@jbrowse/react-app2 3.2.0

package/dist/sessionModel/index.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = sessionModelFactory;
+const web_core_1 = require("@jbrowse/web-core");
+function sessionModelFactory({ pluginManager, assemblyConfigSchema, }) {
+    return (0, web_core_1.BaseWebSession)({ pluginManager, assemblyConfigSchema });
+}
+function z(x) {
+    return x;
+}

package/dist/util.d.ts

@@ -0,0 +1,5 @@
+import type { IAnyStateTreeNode, IAnyType } from 'mobx-state-tree';
+export declare function b64PadSuffix(b64: string): string;
+export declare function fromUrlSafeB64(b64: string): Promise<string>;
+export declare function toUrlSafeB64(str: string): Promise<string>;
+export declare function filterSessionInPlace(node: IAnyStateTreeNode | undefined, type: IAnyType): void;

package/dist/util.js

@@ -0,0 +1,119 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.b64PadSuffix = b64PadSuffix;
+exports.fromUrlSafeB64 = fromUrlSafeB64;
+exports.toUrlSafeB64 = toUrlSafeB64;
+exports.filterSessionInPlace = filterSessionInPlace;
+const mobx_state_tree_1 = require("mobx-state-tree");
+function b64PadSuffix(b64) {
+    let num = 0;
+    const mo = b64.length % 4;
+    switch (mo) {
+        case 3:
+            num = 1;
+            break;
+        case 2:
+            num = 2;
+            break;
+        case 0:
+            num = 0;
+            break;
+        default:
+            throw new Error('base64 not a valid length');
+    }
+    return b64 + '='.repeat(num);
+}
+async function fromUrlSafeB64(b64) {
+    const originalB64 = b64PadSuffix(b64.replaceAll('-', '+').replaceAll('_', '/'));
+    const { toByteArray } = await Promise.resolve().then(() => __importStar(require('base64-js')));
+    const { inflate } = await Promise.resolve().then(() => __importStar(require('pako')));
+    const bytes = toByteArray(originalB64);
+    const inflated = inflate(bytes);
+    return new TextDecoder().decode(inflated);
+}
+async function toUrlSafeB64(str) {
+    const bytes = new TextEncoder().encode(str);
+    const { deflate } = await Promise.resolve().then(() => __importStar(require('pako')));
+    const { fromByteArray } = await Promise.resolve().then(() => __importStar(require('base64-js')));
+    const deflated = deflate(bytes);
+    const encoded = fromByteArray(deflated);
+    const pos = encoded.indexOf('=');
+    return pos > 0
+        ? encoded.slice(0, pos).replaceAll('+', '-').replaceAll('/', '_')
+        : encoded.replaceAll('+', '-').replaceAll('/', '_');
+}
+function filterSessionInPlace(node, type) {
+    if (node === undefined) {
+        return;
+    }
+    if ((0, mobx_state_tree_1.isArrayType)(type)) {
+        const array = node;
+        const childType = (0, mobx_state_tree_1.getChildType)(node);
+        if ((0, mobx_state_tree_1.isReferenceType)(childType)) {
+            for (let i = 0; i < array.length;) {
+                if (!(0, mobx_state_tree_1.isValidReference)(() => array[i])) {
+                    array.splice(i, 1);
+                }
+                else {
+                    i += 1;
+                }
+            }
+        }
+        for (const el of array) {
+            filterSessionInPlace(el, childType);
+        }
+    }
+    else if ((0, mobx_state_tree_1.isMapType)(type)) {
+        const map = node;
+        const childType = (0, mobx_state_tree_1.getChildType)(map);
+        if ((0, mobx_state_tree_1.isReferenceType)(childType)) {
+            for (const key in map.keys()) {
+                if (!(0, mobx_state_tree_1.isValidReference)(() => map.get(key))) {
+                    map.delete(key);
+                }
+            }
+        }
+        for (const child of map) {
+            filterSessionInPlace(child, childType);
+        }
+    }
+    else if ((0, mobx_state_tree_1.isModelType)(type)) {
+        const { properties } = (0, mobx_state_tree_1.getPropertyMembers)(node);
+        for (const [pname, ptype] of Object.entries(properties)) {
+            filterSessionInPlace(node[pname], ptype);
+        }
+    }
+}

package/dist/version.d.ts

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+export const version: "3.2.0";

package/dist/version.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.version = void 0;
+exports.version = '3.2.0';

