@jbrowse/react-linear-genome-view2 3.2.0

package/dist/rpcWorker.d.ts

@@ -0,0 +1,2 @@
+import './workerPolyfill';
+export default function doNothing(): void;

package/dist/rpcWorker.js

@@ -0,0 +1,49 @@
+"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 __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = doNothing;
+require("./workerPolyfill");
+const product_core_1 = require("@jbrowse/product-core");
+const mobx_react_1 = require("mobx-react");
+const corePlugins_1 = __importDefault(require("./corePlugins"));
+(0, mobx_react_1.enableStaticRendering)(true);
+(0, product_core_1.initializeWorker)(corePlugins_1.default, {
+    fetchESM: url => Promise.resolve(`${url}`).then(s => __importStar(require(s))),
+});
+function doNothing() {
+}

package/dist/types.d.ts

@@ -0,0 +1,5 @@
+import type { IAnyStateTreeNode } from 'mobx-state-tree';
+export interface ReferringNode {
+    node: IAnyStateTreeNode;
+    key: string;
+}

package/dist/types.js

@@ -0,0 +1,2 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });

package/dist/version.d.ts

@@ -0,0 +1 @@
+export const version: "3.2.0";

package/dist/version.js

@@ -0,0 +1,4 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.version = void 0;
+exports.version = '3.2.0';

package/dist/webpack.d.ts

@@ -0,0 +1,8 @@
+import * as React from 'react';
+export { default as JBrowseLinearGenomeView } from './JBrowseLinearGenomeView';
+export { default as createModel } from './createModel';
+export { default as createViewState } from './createViewState';
+export { default as loadPlugins } from './loadPlugins';
+export type { ViewModel } from './createModel/createModel';
+export * from 'react-dom/client';
+export { React };

package/dist/webpack.js

@@ -0,0 +1,53 @@
+"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.JBrowseLinearGenomeView = void 0;
+const React = __importStar(require("react"));
+exports.React = React;
+var JBrowseLinearGenomeView_1 = require("./JBrowseLinearGenomeView");
+Object.defineProperty(exports, "JBrowseLinearGenomeView", { enumerable: true, get: function () { return __importDefault(JBrowseLinearGenomeView_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

@@ -0,0 +1,32 @@
+"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/docs/example.md

@@ -0,0 +1,91 @@
+This is an example of an assembly and tracks configuration for a simple human
+genome example using publicly hosted data files. It includes the GRCh38
+reference sequence and a genes track.
+
+```tsx
+import '@fontsource/roboto'
+import {
+  createViewState,
+  JBrowseLinearGenomeView,
+} from '@jbrowse/react-linear-genome-view2'
+
+const assembly = {
+  name: 'GRCh38',
+  sequence: {
+    type: 'ReferenceSequenceTrack',
+    trackId: 'GRCh38-ReferenceSequenceTrack',
+    adapter: {
+      type: 'BgzipFastaAdapter',
+      uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz',
+    },
+  },
+  aliases: ['hg38'],
+  refNameAliases: {
+    adapter: {
+      type: 'RefNameAliasAdapter',
+      uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt',
+    },
+  },
+}
+
+const tracks = [
+  {
+    type: 'FeatureTrack',
+    trackId: 'ncbi_refseq_109_hg38',
+    name: 'NCBI RefSeq (GFF3Tabix)',
+    assemblyNames: ['GRCh38'],
+    category: ['Annotation'],
+    adapter: {
+      type: 'Gff3TabixAdapter',
+      uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz',
+    },
+  },
+]
+
+const defaultSession = {
+  name: 'My session',
+  view: {
+    id: 'linearGenomeView',
+    type: 'LinearGenomeView',
+    tracks: [
+      {
+        type: 'ReferenceSequenceTrack',
+        configuration: 'GRCh38-ReferenceSequenceTrack',
+        displays: [
+          {
+            type: 'LinearReferenceSequenceDisplay',
+            configuration:
+              'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay',
+          },
+        ],
+      },
+      {
+        type: 'FeatureTrack',
+        configuration: 'ncbi_refseq_109_hg38',
+        displays: [
+          {
+            type: 'LinearBasicDisplay',
+            configuration: 'ncbi_refseq_109_hg38-LinearBasicDisplay',
+          },
+        ],
+      },
+    ],
+  },
+}
+
+function View() {
+  const state = createViewState({
+    assembly,
+    tracks,
+    location: '10:29,838,737..29,838,819',
+    defaultSession,
+  })
+  return <JBrowseLinearGenomeView viewState={state} />
+}
+
+export default View
+```
+
+This is what the component should look like:
+
+![a view](./img/exampleView.png)

