@jbrowse/react-app2 3.7.0 → 4.0.0

package/esm/createViewState.js

@@ -1,5 +1,5 @@
-import { onPatch } from 'mobx-state-tree';
-import createModel from './createModel';
+import { onPatch } from '@jbrowse/mobx-state-tree';
+import createModel from "./createModel.js";
 export default function createViewState(opts) {
     const { config, plugins = [], onChange, makeWorkerInstance } = opts;
     const { defaultSession = { name: 'NewSession' } } = config;

package/esm/index.d.ts

@@ -1,4 +1,4 @@
-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 { default as JBrowseApp } from './JBrowseApp/index.ts';
+export { default as createModel } from './createModel.ts';
+export { default as createViewState } from './createViewState.ts';
+export { default as loadPlugins } from './loadPlugins.ts';

package/esm/index.js

@@ -1,4 +1,4 @@
-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 { default as JBrowseApp } from "./JBrowseApp/index.js";
+export { default as createModel } from "./createModel.js";
+export { default as createViewState } from "./createViewState.js";
+export { default as loadPlugins } from "./loadPlugins.js";

package/esm/jbrowseModel.d.ts

@@ -1,23 +1,24 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-export default function JBrowseWeb({ pluginManager, assemblyConfigSchema, }: {
+export default function JBrowseWeb({ pluginManager, assemblyConfigSchema, adminMode, }: {
     pluginManager: PluginManager;
     assemblyConfigSchema: AnyConfigurationSchemaType;
-}): import("mobx-state-tree").IModelType<{
-    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    adminMode?: boolean;
+}): import("@jbrowse/mobx-state-tree").IModelType<{
+    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+        rpc: import("node_modules/@jbrowse/core/src/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>>;
+            drivers: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> | undefined, import("@jbrowse/mobx-state-tree").ModelSnapshotType<Record<string, any>>, ({} & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject) | undefined>>, [undefined]>;
+        }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
         highResolutionScaling: {
             type: string;
             defaultValue: number;
         };
-        formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        formatDetails: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
             feature: {
                 type: string;
                 description: string;
@@ -40,8 +41,8 @@ export default function JBrowseWeb({ pluginManager, assemblyConfigSchema, }: {
                 defaultValue: number;
                 description: string;
             };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-        formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        formatAbout: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
             config: {
                 type: string;
                 description: string;
@@ -52,7 +53,7 @@ export default function JBrowseWeb({ pluginManager, assemblyConfigSchema, }: {
                 type: string;
                 defaultValue: boolean;
             };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
         shareURL: {
             type: string;
             defaultValue: string;
@@ -61,8 +62,8 @@ export default function JBrowseWeb({ pluginManager, assemblyConfigSchema, }: {
             type: string;
             defaultValue: boolean;
         };
-        hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        hierarchical: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+            sort: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
                 trackNames: {
                     type: string;
                     defaultValue: boolean;
@@ -71,8 +72,8 @@ export default function JBrowseWeb({ pluginManager, assemblyConfigSchema, }: {
                     type: string;
                     defaultValue: boolean;
                 };
-            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-            defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+            defaultCollapsed: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
                 categoryNames: {
                     type: string;
                     defaultValue: never[];
@@ -85,8 +86,8 @@ export default function JBrowseWeb({ pluginManager, assemblyConfigSchema, }: {
                     type: string;
                     defaultValue: boolean;
                 };
-            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+            }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
         theme: {
             type: string;
             defaultValue: {};
@@ -102,38 +103,55 @@ export default function JBrowseWeb({ pluginManager, assemblyConfigSchema, }: {
                 locationType: string;
             };
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    plugins: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/core/PluginLoader").PluginDefinition, import("@jbrowse/core/PluginLoader").PluginDefinition, import("@jbrowse/core/PluginLoader").PluginDefinition>>;
-    assemblies: import("mobx-state-tree").IArrayType<AnyConfigurationSchemaType>;
-    tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-    internetAccounts: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-    aggregateTextSearchAdapters: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-    connections: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-    defaultSession: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<any, any, any>, [undefined]>;
-    preConfiguredSessions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<any, any, any>>;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    plugins: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/PluginLoader").PluginDefinition, import("@jbrowse/core/PluginLoader").PluginDefinition, import("@jbrowse/core/PluginLoader").PluginDefinition>>;
+    assemblies: import("@jbrowse/mobx-state-tree").IArrayType<AnyConfigurationSchemaType>;
+    tracks: import("@jbrowse/mobx-state-tree").IType<{
+        [key: string]: unknown;
+        trackId: string;
+    }[] | null | undefined, {
+        [key: string]: unknown;
+        trackId: string;
+    }[], {
+        [key: string]: unknown;
+        trackId: string;
+    }[]>;
+    internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
+    aggregateTextSearchAdapters: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
+    connections: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
+    defaultSession: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<any, any, any>, [undefined]>;
+    preConfiguredSessions: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<any, any, any>>;
 }, {
     readonly assemblyNames: string[];
     readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
 } & {
     addAssemblyConf(conf: import("@jbrowse/core/configuration").AnyConfigurationModel): ({
         [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+    } & import("@jbrowse/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>) | undefined;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>) | undefined;
     removeAssemblyConf(assemblyName: string): void;
-    addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
+    addTrackConf(trackConf: {
+        trackId: string;
+        type: string;
+    }): {
+        [key: string]: unknown;
+        trackId: string;
+    } | undefined;
     addConnectionConf(connectionConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
     deleteConnectionConf(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): boolean;
-    deleteTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): boolean;
+    deleteTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel | {
+        trackId: string;
+    }): void;
+    updateTrackConf(trackConf: {
+        trackId: string;
+        [key: string]: unknown;
+    }): void;
     addPlugin(pluginDefinition: import("@jbrowse/core/PluginLoader").PluginDefinition): void;
     removePlugin(pluginDefinition: import("@jbrowse/core/PluginLoader").PluginDefinition): void;
     setDefaultSessionConf(sessionConf: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
     addInternetAccountConf(internetAccountConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
     deleteInternetAccountConf(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): boolean;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;