package/dist/webpack.d.ts

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+import * as React from 'react';
+export { default as JBrowseApp } from './JBrowseApp';
+export { default as createModel } from './createModel';
+export { default as createViewState } from './createViewState';
+export { default as loadPlugins } from './loadPlugins';
+export * from 'react-dom/client';
+export { React };

package/dist/webpack.js

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+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+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);
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.React = exports.loadPlugins = exports.createViewState = exports.createModel = exports.JBrowseApp = void 0;
+const React = __importStar(require("react"));
+exports.React = React;
+var JBrowseApp_1 = require("./JBrowseApp");
+Object.defineProperty(exports, "JBrowseApp", { enumerable: true, get: function () { return __importDefault(JBrowseApp_1).default; } });
+var createModel_1 = require("./createModel");
+Object.defineProperty(exports, "createModel", { enumerable: true, get: function () { return __importDefault(createModel_1).default; } });
+var createViewState_1 = require("./createViewState");
+Object.defineProperty(exports, "createViewState", { enumerable: true, get: function () { return __importDefault(createViewState_1).default; } });
+var loadPlugins_1 = require("./loadPlugins");
+Object.defineProperty(exports, "loadPlugins", { enumerable: true, get: function () { return __importDefault(loadPlugins_1).default; } });
+__exportStar(require("react-dom/client"), exports);

package/dist/workerPolyfill.js

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+"use strict";
+self.window = {
+    addEventListener() { },
+    fetch: self.fetch.bind(self),
+    location: self.location,
+    Date: self.Date,
+    requestIdleCallback: cb => {
+        cb();
+    },
+    cancelIdleCallback: () => { },
+    requestAnimationFrame: cb => {
+        cb();
+    },
+    cancelAnimationFrame: () => { },
+    navigator: {},
+};
+self.document = {
+    createTextNode() { },
+    querySelector() {
+        return { appendChild() { } };
+    },
+    documentElement: {},
+    querySelectorAll: () => [],
+    createElement() {
+        return {
+            style: {},
+            setAttribute() { },
+            removeAttribute() { },
+            appendChild() { },
+        };
+    },
+};

package/esm/JBrowseApp/AppReExport.d.ts

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+export { App as default } from '@jbrowse/app-core';

package/esm/JBrowseApp/AppReExport.js

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+export { App as default } from '@jbrowse/app-core';

package/esm/JBrowseApp/JBrowseApp.d.ts

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+import type { ViewModel } from '../createModel';
+declare const JBrowseApp: ({ viewState }: {
+    viewState: ViewModel;
+}) => import("react/jsx-runtime").JSX.Element;
+export default JBrowseApp;

package/esm/JBrowseApp/JBrowseApp.js

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+import { jsx as _jsx } from "react/jsx-runtime";
+import { Suspense, lazy } from 'react';
+import { getConf } from '@jbrowse/core/configuration';
+import { LoadingEllipses, createJBrowseTheme } from '@jbrowse/core/ui';
+import { ScopedCssBaseline, ThemeProvider } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+const App = lazy(() => import('./AppReExport'));
+const useStyles = makeStyles()({
+    avoidParentStyle: {
+        all: 'initial',
+    },
+});
+const JBrowseApp = observer(function ({ viewState }) {
+    const { classes } = useStyles();
+    const session = viewState.session;
+    const theme = createJBrowseTheme(getConf(viewState.jbrowse, 'theme'));
+    return (_jsx(ThemeProvider, { theme: theme, children: _jsx("div", { className: classes.avoidParentStyle, children: _jsx(ScopedCssBaseline, { children: _jsx(Suspense, { fallback: _jsx(LoadingEllipses, {}), children: _jsx(App, { session: session }) }) }) }) }));
+});
+export default JBrowseApp;

package/esm/JBrowseApp/index.d.ts

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+export { default } from './JBrowseApp';

package/esm/JBrowseApp/index.js

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+export { default } from './JBrowseApp';

package/esm/components/AboutDialog.d.ts

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+export { AboutDialog as default } from '@jbrowse/product-core';

package/esm/components/AboutDialog.js

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+export { AboutDialog as default } from '@jbrowse/product-core';

package/esm/components/PreferencesDialog.d.ts

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+import type { ThemeOptions } from '@mui/material';
+declare const PreferencesDialog: ({ handleClose, session, }: {
+    handleClose: () => void;
+    session: {
+        allThemes: () => Record<string, ThemeOptions & {
+            name?: string;
+        }>;
+        themeName?: string;
+        stickyViewHeaders: boolean;
+        setStickyViewHeaders(sticky: boolean): void;
+        setThemeName: (arg: string) => void;
+    };
+}) => import("react/jsx-runtime").JSX.Element;
+export default PreferencesDialog;

