@jbrowse/core 2.10.3 → 2.11.1

package/BaseFeatureWidget/SequenceFeatureDetails/{CDNASequence.js → seqtypes/CDNASequence.js}

@@ -4,22 +4,31 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const util_1 = require("./util");
-function CDNASequence({ utr, cds, exons, sequence, upstream, downstream, includeIntrons, collapseIntron, intronBp, }) {
+const mobx_react_1 = require("mobx-react");
+const util_1 = require("../util");
+const CDNASequence = (0, mobx_react_1.observer)(function ({ utr, cds, exons, sequence, upstream, downstream, includeIntrons, collapseIntron, model, }) {
+    const { upperCaseCDS, intronBp } = model;
+    const hasCds = cds.length > 0;
     const chunks = (cds.length ? [...cds, ...utr].sort((a, b) => a.start - b.start) : exons).filter(f => f.start !== f.end);
+    const toLower = (s) => (upperCaseCDS ? s.toLowerCase() : s);
+    const toUpper = (s) => (upperCaseCDS ? s.toUpperCase() : s);
     return (react_1.default.createElement(react_1.default.Fragment, null,
-        upstream ? (react_1.default.createElement("span", { style: { background: util_1.updownstreamColor } }, upstream)) : null,
+        upstream ? (react_1.default.createElement("span", { style: { background: util_1.updownstreamColor } }, toLower(upstream))) : null,
         chunks.map((chunk, idx) => {
             var _a;
             const intron = sequence.slice(chunk.end, (_a = chunks[idx + 1]) === null || _a === void 0 ? void 0 : _a.start);
             return (react_1.default.createElement(react_1.default.Fragment, { key: JSON.stringify(chunk) },
                 react_1.default.createElement("span", { style: {
                         background: chunk.type === 'CDS' ? util_1.cdsColor : util_1.utrColor,
-                    } }, sequence.slice(chunk.start, chunk.end)),
-                includeIntrons && idx < chunks.length - 1 ? (react_1.default.createElement("span", { style: { background: util_1.intronColor } }, collapseIntron && intron.length > intronBp * 2
+                    } }, hasCds
+                    ? chunk.type === 'CDS'
+                        ? toUpper(sequence.slice(chunk.start, chunk.end))
+                        : toLower(sequence.slice(chunk.start, chunk.end))
+                    : toUpper(sequence.slice(chunk.start, chunk.end))),
+                includeIntrons && idx < chunks.length - 1 ? (react_1.default.createElement("span", { style: { background: util_1.intronColor } }, toLower(collapseIntron && intron.length > intronBp * 2
                     ? `${intron.slice(0, intronBp)}...${intron.slice(-intronBp)}`
-                    : intron)) : null));
+                    : intron))) : null));
         }),
-        downstream ? (react_1.default.createElement("span", { style: { background: util_1.updownstreamColor } }, downstream)) : null));
-}
+        downstream ? (react_1.default.createElement("span", { style: { background: util_1.updownstreamColor } }, toLower(downstream))) : null));
+});
 exports.default = CDNASequence;

package/BaseFeatureWidget/SequenceFeatureDetails/{CDSSequence.d.ts → seqtypes/CDSSequence.d.ts}

@@ -1,5 +1,5 @@
 import React from 'react';
-import { Feat } from '../util';
+import { Feat } from '../../util';
 export default function CDSSequence({ cds, sequence, }: {
     cds: Feat[];
     sequence: string;

package/BaseFeatureWidget/SequenceFeatureDetails/{CDSSequence.js → seqtypes/CDSSequence.js}

@@ -4,8 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const util_1 = require("./util");
-const util_2 = require("../util");
+const util_1 = require("../util");
+const util_2 = require("../../util");
 function CDSSequence({ cds, sequence, }) {
     return react_1.default.createElement("span", { style: { background: util_1.cdsColor } }, (0, util_2.stitch)(cds, sequence));
 }

package/BaseFeatureWidget/SequenceFeatureDetails/{GenomicSequence.js → seqtypes/GenomicSequence.js}