package/esm/JBrowseLinearGenomeView/JBrowseLinearGenomeView.d.ts

@@ -0,0 +1,5 @@
+import type { ViewModel } from '../createModel/createModel';
+declare const JBrowseLinearGenomeView: ({ viewState, }: {
+    viewState: ViewModel;
+}) => import("react/jsx-runtime").JSX.Element;
+export default JBrowseLinearGenomeView;

package/esm/JBrowseLinearGenomeView/JBrowseLinearGenomeView.js

@@ -0,0 +1,17 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { Suspense } from 'react';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { LoadingEllipses, createJBrowseTheme } from '@jbrowse/core/ui';
+import { EmbeddedViewContainer, ModalWidget } from '@jbrowse/embedded-core';
+import { ThemeProvider } from '@mui/material';
+import { observer } from 'mobx-react';
+import { getEnv } from 'mobx-state-tree';
+const JBrowseLinearGenomeView = observer(function ({ viewState, }) {
+    const { session } = viewState;
+    const { view } = session;
+    const { pluginManager } = getEnv(session);
+    const { ReactComponent } = pluginManager.getViewType(view.type);
+    const theme = createJBrowseTheme(readConfObject(viewState.config.configuration, 'theme'));
+    return (_jsxs(ThemeProvider, { theme: theme, children: [_jsx(EmbeddedViewContainer, { view: view, children: _jsx(Suspense, { fallback: _jsx(LoadingEllipses, {}), children: _jsx(ReactComponent, { model: view, session: session }) }) }, `view-${view.id}`), _jsx(ModalWidget, { session: session })] }));
+});
+export default JBrowseLinearGenomeView;

package/esm/JBrowseLinearGenomeView/index.d.ts

@@ -0,0 +1 @@
+export { default } from './JBrowseLinearGenomeView';

package/esm/JBrowseLinearGenomeView/index.js

@@ -0,0 +1 @@
+export { default } from './JBrowseLinearGenomeView';

package/esm/corePlugins.d.ts

@@ -0,0 +1,3 @@
+import Arc from '@jbrowse/plugin-arc';
+declare const corePlugins: (typeof Arc)[];
+export default corePlugins;

package/esm/corePlugins.js

@@ -0,0 +1,33 @@
+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 Config from '@jbrowse/plugin-config';
+import DataManagement from '@jbrowse/plugin-data-management';
+import GCContent from '@jbrowse/plugin-gccontent';
+import GFF3 from '@jbrowse/plugin-gff3';
+import LegacyJBrowse from '@jbrowse/plugin-legacy-jbrowse';
+import LinearGenomeView from '@jbrowse/plugin-linear-genome-view';
+import Sequence from '@jbrowse/plugin-sequence';
+import SVG from '@jbrowse/plugin-svg';
+import Trix from '@jbrowse/plugin-trix';
+import Variants from '@jbrowse/plugin-variants';
+import Wiggle from '@jbrowse/plugin-wiggle';
+const corePlugins = [
+    SVG,
+    Alignments,
+    Authentication,
+    BED,
+    Config,
+    DataManagement,
+    GFF3,
+    LegacyJBrowse,
+    LinearGenomeView,
+    Sequence,
+    Variants,
+    Wiggle,
+    GCContent,
+    Trix,
+    Arc,
+];
+export default corePlugins;

package/esm/createModel/AboutDialog.d.ts

@@ -0,0 +1 @@
+export { AboutDialog as default } from '@jbrowse/product-core';