package/esm/components/PreferencesDialog.js

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+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { Dialog } from '@jbrowse/core/ui';
+import { Button, Checkbox, DialogActions, DialogContent, FormControlLabel, FormGroup, MenuItem, TextField, } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()(() => ({
+    container: {
+        width: 800,
+    },
+}));
+const PreferencesDialog = observer(function ({ handleClose, session, }) {
+    const { classes } = useStyles();
+    return (_jsxs(Dialog, { title: "Preferences", open: true, onClose: handleClose, maxWidth: "xl", children: [_jsxs(DialogContent, { className: classes.container, children: [_jsx(TextField, { select: true, label: "Theme", value: session.themeName, onChange: event => {
+                            session.setThemeName(event.target.value);
+                        }, children: Object.entries(session.allThemes()).map(([key, val]) => (_jsx(MenuItem, { value: key, children: val.name || '(Unknown name)' }, key))) }), _jsx(FormGroup, { children: _jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: session.stickyViewHeaders }), onChange: (_, checked) => {
+                                session.setStickyViewHeaders(checked);
+                            }, label: "Keep view header visible" }) })] }), _jsx(DialogActions, { children: _jsx(Button, { onClick: handleClose, children: "Close" }) })] }));
+});
+export default PreferencesDialog;

package/esm/corePlugins.d.ts

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+import Arc from '@jbrowse/plugin-arc';
+declare const corePlugins: (typeof Arc)[];
+export default corePlugins;

package/esm/corePlugins.js

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+import Alignments from '@jbrowse/plugin-alignments';
+import Arc from '@jbrowse/plugin-arc';
+import Authentication from '@jbrowse/plugin-authentication';
+import Bed from '@jbrowse/plugin-bed';
+import BreakpointSplitView from '@jbrowse/plugin-breakpoint-split-view';
+import CircularView from '@jbrowse/plugin-circular-view';
+import ComparativeAdapters from '@jbrowse/plugin-comparative-adapters';
+import Config from '@jbrowse/plugin-config';
+import DataManagement from '@jbrowse/plugin-data-management';
+import DotplotView from '@jbrowse/plugin-dotplot-view';
+import GCContent from '@jbrowse/plugin-gccontent';
+import Gff3 from '@jbrowse/plugin-gff3';
+import GridBookmarkPlugin from '@jbrowse/plugin-grid-bookmark';
+import GtfPlugin from '@jbrowse/plugin-gtf';
+import HicPlugin from '@jbrowse/plugin-hic';
+import LegacyJBrowse from '@jbrowse/plugin-legacy-jbrowse';
+import LinearComparativeView from '@jbrowse/plugin-linear-comparative-view';
+import LinearGenomeView from '@jbrowse/plugin-linear-genome-view';
+import Lollipop from '@jbrowse/plugin-lollipop';
+import Menus from '@jbrowse/plugin-menus';
+import RDF from '@jbrowse/plugin-rdf';
+import Sequence from '@jbrowse/plugin-sequence';
+import SpreadsheetViewPlugin from '@jbrowse/plugin-spreadsheet-view';
+import SvInspectorPlugin from '@jbrowse/plugin-sv-inspector';
+import SVG from '@jbrowse/plugin-svg';
+import TrixPlugin from '@jbrowse/plugin-trix';
+import Variants from '@jbrowse/plugin-variants';
+import Wiggle from '@jbrowse/plugin-wiggle';
+const corePlugins = [
+    SVG,
+    LinearGenomeView,
+    Alignments,
+    Authentication,
+    Bed,
+    CircularView,
+    Config,
+    DataManagement,
+    DotplotView,
+    GtfPlugin,
+    Gff3,
+    LegacyJBrowse,
+    LinearComparativeView,
+    Lollipop,
+    Menus,
+    RDF,
+    Sequence,
+    Variants,
+    Wiggle,
+    GCContent,
+    SpreadsheetViewPlugin,
+    SvInspectorPlugin,
+    BreakpointSplitView,
+    HicPlugin,
+    TrixPlugin,
+    GridBookmarkPlugin,
+    ComparativeAdapters,
+    Arc,
+];
+export default corePlugins;