@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const util_1 = require("./util");
+const util_1 = require("../util");
 function GenomicSequence({ sequence, upstream, downstream, }) {
     return (react_1.default.createElement(react_1.default.Fragment, null,
         upstream ? (react_1.default.createElement("span", { style: { background: util_1.updownstreamColor } }, upstream)) : null,

package/BaseFeatureWidget/SequenceFeatureDetails/{ProteinSequence.d.ts → seqtypes/ProteinSequence.d.ts}

@@ -1,5 +1,5 @@
 import React from 'react';
-import { Feat } from '../util';
+import { Feat } from '../../util';
 export default function ProteinSequence({ cds, sequence, codonTable, }: {
     cds: Feat[];
     sequence: string;

package/BaseFeatureWidget/SequenceFeatureDetails/{ProteinSequence.js → seqtypes/ProteinSequence.js}

@@ -4,8 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const util_1 = require("../util");
-const util_2 = require("./util");
+const util_1 = require("../../util");
+const util_2 = require("../util");
 function ProteinSequence({ cds, sequence, codonTable, }) {
     const str = (0, util_1.stitch)(cds, sequence);
     let protein = '';

package/BaseFeatureWidget/stateModelFactory.d.ts

@@ -1,3 +1,4 @@
+import { Instance } from 'mobx-state-tree';
 import PluginManager from '../PluginManager';
 /**
  * #stateModel BaseFeatureWidget
@@ -47,6 +48,20 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #property
      */
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    /**
+     * #property
+     */
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }, {
     error: unknown;
 } & {
@@ -113,6 +128,20 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #property
      */
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    /**
+     * #property
+     */
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }>>, {
     id: string;
     type: "BaseFeatureWidget";
@@ -122,5 +151,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackType: string | undefined;
     maxDepth: number | undefined;
     formattedFields: any;
+    sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
     finalizedFeatureData: any;
 }>;
+export type BaseFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;
+export type BaseFeatureWidgetModel = Instance<BaseFeatureWidgetStateModel>;

package/BaseFeatureWidget/stateModelFactory.js

@@ -10,6 +10,7 @@ const clone_1 = __importDefault(require("clone"));
 const configuration_1 = require("../configuration");
 const util_1 = require("../util");
 const mst_1 = require("../util/types/mst");
+const model_1 = require("./SequenceFeatureDetails/model");
 function formatSubfeatures(obj, depth, parse, currentDepth = 0, returnObj = {}) {
     var _a;
     if (depth <= currentDepth) {
@@ -70,6 +71,10 @@ function stateModelFactory(pluginManager) {
          * #property
          */
         maxDepth: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
+        /**
+         * #property
+         */
+        sequenceFeatureDetails: mobx_state_tree_1.types.optional((0, model_1.SequenceFeatureDetailsF)(), {}),
     })
         .volatile(() => ({
         error: undefined,

package/BaseFeatureWidget/types.d.ts

@@ -1,16 +1,11 @@
 import React from 'react';
-import { IAnyStateTreeNode } from 'mobx-state-tree';
 import { SimpleFeatureSerialized } from '../util/simpleFeature';
-import { AbstractViewModel } from '../util';
+import { BaseFeatureWidgetModel } from './stateModelFactory';
 export interface BaseProps extends BaseCardProps {
     feature: SimpleFeatureSerialized;
     formatter?: (val: unknown, key: string) => React.ReactNode;
     descriptions?: Record<string, React.ReactNode>;
-    model?: IAnyStateTreeNode & {
-        view?: AbstractViewModel & {
-            assemblyNames?: string[];
-        };
-    };
+    model?: BaseFeatureWidgetModel;
 }
 export interface BaseCardProps {
     title?: string;

