@jbrowse/core 2.10.1 → 2.10.3

package/BaseFeatureWidget/BaseFeatureDetail/index.d.ts

@@ -1,7 +1,7 @@
 import React from 'react';
 import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { BaseCardProps, BaseProps } from '../types';
 import { SimpleFeatureSerialized } from '../../util';
+import { BaseCardProps, BaseProps } from '../types';
 export declare function BaseCard({ children, title, defaultExpanded, }: BaseCardProps): React.JSX.Element;
 export declare const BaseCoreDetails: (props: BaseProps) => React.JSX.Element;
 export declare const BaseAttributes: (props: BaseProps) => React.JSX.Element;

package/BaseFeatureWidget/BaseFeatureDetail/index.js

@@ -96,7 +96,7 @@ function CoreDetails(props) {
     const { start, end } = formattedFeat;
     const displayedDetails = {
         ...formattedFeat,
-        length: (0, util_2.toLocale)(end - start),
+        length: (0, util_1.toLocale)(end - start),
     };
     const coreRenderedDetails = {
         description: 'Description',

package/BaseFeatureWidget/BaseFeatureDetail/util.d.ts

@@ -1,5 +1,4 @@
 export declare function isEmpty(obj: Record<string, unknown>): boolean;
 export declare function generateTitle(name: unknown, id: unknown, type: unknown): string;
 export declare function generateMaxWidth(array: unknown[][], prefix: string[]): number;
-export declare function toLocale(n: number): string;
 export declare function accessNested(arr: string[], obj?: Record<string, unknown>): string | undefined;

package/BaseFeatureWidget/BaseFeatureDetail/util.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.accessNested = exports.toLocale = exports.generateMaxWidth = exports.generateTitle = exports.isEmpty = void 0;
+exports.accessNested = exports.generateMaxWidth = exports.generateTitle = exports.isEmpty = void 0;
 const is_object_1 = __importDefault(require("is-object"));
 const util_1 = require("../../util");
 const util_2 = require("../util");
@@ -21,10 +21,6 @@ function generateMaxWidth(array, prefix) {
     return (Math.ceil((0, util_1.max)(array.map(key => (0, util_1.measureText)([...prefix, key[0]].join('.'), 12)))) + 10);
 }
 exports.generateMaxWidth = generateMaxWidth;
-function toLocale(n) {
-    return n.toLocaleString('en-US');
-}
-exports.toLocale = toLocale;
 // pick using a path from an object, similar to _.get from lodash with special
 // logic for Descriptions from e.g. VCF headers
 //

package/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js

@@ -37,7 +37,7 @@ const ui_1 = require("../../ui");
 const Settings_1 = __importDefault(require("@mui/icons-material/Settings"));
 const hooks_1 = require("./hooks");
 // lazies
-const SettingsDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SequenceFeatureSettingsDialog'))));
+const SettingsDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SequenceFeatureSettingsDialog'))));
 const SequencePanel = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SequencePanel'))));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     button: {
@@ -126,18 +126,18 @@ function SequenceFeatureDetails({ model, feature: prefeature, }) {
 exports.default = SequenceFeatureDetails;
 function Settings({ intronBp, upDownBp, setIntronBp, setUpDownBp, }) {
     const { classes } = useStyles();
-    const [settingsDlgOpen, setSettingsDlgOpen] = (0, react_1.useState)(false);
+    const [settingsDialogOpen, setSettingsDialogOpen] = (0, react_1.useState)(false);
     return (react_1.default.createElement(react_1.default.Fragment, null,
         react_1.default.createElement(material_1.FormControl, { className: classes.formControl },
-            react_1.default.createElement(material_1.IconButton, { onClick: () => setSettingsDlgOpen(true) },
+            react_1.default.createElement(material_1.IconButton, { onClick: () => setSettingsDialogOpen(true) },
                 react_1.default.createElement(Settings_1.default, null))),
-        settingsDlgOpen ? (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
-            react_1.default.createElement(SettingsDlg, { handleClose: arg => {
+        settingsDialogOpen ? (react_1.default.createElement(react_1.Suspense, { fallback: null },
+            react_1.default.createElement(SettingsDialog, { handleClose: arg => {
                     if (arg) {
                         const { upDownBp, intronBp } = arg;
                         setIntronBp(intronBp);
                         setUpDownBp(upDownBp);
                     }
-                    setSettingsDlgOpen(false);
+                    setSettingsDialogOpen(false);
                 }, upDownBp: upDownBp, intronBp: intronBp }))) : null));
 }