package/esm/jbrowseModel.js

@@ -1,4 +1,4 @@
 import { JBrowseModelF } from '@jbrowse/app-core';
-export default function JBrowseWeb({ pluginManager, assemblyConfigSchema, }) {
-    return JBrowseModelF({ pluginManager, assemblyConfigSchema });
+export default function JBrowseWeb({ pluginManager, assemblyConfigSchema, adminMode = false, }) {
+    return JBrowseModelF({ pluginManager, assemblyConfigSchema, adminMode });
 }

package/esm/rootModel/rootModel.d.ts

@@ -3,8 +3,8 @@ import assemblyConfigSchemaFactory from '@jbrowse/core/assemblyManager/assemblyC
 import RpcManager from '@jbrowse/core/rpc/RpcManager';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { MenuItem } from '@jbrowse/core/ui';
+import type { IAnyType, Instance, SnapshotIn } from '@jbrowse/mobx-state-tree';
 import type { BaseSessionType } from '@jbrowse/product-core';
-import type { IAnyType, Instance, SnapshotIn } from 'mobx-state-tree';
 export interface Menu {
     label: string;
     menuItems: MenuItem[];
@@ -18,13 +18,13 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
     pluginManager: PluginManager;
     sessionModelFactory: SessionModelFactory;
     makeWorkerInstance?: () => Worker;
-}): import("mobx-state-tree").IModelType<{
+}): import("@jbrowse/mobx-state-tree").IModelType<{
     jbrowse: IAnyType;
-    session: import("mobx-state-tree").IMaybe<IAnyType>;
-    sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
-        assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-            configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
+    session: import("@jbrowse/mobx-state-tree").IMaybe<IAnyType>;
+    sessionPath: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    assemblyManager: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
+        assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -32,6 +32,7 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -55,9 +56,10 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
             readonly refNames: string[] | undefined;
         } & {
             getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(asmName: string): string;
+            getCanonicalRefName2(refName: string): string;
             getRefNameColor(refName: string): string | undefined;
             isValidRefName(refName: string): boolean;
+            getSeqAdapterRefName(canonicalRefName: string): string;
         } & {
             setLoaded({ regions, refNameAliases, cytobands, }: {
                 regions: import("@jbrowse/core/util").Region[];
@@ -72,6 +74,7 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
                 [x: string]: string;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
@@ -90,17 +93,18 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
                 [x: string]: string;
             }>;
             afterCreate(): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     }, {
         readonly assemblyNameMap: Record<string, {
             configuration: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
             error: unknown;
             loadingP: Promise<void> | undefined;
             volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -124,9 +128,10 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
             readonly refNames: string[] | undefined;
         } & {
             getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(asmName: string): string;
+            getCanonicalRefName2(refName: string): string;
             getRefNameColor(refName: string): string | undefined;
             isValidRefName(refName: string): boolean;
+            getSeqAdapterRefName(canonicalRefName: string): string;
         } & {
             setLoaded({ regions, refNameAliases, cytobands, }: {
                 regions: import("@jbrowse/core/util").Region[];
@@ -141,6 +146,7 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
                 [x: string]: string;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
@@ -159,8 +165,8 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
                 [x: string]: string;
             }>;
             afterCreate(): void;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -168,6 +174,7 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -191,9 +198,10 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
             readonly refNames: string[] | undefined;
         } & {
             getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(asmName: string): string;
+            getCanonicalRefName2(refName: string): string;
             getRefNameColor(refName: string): string | undefined;
             isValidRefName(refName: string): boolean;
+            getSeqAdapterRefName(canonicalRefName: string): string;
         } & {
             setLoaded({ regions, refNameAliases, cytobands, }: {
                 regions: import("@jbrowse/core/util").Region[];
@@ -208,6 +216,7 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
                 [x: string]: string;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
@@ -226,19 +235,20 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
                 [x: string]: string;
             }>;
             afterCreate(): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
     } & {
         getCanonicalAssemblyName(asmName: string): string | undefined;
         getCanonicalAssemblyName2(asmName: string): string;
         get(asmName: string): ({
             configuration: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
             error: unknown;
             loadingP: Promise<void> | undefined;
             volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -262,9 +272,10 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
             readonly refNames: string[] | undefined;
         } & {
             getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(asmName: string): string;
+            getCanonicalRefName2(refName: string): string;