package/BaseFeatureWidget/util.d.ts

@@ -1,7 +1,7 @@
 export interface Feat {
     start: number;
     end: number;
-    type: string;
+    type?: string;
     name?: string;
     id?: string;
 }
@@ -25,7 +25,7 @@ export declare function dedupe(list: Feat[]): Feat[];
 export declare function revlist(list: Feat[], seqlen: number): {
     start: number;
     end: number;
-    type: string;
+    type?: string | undefined;
     name?: string | undefined;
     id?: string | undefined;
 }[];
@@ -33,6 +33,8 @@ export declare function calculateUTRs(cds: Feat[], exons: Feat[]): {
     type: string;
     start: number;
     end: number;
+    name?: string | undefined;
+    id?: string | undefined;
 }[];
 export declare function calculateUTRs2(cds: Feat[], parentFeat: Feat): {
     type: string;

package/PluginLoader.d.ts

@@ -55,7 +55,7 @@ export default class PluginLoader {
         default: PluginConstructor;
     }>;
     loadPlugin(def: PluginDefinition, baseUri?: string): Promise<PluginConstructor>;
-    installGlobalReExports(target: WindowOrWorkerGlobalScope): void;
+    installGlobalReExports(target: WindowOrWorkerGlobalScope): this;
     load(baseUri?: string): Promise<{
         plugin: PluginConstructor;
         definition: PluginDefinition;

package/PluginLoader.js

@@ -152,6 +152,7 @@ class PluginLoader {
         target.JBrowseExports = Object.fromEntries(Object.entries(ReExports_1.default).map(([moduleName, module]) => {
             return [moduleName, module];
         }));
+        return this;
     }
     async load(baseUri) {
         return Promise.all(this.definitions.map(async (definition) => ({

package/PluginManager.d.ts

@@ -17,8 +17,6 @@ import ReExports from './ReExports';
 import { PluggableElementType, PluggableElementMember } from './pluggableElementTypes';
 import { AbstractRootModel } from './util';
 import { PluginDefinition } from './PluginLoader';
-/** little helper class that keeps groups of callbacks that are
-then run in a specified order by group */
 declare class PhasedScheduler<PhaseName extends string> {
     phaseCallbacks: Map<PhaseName, Function[]>;
     phaseOrder: PhaseName[];
@@ -44,11 +42,11 @@ declare class TypeRecord<ElementClass extends PluggableElementBase> {
 }
 type AnyFunction = (...args: any) => any;
 /**
- * free-form string-to-unknown mapping of metadata related to the instance
- * of this plugin. `isCore` is typically set to `Boolean(true)` if the plugin was
- * loaded as part of the "core" set of plugins for this application.
- * Can also use this metadata to stash other things about why the plugin is
- * loaded, such as where it came from, what plugin depends on it, etc.
+ * free-form string-to-unknown mapping of metadata related to the instance of
+ * this plugin. `isCore` is typically set to `Boolean(true)` if the plugin was
+ * loaded as part of the "core" set of plugins for this application. Can also
+ * use this metadata to stash other things about why the plugin is loaded, such
+ * as where it came from, what plugin depends on it, etc.
  */
 export type PluginMetadata = Record<string, unknown>;
 export interface PluginLoadRecord {
@@ -232,7 +230,7 @@ export default class PluginManager {
         '@mui/x-data-grid': {
             useGridApiContext: typeof import("@mui/x-data-grid").useGridApiContext;
             useGridApiRef: <Api extends import("@mui/x-data-grid").GridApiCommon<any, any> = import("@mui/x-data-grid/internals").GridApiCommunity>() => import("react").MutableRefObject<Api>;
-            useGridRootProps: () => import("@mui/x-data-grid/models/props/DataGridProps").DataGridProcessedProps<any>;
+            useGridRootProps: () => import("@mui/x-data-grid/internals").DataGridProcessedProps<any>;
         };
         '@mui/material/utils': typeof import("@mui/material/utils");
         '@material-ui/core/utils': typeof import("@mui/material/utils");
@@ -260,8 +258,14 @@ export default class PluginManager {
             useTheme: typeof import("@mui/material").useTheme;
         };
         'prop-types': typeof import("prop-types");
-        '@mui/material/styles': typeof import("@mui/material/styles");
-        '@material-ui/core/styles': typeof import("@mui/material/styles");
+        '@mui/material/styles': {
+            MUIStyles: typeof import("@mui/material/styles");
+            makeStyles: (args: any) => () => Record<string, string>;
+        };
+        '@material-ui/core/styles': {
+            MUIStyles: typeof import("@mui/material/styles");
+            makeStyles: (args: any) => () => Record<string, string>;
+        };
     };
     load: <FTYPE extends AnyFunction>(lib: FTYPE) => ReturnType<FTYPE>;
     /**

