@jbrowse/react-circular-genome-view2 3.2.0

package/dist/types.d.ts

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

package/dist/types.js

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+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });

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 JBrowseCircularGenomeView } from './JBrowseCircularGenomeView';
+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.JBrowseCircularGenomeView = void 0;
+const React = __importStar(require("react"));
+exports.React = React;
+var JBrowseCircularGenomeView_1 = require("./JBrowseCircularGenomeView");
+Object.defineProperty(exports, "JBrowseCircularGenomeView", { enumerable: true, get: function () { return __importDefault(JBrowseCircularGenomeView_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/docs/example.md

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+This is an example of an assembly and tracks configuration for a simple human
+genome example using publicly hosted data files. It includes the hg19 reference
+sequence and a structural variant track.
+
+```tsx
+import '@fontsource/roboto'
+import {
+  createViewState,
+  JBrowseCircularGenomeView,
+} from '@jbrowse/react-circular-genome-view2'
+
+const assembly = {
+  name: 'hg19',
+  aliases: ['GRCh37'],
+  sequence: {
+    type: 'ReferenceSequenceTrack',
+    trackId: 'Pd8Wh30ei9R',
+    adapter: {
+      type: 'BgzipFastaAdapter',
+      fastaLocation: {
+        uri: 'https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz',
+        locationType: 'UriLocation',
+      },
+      faiLocation: {
+        uri: 'https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.fai',
+        locationType: 'UriLocation',
+      },
+      gziLocation: {
+        uri: 'https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.gzi',
+        locationType: 'UriLocation',
+      },
+    },
+  },
+  refNameAliases: {
+    adapter: {
+      type: 'RefNameAliasAdapter',
+      location: {
+        uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/hg19/hg19_aliases.txt',
+        locationType: 'UriLocation',
+      },
+    },
+  },
+}
+
+const tracks = [
+  {
+    type: 'VariantTrack',
+    trackId: 'pacbio_sv_vcf',
+    name: 'HG002 Pacbio SV (VCF)',
+    assemblyNames: ['hg19'],
+    category: ['GIAB'],
+    adapter: {
+      type: 'VcfTabixAdapter',
+      vcfGzLocation: {
+        uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/hg19/pacbio/hs37d5.HG002-SequelII-CCS.bnd-only.sv.vcf.gz',
+        locationType: 'UriLocation',
+      },
+      index: {
+        location: {
+          uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/hg19/pacbio/hs37d5.HG002-SequelII-CCS.bnd-only.sv.vcf.gz.tbi',
+          locationType: 'UriLocation',
+        },
+      },
+    },
+  },
+]
+
+const defaultSession = {
+  name: 'My session',
+  view: {
+    id: 'circularView',
+    type: 'CircularView',
+    bpPerPx: 5000000,
+    tracks: [
+      {
+        id: 'uPdLKHik1',
+        type: 'VariantTrack',
+        configuration: 'pacbio_sv_vcf',
+        displays: [
+          {
+            id: 'v9QVAR3oaB',
+            type: 'ChordVariantDisplay',
+            configuration: 'pacbio_sv_vcf-ChordVariantDisplay',
+          },
+        ],
+      },
+    ],
+  },
+}
+
+function View() {
+  const state = createViewState({
+    assembly,
+    tracks,
+    defaultSession,
+  })
+  return <JBrowseCircularGenomeView viewState={state} />
+}
+
+export default View
+```
+
+This is what the component should look like:
+
+![a view](./img/exampleView.png)

package/esm/JBrowseCircularGenomeView/JBrowseCircularGenomeView.d.ts

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

package/esm/JBrowseCircularGenomeView/JBrowseCircularGenomeView.js

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+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { Suspense } from 'react';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { createJBrowseTheme } from '@jbrowse/core/ui';
+import { getEnv } from '@jbrowse/core/util';
+import { EmbeddedViewContainer, ModalWidget } from '@jbrowse/embedded-core';
+import { ThemeProvider } from '@mui/material';
+import { observer } from 'mobx-react';
+const JBrowseCircularGenomeView = observer(function ({ viewState, }) {
+    const { session } = viewState;
+    const { view } = session;
+    const { pluginManager } = getEnv(session);
+    const viewType = pluginManager.getViewType(view.type);
+    if (!viewType) {
+        throw new Error(`unknown view type ${view.type}`);
+    }
+    const { ReactComponent } = viewType;
+    const theme = createJBrowseTheme(readConfObject(viewState.config.configuration, 'theme'));
+    return (_jsxs(ThemeProvider, { theme: theme, children: [_jsx(EmbeddedViewContainer, { view: view, children: _jsx(Suspense, { fallback: _jsx("div", { children: "Loading..." }), children: _jsx(ReactComponent, { model: view, session: session }) }) }, `view-${view.id}`), _jsx(ModalWidget, { session: session })] }));
+});
+export default JBrowseCircularGenomeView;

package/esm/JBrowseCircularGenomeView/index.d.ts

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

package/esm/JBrowseCircularGenomeView/index.js

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

package/esm/corePlugins.d.ts

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

package/esm/corePlugins.js

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+import Authentication from '@jbrowse/plugin-authentication';
+import CircularGenomeView from '@jbrowse/plugin-circular-view';
+import Config from '@jbrowse/plugin-config';
+import DataManagement from '@jbrowse/plugin-data-management';
+import Sequence from '@jbrowse/plugin-sequence';
+import Variants from '@jbrowse/plugin-variants';
+import Wiggle from '@jbrowse/plugin-wiggle';
+const corePlugins = [
+    Authentication,
+    Config,
+    DataManagement,
+    CircularGenomeView,
+    Sequence,
+    Variants,
+    Wiggle,
+];
+export default corePlugins;

package/esm/createModel/AboutDialog.d.ts

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

package/esm/createModel/AboutDialog.js

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

package/esm/createModel/createConfigModel.d.ts

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+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+export default function createConfigModel(pluginManager: PluginManager, assemblyConfigSchemasType: AnyConfigurationSchemaType): 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;
+        };
+        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>>;
+        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>>;
+        theme: {
+            type: string;
+            defaultValue: {};
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    assembly: AnyConfigurationSchemaType;
+    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: ({
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>)[];
+    readonly assemblyName: string;
+    readonly rpcManager: any;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/createModel/createConfigModel.js

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+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,
+            },
+            formatDetails: FormatDetailsConfigSchemaFactory(),
+            formatAbout: FormatAboutConfigSchemaFactory(),
+            hierarchical: HierarchicalConfigSchemaFactory(),
+            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;
+        },
+    }));
+}