package/BaseFeatureWidget/SequenceFeatureDetails/index.js

@@ -29,11 +29,13 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
+const mobx_react_1 = require("mobx-react");
 const ui_1 = require("../../ui");
+const util_1 = require("../../util");
 // icons
 const Help_1 = __importDefault(require("@mui/icons-material/Help"));
 // lazies
-const HelpDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SequenceHelpDialog'))));
+const HelpDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SequenceHelpDialog'))));
 const SequenceFeatureDetails = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SequenceFeatureDetails'))));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     formControl: {
@@ -44,25 +46,27 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         marginBottom: theme.spacing(4),
     },
 }));
+const SequenceFeatureDetailsHelpButton = (0, mobx_react_1.observer)(function ({ model, }) {
+    const { classes } = useStyles();
+    const session = (0, util_1.getSession)(model);
+    return (react_1.default.createElement(material_1.FormControl, { className: classes.formControl },
+        react_1.default.createElement(material_1.IconButton, { onClick: () => session.queueDialog(handleClose => [HelpDialog, { handleClose }]) },
+            react_1.default.createElement(Help_1.default, null))));
+});
 // display the stitched-together sequence of a gene's CDS, cDNA, or protein
 // sequence. this is a best effort and weird genomic phenomena could lead these
 // to not be 100% accurate
 function SequenceFeaturePanel({ model, feature }) {
     const { classes } = useStyles();
     const [shown, setShown] = (0, react_1.useState)(false);
-    const [helpShown, setHelpShown] = (0, react_1.useState)(false);
     return !model ? null : (react_1.default.createElement("div", { className: classes.container },
         react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => setShown(!shown) }, shown ? 'Hide feature sequence' : 'Show feature sequence'),
-        react_1.default.createElement(material_1.FormControl, { className: classes.formControl },
-            react_1.default.createElement(material_1.IconButton, { onClick: () => setHelpShown(true) },
-                react_1.default.createElement(Help_1.default, null))),
+        react_1.default.createElement(SequenceFeatureDetailsHelpButton, { model: model }),
         shown ? (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement(ui_1.LoadingEllipses, null) },
             react_1.default.createElement(SequenceFeatureDetails
             /* eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion */
             , { 
                 /* eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion */
-                key: feature.uniqueId, model: model, feature: feature }))) : null,
-        helpShown ? (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
-            react_1.default.createElement(HelpDlg, { handleClose: () => setHelpShown(false) }))) : null));
+                key: feature.uniqueId, model: model, feature: feature }))) : null));
 }
 exports.default = SequenceFeaturePanel;

package/BaseFeatureWidget/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const configSchema: import("../configuration/configurationSchema").ConfigurationSchemaType<{}, import("../configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export { configSchema };

package/BaseFeatureWidget/configSchema.js

@@ -0,0 +1,6 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.configSchema = void 0;
+const configuration_1 = require("../configuration");
+const configSchema = (0, configuration_1.ConfigurationSchema)('BaseFeatureWidget', {});
+exports.configSchema = configSchema;

package/BaseFeatureWidget/index.d.ts

@@ -1,128 +1,2 @@
-import PluginManager from '../PluginManager';
-declare const configSchema: import("../configuration/configurationSchema").ConfigurationSchemaType<{}, import("../configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-/**
- * #stateModel BaseFeatureWidget
- * displays data about features, allowing configuration callbacks to modify the
- * contents of what is displayed
- *
- * see: formatDetails-\>feature,formatDetails-\>subfeatures
- */
-export default function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    /**
-     * #property
-     */
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    /**
-     * #property
-     */
-    type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
-    /**
-     * #property
-     */
-    featureData: import("mobx-state-tree").IType<any, any, any>;
-    /**
-     * #property
-     */
-    formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    /**
-     * #property
-     */
-    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
-    /**
-     * #property
-     */
-    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    /**
-     * #property
-     */
-    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    /**
-     * #property
-     */
-    trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    /**
-     * #property
-     */
-    trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    /**
-     * #property
-     */
-    maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-}, {
-    error: unknown;
-} & {
-    /**
-     * #action
-     */
-    setFeatureData(featureData: Record<string, unknown>): void;
-    /**
-     * #action
-     */
-    clearFeatureData(): void;
-    /**
-     * #action
-     */
-    setFormattedData(feat: Record<string, unknown>): void;
-    /**
-     * #action
-     */
-    setExtra(type?: string, trackId?: string, maxDepth?: number): void;
-    /**
-     * #action
-     */
-    setError(e: unknown): void;
-} & {
-    afterCreate(): void;
-}, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-    /**
-     * #property
-     */
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    /**
-     * #property
-     */
-    type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
-    /**
-     * #property
-     */
-    featureData: import("mobx-state-tree").IType<any, any, any>;
-    /**
-     * #property
-     */
-    formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    /**
-     * #property
-     */
-    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
-    /**
-     * #property
-     */
-    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    /**
-     * #property
-     */
-    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    /**
-     * #property
-     */
-    trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    /**
-     * #property
-     */
-    trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    /**
-     * #property
-     */
-    maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-}>>, {
-    type: "BaseFeatureWidget";
-    id: string;
-    track: import("mobx-state-tree").ReferenceIdentifier | undefined;
-    view: import("mobx-state-tree").ReferenceIdentifier | undefined;
-    trackId: string | undefined;
-    trackType: string | undefined;
-    maxDepth: number | undefined;
-    formattedFields: any;
-    finalizedFeatureData: any;
-}>;
-export { configSchema, stateModelFactory };
+export { configSchema } from './configSchema';
+export { stateModelFactory } from './stateModelFactory';