package/PluginManager.js

@@ -19,8 +19,8 @@ const configuration_1 = require("./configuration");
 const ReExports_1 = __importDefault(require("./ReExports"));
 const CorePlugin_1 = __importDefault(require("./CorePlugin"));
 const jexl_1 = __importDefault(require("./util/jexl"));
-/** little helper class that keeps groups of callbacks that are
-then run in a specified order by group */
+// helper class that keeps groups of callbacks that are then run in a specified
+// order by group
 class PhasedScheduler {
     constructor(...phaseOrder) {
         this.phaseCallbacks = new Map();
@@ -119,7 +119,12 @@ class PluginManager {
             throw new TypeError('lib passed to jbrequire must be either a string or a function');
         };
         // add the core plugin
-        this.addPlugin({ plugin: new CorePlugin_1.default(), metadata: { isCore: true } });
+        this.addPlugin({
+            plugin: new CorePlugin_1.default(),
+            metadata: {
+                isCore: true,
+            },
+        });
         // add all the initial plugins
         initialPlugins.forEach(plugin => {
             this.addPlugin(plugin);

package/ReExports/modules.d.ts

@@ -138,7 +138,7 @@ declare const libs: {
     '@mui/x-data-grid': {
         useGridApiContext: typeof useGridApiContext;
         useGridApiRef: <Api extends import("@mui/x-data-grid").GridApiCommon<any, any> = import("@mui/x-data-grid/internals").GridApiCommunity>() => React.MutableRefObject<Api>;
-        useGridRootProps: () => import("@mui/x-data-grid/models/props/DataGridProps").DataGridProcessedProps<any>;
+        useGridRootProps: () => import("@mui/x-data-grid/internals").DataGridProcessedProps<any>;
     };
     '@mui/material/utils': typeof MUIUtils;
     '@material-ui/core/utils': typeof MUIUtils;
@@ -166,7 +166,13 @@ declare const libs: {
         useTheme: typeof MUIStyles.useTheme;
     };
     'prop-types': typeof PropTypes;
-    '@mui/material/styles': typeof MUIStyles;
-    '@material-ui/core/styles': typeof MUIStyles;
+    '@mui/material/styles': {
+        MUIStyles: typeof MUIStyles;
+        makeStyles: (args: any) => () => Record<string, string>;
+    };
+    '@material-ui/core/styles': {
+        MUIStyles: typeof MUIStyles;
+        makeStyles: (args: any) => () => Record<string, string>;
+    };
 };
 export default libs;

package/ReExports/modules.js

@@ -295,9 +295,6 @@ const DataGridEntries = {
     GridPanelWrapper: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/x-data-grid'))).then(module => ({
         default: module.GridPanelWrapper,
     }))),
-    GridPreferencesPanel: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/x-data-grid'))).then(module => ({
-        default: module.GridPreferencesPanel,
-    }))),
     GridRemoveIcon: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/x-data-grid'))).then(module => ({
         default: module.GridRemoveIcon,
     }))),
@@ -405,8 +402,22 @@ const libs = {
     'prop-types': prop_types_1.default,
     // end special case
     // material-ui subcomponents, should get rid of these
-    '@mui/material/styles': MUIStyles,
-    '@material-ui/core/styles': MUIStyles,
+    '@mui/material/styles': {
+        MUIStyles,
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        makeStyles: (args) => {
+            const useStyles = (0, mui_1.makeStyles)()(args);
+            return () => useStyles().classes;
+        },
+    },
+    '@material-ui/core/styles': {
+        MUIStyles,
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        makeStyles: (args) => {
+            const useStyles = (0, mui_1.makeStyles)()(args);
+            return () => useStyles().classes;
+        },
+    },
     ...MaterialPrefixMUI,
     ...MuiPrefixMUI,
     // these are core in @mui/material, but used to be in @material-ui/lab

