', (_file, _index, _adapterHint) => {
             return undefined;
         });
@@ -144,7 +143,7 @@ function guessTrackType(adapterType, model) {
     if (model) {
         // @ts-ignore
         const session = (0, index_1.getSession)(model);
-        const trackTypeGuesser = (0, mobx_state_tree_1.getEnv)(session).pluginManager.evaluateExtensionPoint('Core-guessTrackTypeForLocation', (_adapterName) => {
+        const trackTypeGuesser = (0, index_1.getEnv)(session).pluginManager.evaluateExtensionPoint('Core-guessTrackTypeForLocation', (_adapterName) => {
             return undefined;
         });
         const trackType = trackTypeGuesser(adapterType);
@@ -179,3 +178,14 @@ function generateUnknownTrackConf(trackName, trackUrl, categories) {
     return conf;
 }
 exports.generateUnknownTrackConf = generateUnknownTrackConf;
+function getTrackName(conf, session) {
+    const trackName = (0, configuration_1.readConfObject)(conf, 'name');
+    if (!trackName && (0, configuration_1.readConfObject)(conf, 'type') === 'ReferenceSequenceTrack') {
+        const asm = session.assemblies.find(a => a.sequence === conf);
+        return asm
+            ? `Reference sequence (${(0, configuration_1.readConfObject)(asm, 'displayName') || (0, configuration_1.readConfObject)(asm, 'name')})`
+            : 'Reference sequence';
+    }
+    return trackName;
+}
+exports.getTrackName = getTrackName;

package/util/types/index.d.ts

@@ -73,7 +73,7 @@ export interface AbstractSessionModel extends AbstractViewContainer {
     addWidget?: Function;
     DialogComponent?: DialogComponentType;
     DialogProps: any;
-    queueDialog: (callback: (doneCallback: Function) => [DialogComponentType, any]) => void;
+    queueDialog<T extends DialogComponentType>(callback: (doneCallback: () => void) => [T, React.ComponentProps<T>]): void;
     name: string;
     id?: string;
     tracks: AnyConfigurationModel[];

package/util/types/index.js

@@ -36,7 +36,9 @@ function isSessionModelWithConfigEditing(thing) {
 }
 exports.isSessionModelWithConfigEditing = isSessionModelWithConfigEditing;
 function isSessionWithAddTracks(thing) {
-    return isSessionModel(thing) && 'addTrackConf' in thing;
+    return (
+    // @ts-ignore
+    isSessionModel(thing) && 'addTrackConf' in thing && !thing.disableAddTracks);
 }
 exports.isSessionWithAddTracks = isSessionWithAddTracks;
 function isSessionModelWithWidgets(thing) {