package/BaseFeatureWidget/index.js

@@ -1,171 +1,7 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.stateModelFactory = exports.configSchema = void 0;
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mobx_1 = require("mobx");
-const clone_1 = __importDefault(require("clone"));
-const configuration_1 = require("../configuration");
-const util_1 = require("../util");
-const mst_1 = require("../util/types/mst");
-const configSchema = (0, configuration_1.ConfigurationSchema)('BaseFeatureWidget', {});
-exports.configSchema = configSchema;
-function formatSubfeatures(obj, depth, parse, currentDepth = 0, returnObj = {}) {
-    var _a;
-    if (depth <= currentDepth) {
-        return;
-    }
-    (_a = obj.subfeatures) === null || _a === void 0 ? void 0 : _a.map(sub => {
-        formatSubfeatures(sub, depth, parse, currentDepth + 1, returnObj);
-        parse(sub);
-    });
-}
-/**
- * #stateModel BaseFeatureWidget
- * displays data about features, allowing configuration callbacks to modify the
- * contents of what is displayed
- *
- * see: formatDetails-\>feature,formatDetails-\>subfeatures
- */
-function stateModelFactory(pluginManager) {
-    return mobx_state_tree_1.types
-        .model('BaseFeatureWidget', {
-        /**
-         * #property
-         */
-        id: mst_1.ElementId,
-        /**
-         * #property
-         */
-        type: mobx_state_tree_1.types.literal('BaseFeatureWidget'),
-        /**
-         * #property
-         */
-        featureData: mobx_state_tree_1.types.frozen(),
-        /**
-         * #property
-         */
-        formattedFields: mobx_state_tree_1.types.frozen(),
-        /**
-         * #property
-         */
-        unformattedFeatureData: mobx_state_tree_1.types.frozen(),
-        /**
-         * #property
-         */
-        view: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
-        /**
-         * #property
-         */
-        track: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('track', 'stateModel')),
-        /**
-         * #property
-         */
-        trackId: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        /**
-         * #property
-         */
-        trackType: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        /**
-         * #property
-         */
-        maxDepth: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-    })
-        .volatile(() => ({
-        error: undefined,
-    }))
-        .actions(self => ({
-        /**
-         * #action
-         */
-        setFeatureData(featureData) {
-            self.unformattedFeatureData = featureData;
-        },
-        /**
-         * #action
-         */
-        clearFeatureData() {
-            self.featureData = undefined;
-        },
-        /**
-         * #action
-         */
-        setFormattedData(feat) {
-            self.featureData = feat;
-        },
-        /**
-         * #action
-         */
-        setExtra(type, trackId, maxDepth) {
-            self.trackId = trackId;
-            self.trackType = type;
-            self.maxDepth = maxDepth;
-        },
-        /**
-         * #action
-         */
-        setError(e) {
-            self.error = e;
-        },
-    }))
-        .actions(self => ({
-        afterCreate() {
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-                try {
-                    const { unformattedFeatureData, track } = self;
-                    const session = (0, util_1.getSession)(self);
-                    if (track) {
-                        self.setExtra(track.type, track.configuration.trackId, (0, configuration_1.getConf)(track, ['formatDetails', 'maxDepth']));
-                    }
-                    if (unformattedFeatureData) {
-                        const feature = (0, clone_1.default)(unformattedFeatureData);
-                        const combine = (arg2, feature) => ({
-                            ...(0, configuration_1.getConf)(session, ['formatDetails', arg2], { feature }),
-                            ...(0, configuration_1.getConf)(track, ['formatDetails', arg2], { feature }),
-                        });
-                        if (track) {
-                            // eslint-disable-next-line no-underscore-dangle
-                            feature.__jbrowsefmt = combine('feature', feature);
-                            formatSubfeatures(feature, (0, configuration_1.getConf)(track, ['formatDetails', 'depth']), sub => {
-                                // eslint-disable-next-line no-underscore-dangle
-                                sub.__jbrowsefmt = combine('subfeatures', sub);
-                            });
-                        }
-                        self.setFormattedData(feature);
-                    }
-                }
-                catch (e) {
-                    console.error(e);
-                    self.setError(e);
-                }
-            }));
-        },
-    }))
-        .preProcessSnapshot(snap => {
-        // @ts-expect-error
-        const { featureData, finalizedFeatureData, ...rest } = snap;
-        return {
-            unformattedFeatureData: featureData,
-            featureData: finalizedFeatureData,
-            ...rest,
-        };
-    })
-        .postProcessSnapshot(snap => {
-        // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
-        const { unformattedFeatureData, featureData, ...rest } = snap;
-        // finalizedFeatureData avoids running formatter twice if loading from
-        // snapshot
-        return {
-            // replacing undefined with null helps with allowing fields to be
-            // hidden, setting null is not allowed by jexl so we set it to
-            // undefined to hide. see config guide. this replacement happens both
-            // here and when displaying the featureData in base feature widget
-            finalizedFeatureData: JSON.parse(JSON.stringify(featureData, (_, v) => (v === undefined ? null : v))),
-            ...rest,
-        };
-    });
-}
-exports.default = stateModelFactory;
-exports.stateModelFactory = stateModelFactory;
+var configSchema_1 = require("./configSchema");
+Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return configSchema_1.configSchema; } });
+var stateModelFactory_1 = require("./stateModelFactory");
+Object.defineProperty(exports, "stateModelFactory", { enumerable: true, get: function () { return stateModelFactory_1.stateModelFactory; } });