             getRefNameColor(refName: string): string | undefined;
             isValidRefName(refName: string): boolean;
+            getSeqAdapterRefName(canonicalRefName: string): string;
         } & {
             setLoaded({ regions, refNameAliases, cytobands, }: {
                 regions: import("@jbrowse/core/util").Region[];
@@ -279,6 +290,7 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
                 [x: string]: string;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
@@ -297,8 +309,8 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
                 [x: string]: string;
             }>;
             afterCreate(): void;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -306,6 +318,7 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -329,9 +342,10 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
             readonly refNames: string[] | undefined;
         } & {
             getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(asmName: string): string;
+            getCanonicalRefName2(refName: string): string;
             getRefNameColor(refName: string): string | undefined;
             isValidRefName(refName: string): boolean;
+            getSeqAdapterRefName(canonicalRefName: string): string;
         } & {
             setLoaded({ regions, refNameAliases, cytobands, }: {
                 regions: import("@jbrowse/core/util").Region[];
@@ -346,6 +360,7 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
                 [x: string]: string;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
@@ -364,20 +379,21 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
                 [x: string]: string;
             }>;
             afterCreate(): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
         readonly assemblyNamesList: any[];
         readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
         readonly rpcManager: RpcManager;
     } & {
         waitForAssembly(assemblyName: string): Promise<({
             configuration: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
             error: unknown;
             loadingP: Promise<void> | undefined;
             volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -401,9 +417,10 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
             readonly refNames: string[] | undefined;
         } & {
             getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(asmName: string): string;
+            getCanonicalRefName2(refName: string): string;
             getRefNameColor(refName: string): string | undefined;
             isValidRefName(refName: string): boolean;
+            getSeqAdapterRefName(canonicalRefName: string): string;
         } & {
             setLoaded({ regions, refNameAliases, cytobands, }: {
                 regions: import("@jbrowse/core/util").Region[];
@@ -418,6 +435,7 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
                 [x: string]: string;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
@@ -436,8 +454,8 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
                 [x: string]: string;
             }>;
             afterCreate(): void;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
@@ -445,6 +463,7 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
             refNameAliases: {
                 [x: string]: string;
             } | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
         } & {
             getConf(arg: string): any;
@@ -468,9 +487,10 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
             readonly refNames: string[] | undefined;
         } & {
             getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(asmName: string): string;
+            getCanonicalRefName2(refName: string): string;
             getRefNameColor(refName: string): string | undefined;
             isValidRefName(refName: string): boolean;
+            getSeqAdapterRefName(canonicalRefName: string): string;
         } & {
             setLoaded({ regions, refNameAliases, cytobands, }: {
                 regions: import("@jbrowse/core/util").Region[];
@@ -485,6 +505,7 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
                 [x: string]: string;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
@@ -503,21 +524,15 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
                 [x: string]: string;
             }>;
             afterCreate(): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
-        }, assemblyName: string | undefined, opts: {
-            stopToken?: string;
-            sessionId: string;
-        }): Promise<{
+        }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
             [x: string]: string;
         } | undefined>;
         getReverseRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
-        }, assemblyName: string | undefined, opts: {
-            stopToken?: string;
-            sessionId: string;
-        }): Promise<{
+        }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
             [x: string]: string;
         } | undefined>;
         isValidRefName(refName: string, assemblyName: string): boolean;
@@ -525,9 +540,9 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
         afterAttach(): void;
         removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
         addAssembly(configuration: any): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
 } & {
-    internetAccounts: import("mobx-state-tree").IArrayType<IAnyType>;
+    internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<IAnyType>;
 }, {
     rpcManager: RpcManager;
     adminMode: boolean;
@@ -571,7 +586,7 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
     setError(error?: unknown): void;
 } & {
     menus(): import("@jbrowse/app-core").Menu[];
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export type WebRootModelType = ReturnType<typeof RootModel>;
 export type WebRootModel = Instance<WebRootModelType>;
 export {};