package/data_adapters/CytobandAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '../../PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function CytobandAdapterF(pluginManager: PluginManager): void;

package/data_adapters/CytobandAdapter/index.js

@@ -28,10 +28,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const pluggableElementTypes_1 = require("../../pluggableElementTypes");
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pluginManager) => {
+function CytobandAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new pluggableElementTypes_1.AdapterType({
         name: 'CytobandAdapter',
         configSchema: configSchema_1.default,
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./CytobandAdapter'))).then(f => f.default),
     }));
-};
+}
+exports.default = CytobandAdapterF;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.10.3",
+  "version": "2.11.1",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -58,7 +58,7 @@
   },
   "peerDependencies": {
     "@mui/material": "^5.0.0",
-    "@mui/x-data-grid": "^6.0.1",
+    "@mui/x-data-grid": "^7.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
@@ -72,5 +72,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "c8fc800cd17decd72b2e971c7a6add3b95214e72"
+  "gitHead": "11b28d66d782eb06f92ccb993108bb6c3c82819e"
 }

package/pluggableElementTypes/models/BaseTrackModel.d.ts

@@ -10,6 +10,7 @@ export declare function getCompatibleDisplays(self: IAnyStateTreeNode): ({
 /**
  * #stateModel BaseTrackModel
  * #category track
+ *
  * these MST models only exist for tracks that are *shown*. they should contain
  * only UI state for the track, and have a reference to a track configuration.
  * note that multiple displayed tracks could use the same configuration.

package/pluggableElementTypes/models/BaseTrackModel.js

@@ -20,6 +20,7 @@ exports.getCompatibleDisplays = getCompatibleDisplays;
 /**
  * #stateModel BaseTrackModel
  * #category track
+ *
  * these MST models only exist for tracks that are *shown*. they should contain
  * only UI state for the track, and have a reference to a track configuration.
  * note that multiple displayed tracks could use the same configuration.
@@ -97,7 +98,7 @@ function createBaseTrackModel(pm, trackType, baseTrackConfig) {
             const { sessionTracks, adminMode } = session;
             return ((0, types_1.isSessionModelWithConfigEditing)(session) &&
                 (adminMode ||
-                    (sessionTracks === null || sessionTracks === void 0 ? void 0 : sessionTracks.find(track => { var _a; return track.trackId === ((_a = self.configuration) === null || _a === void 0 ? void 0 : _a.trackId); }))));
+                    (sessionTracks === null || sessionTracks === void 0 ? void 0 : sessionTracks.find(t => { var _a; return t.trackId === ((_a = self.configuration) === null || _a === void 0 ? void 0 : _a.trackId); }))));
         },
     }))
         .actions(self => ({

package/pluggableElementTypes/models/InternetAccountModel.d.ts

@@ -156,6 +156,7 @@ export declare const InternetAccount: import("mobx-state-tree").IModelType<{
         keepalive?: boolean | undefined;
         method?: string | undefined;
         mode?: RequestMode | undefined;
+        priority?: RequestPriority | undefined;
         redirect?: RequestRedirect | undefined;
         referrer?: string | undefined;
         referrerPolicy?: ReferrerPolicy | undefined;

package/rpc/BaseRpcDriver.js

@@ -12,6 +12,7 @@ function isClonable(thing) {
 // the worker times out
 async function watchWorker(worker, pingTime, rpcDriverClassName) {
     // after first ping succeeds, apply wait for timeout
+    // eslint-disable-next-line no-constant-condition
     while (true) {
         await worker.call('ping', [], {
             timeout: pingTime * 2,