package/BaseFeatureWidget/stateModelFactory.d.ts

@@ -0,0 +1,126 @@
+import PluginManager from '../PluginManager';
+/**
+ * #stateModel BaseFeatureWidget
+ * displays data about features, allowing configuration callbacks to modify the
+ * contents of what is displayed
+ *
+ * see: formatDetails-\>feature,formatDetails-\>subfeatures
+ */
+export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
+    /**
+     * #property
+     */
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    /**
+     * #property
+     */
+    type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
+    /**
+     * #property
+     */
+    featureData: import("mobx-state-tree").IType<any, any, any>;
+    /**
+     * #property
+     */
+    formattedFields: import("mobx-state-tree").IType<any, any, any>;
+    /**
+     * #property
+     */
+    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
+    /**
+     * #property
+     */
+    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    /**
+     * #property
+     */
+    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    /**
+     * #property
+     */
+    trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    /**
+     * #property
+     */
+    trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    /**
+     * #property
+     */
+    maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+}, {
+    error: unknown;
+} & {
+    /**
+     * #action
+     */
+    setFeatureData(featureData: Record<string, unknown>): void;
+    /**
+     * #action
+     */
+    clearFeatureData(): void;
+    /**
+     * #action
+     */
+    setFormattedData(feat: Record<string, unknown>): void;
+    /**
+     * #action
+     */
+    setExtra(type?: string, trackId?: string, maxDepth?: number): void;
+    /**
+     * #action
+     */
+    setError(e: unknown): void;
+} & {
+    afterCreate(): void;
+}, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    /**
+     * #property
+     */
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    /**
+     * #property
+     */
+    type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
+    /**
+     * #property
+     */
+    featureData: import("mobx-state-tree").IType<any, any, any>;
+    /**
+     * #property
+     */
+    formattedFields: import("mobx-state-tree").IType<any, any, any>;
+    /**
+     * #property
+     */
+    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
+    /**
+     * #property
+     */
+    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    /**
+     * #property
+     */
+    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    /**
+     * #property
+     */
+    trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    /**
+     * #property
+     */
+    trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    /**
+     * #property
+     */
+    maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+}>>, {
+    id: string;
+    type: "BaseFeatureWidget";
+    track: import("mobx-state-tree").ReferenceIdentifier | undefined;
+    view: import("mobx-state-tree").ReferenceIdentifier | undefined;
+    trackId: string | undefined;
+    trackType: string | undefined;
+    maxDepth: number | undefined;
+    formattedFields: any;
+    finalizedFeatureData: any;
+}>;