package/esm/rootModel/rootModel.js

@@ -3,17 +3,17 @@ import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
 import assemblyConfigSchemaFactory from '@jbrowse/core/assemblyManager/assemblyConfigSchema';
 import RpcManager from '@jbrowse/core/rpc/RpcManager';
 import { Cable } from '@jbrowse/core/ui/Icons';
+import { addDisposer, cast, getSnapshot, getType, types, } from '@jbrowse/mobx-state-tree';
 import { BaseRootModelFactory, InternetAccountsRootModelMixin, } from '@jbrowse/product-core';
 import AddIcon from '@mui/icons-material/Add';
 import GetAppIcon from '@mui/icons-material/GetApp';
 import PublishIcon from '@mui/icons-material/Publish';
+import SpaceDashboardIcon from '@mui/icons-material/SpaceDashboard';
 import StorageIcon from '@mui/icons-material/Storage';
-import { saveAs } from 'file-saver';
 import { autorun } from 'mobx';
-import { addDisposer, cast, getSnapshot, getType, types } from 'mobx-state-tree';
-import jbrowseWebFactory from '../jbrowseModel';
-import { filterSessionInPlace } from '../util';
-import { version } from '../version';
+import jbrowseWebFactory from "../jbrowseModel.js";
+import { filterSessionInPlace } from "../util.js";
+import { version } from "../version.js";
 export default function RootModel({ pluginManager, sessionModelFactory, makeWorkerInstance = () => {
     throw new Error('no makeWorkerInstance supplied');
 }, }) {
@@ -46,11 +46,11 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
         .actions(self => {
         return {
             afterCreate() {
-                addDisposer(self, autorun(() => {
+                addDisposer(self, autorun(function pluginsUpdatedAutorun() {
                     if (self.pluginsUpdated) {
                         window.location.reload();
                     }
-                }));
+                }, { name: 'PluginsUpdated' }));
             },
             setSession(sessionSnapshot) {
                 const oldSession = self.session;
@@ -112,11 +112,11 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
                         {
                             label: 'Export session',
                             icon: GetAppIcon,
-                            onClick: (session) => {
-                                const sessionBlob = new Blob([
+                            onClick: async (session) => {
+                                const { saveAs } = await import('file-saver-es');
+                                saveAs(new Blob([
                                     JSON.stringify({ session: getSnapshot(session) }, null, 2),
-                                ], { type: 'text/plain;charset=utf-8' });
-                                saveAs(sessionBlob, 'session.json');
+                                ], { type: 'text/plain;charset=utf-8' }), 'session.json');
                             },
                         },
                         { type: 'divider' },
@@ -152,7 +152,18 @@ export default function RootModel({ pluginManager, sessionModelFactory, makeWork
                 },
                 {
                     label: 'Tools',
-                    menuItems: [],
+                    menuItems: [
+                        {
+                            label: 'Use workspaces',
+                            icon: SpaceDashboardIcon,
+                            type: 'checkbox',
+                            checked: self.session?.useWorkspaces ?? false,
+                            helpText: 'Workspaces allow you to organize views into tabs and tiles. You can drag views between tabs or split them side-by-side.',
+                            onClick: () => {
+                                self.session?.setUseWorkspaces(!self.session.useWorkspaces);
+                            },
+                        },
+                    ],
                 },
             ], self.mutableMenuActions);
         },

package/esm/rpcWorker.d.ts

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

package/esm/rpcWorker.js

@@ -6,10 +6,10 @@ var __rewriteRelativeImportExtension = (this && this.__rewriteRelativeImportExte
     }
     return path;
 };
-import './workerPolyfill';
+import './workerPolyfill.js';
 import { initializeWorker } from '@jbrowse/product-core';
 import { enableStaticRendering } from 'mobx-react';
-import corePlugins from './corePlugins';
+import corePlugins from "./corePlugins.js";
 enableStaticRendering(true);
 initializeWorker(corePlugins, {
     fetchESM: url => import(__rewriteRelativeImportExtension(url)),