package/esm/createModel/AboutDialog.js

@@ -0,0 +1 @@
+export { AboutDialog as default } from '@jbrowse/product-core';

package/esm/createModel/createConfigModel.d.ts

@@ -0,0 +1,94 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { IAnyType } from 'mobx-state-tree';
+export default function createConfigModel(pluginManager: PluginManager, assemblyConfigSchemasType: IAnyType): import("mobx-state-tree").IModelType<{
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            defaultDriver: {
+                type: string;
+                description: string;
+                defaultValue: string;
+            };
+            drivers: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IMapType<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> | undefined, import("mobx-state-tree").ModelSnapshotType<Record<string, any>>, ({} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> & import("mobx-state-tree/dist/internal").NonEmptyObject) | undefined>>, [undefined]>;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        highResolutionScaling: {
+            type: string;
+            defaultValue: number;
+        };
+        hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                trackNames: {
+                    type: string;
+                    defaultValue: boolean;
+                };
+                categories: {
+                    type: string;
+                    defaultValue: boolean;
+                };
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+            defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+                categoryNames: {
+                    type: string;
+                    defaultValue: never[];
+                };
+                topLevelCategories: {
+                    type: string;
+                    defaultValue: boolean;
+                };
+                subCategories: {
+                    type: string;
+                    defaultValue: boolean;
+                };
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            feature: {
+                type: string;
+                description: string;
+                defaultValue: {};
+                contextVariable: string[];
+            };
+            subfeatures: {
+                type: string;
+                description: string;
+                defaultValue: {};
+                contextVariable: string[];
+            };
+            depth: {
+                type: string;
+                defaultValue: number;
+                description: string;
+            };
+            maxDepth: {
+                type: string;
+                defaultValue: number;
+                description: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            config: {
+                type: string;
+                description: string;
+                defaultValue: {};
+                contextVariable: string[];
+            };
+            hideUris: {
+                type: string;
+                defaultValue: boolean;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        theme: {
+            type: string;
+            defaultValue: {};
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    assembly: IAnyType;
+    tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    internetAccounts: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    connections: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    aggregateTextSearchAdapters: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    plugins: import("mobx-state-tree").IType<any, any, any>;
+}, {
+    readonly assemblies: any[];
+    readonly assemblyName: string;
+    readonly rpcManager: any;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/createModel/createConfigModel.js

@@ -0,0 +1,37 @@
+import { ConfigurationSchema, readConfObject, } from '@jbrowse/core/configuration';
+import RpcManager from '@jbrowse/core/rpc/RpcManager';
+import { FormatAboutConfigSchemaFactory, FormatDetailsConfigSchemaFactory, HierarchicalConfigSchemaFactory, } from '@jbrowse/product-core';
+import { getParent, types } from 'mobx-state-tree';
+export default function createConfigModel(pluginManager, assemblyConfigSchemasType) {
+    return types
+        .model('Configuration', {
+        configuration: ConfigurationSchema('Root', {
+            rpc: RpcManager.configSchema,
+            highResolutionScaling: {
+                type: 'number',
+                defaultValue: 2,
+            },
+            hierarchical: HierarchicalConfigSchemaFactory(),
+            formatDetails: FormatDetailsConfigSchemaFactory(),
+            formatAbout: FormatAboutConfigSchemaFactory(),
+            theme: { type: 'frozen', defaultValue: {} },
+        }),
+        assembly: assemblyConfigSchemasType,
+        tracks: types.array(pluginManager.pluggableConfigSchemaType('track')),
+        internetAccounts: types.array(pluginManager.pluggableConfigSchemaType('internet account')),
+        connections: types.array(pluginManager.pluggableConfigSchemaType('connection')),
+        aggregateTextSearchAdapters: types.array(pluginManager.pluggableConfigSchemaType('text search adapter')),
+        plugins: types.frozen(),
+    })
+        .views(self => ({
+        get assemblies() {
+            return [self.assembly];
+        },
+        get assemblyName() {
+            return readConfObject(self.assembly, 'name');
+        },
+        get rpcManager() {
+            return getParent(self).rpcManager;
+        },
+    }));
+}