@jbrowse/react-app2 3.7.0 → 4.0.1

package/esm/JBrowseApp/JBrowseApp.d.ts

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

package/esm/JBrowseApp/JBrowseApp.js

@@ -2,16 +2,16 @@ 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 { makeStyles } from '@jbrowse/core/util/tss-react';
 import { ScopedCssBaseline, ThemeProvider } from '@mui/material';
 import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-const App = lazy(() => import('./AppReExport'));
+const App = lazy(() => import("./AppReExport.js"));
 const useStyles = makeStyles()({
     avoidParentStyle: {
         all: 'initial',
     },
 });
-const JBrowseApp = observer(function ({ viewState }) {
+const JBrowseApp = observer(function JBrowseApp({ viewState, }) {
     const { classes } = useStyles();
     const session = viewState.session;
     const theme = createJBrowseTheme(getConf(viewState.jbrowse, 'theme'));

package/esm/JBrowseApp/index.d.ts

@@ -1 +1 @@
-export { default } from './JBrowseApp';
+export { default } from './JBrowseApp.tsx';

package/esm/JBrowseApp/index.js

@@ -1 +1 @@
-export { default } from './JBrowseApp';
+export { default } from "./JBrowseApp.js";

package/esm/components/PreferencesDialog.d.ts

@@ -9,6 +9,8 @@ declare const PreferencesDialog: ({ handleClose, session, }: {
         stickyViewHeaders: boolean;
         setStickyViewHeaders(sticky: boolean): void;
         setThemeName: (arg: string) => void;
+        useWorkspaces: boolean;
+        setUseWorkspaces(useWorkspaces: boolean): void;
     };
 }) => import("react/jsx-runtime").JSX.Element;
 export default PreferencesDialog;

package/esm/components/PreferencesDialog.js

@@ -1,19 +1,21 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { Dialog } from '@jbrowse/core/ui';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
 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 PreferencesDialog = observer(function PreferencesDialog({ 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" }) })] }));
+                        }, children: Object.entries(session.allThemes()).map(([key, val]) => (_jsx(MenuItem, { value: key, children: val.name || '(Unknown name)' }, key))) }), _jsxs(FormGroup, { children: [_jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: session.stickyViewHeaders }), onChange: (_, checked) => {
+                                    session.setStickyViewHeaders(checked);
+                                }, label: "Keep view header visible" }), _jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: session.useWorkspaces }), onChange: (_, checked) => {
+                                    session.setUseWorkspaces(checked);
+                                }, label: "Use workspaces (tabbed/tiled view layout)" })] })] }), _jsx(DialogActions, { children: _jsx(Button, { onClick: handleClose, children: "Close" }) })] }));
 });
 export default PreferencesDialog;

package/esm/corePlugins.d.ts

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

package/esm/corePlugins.js

@@ -3,6 +3,7 @@ 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 Canvas from '@jbrowse/plugin-canvas';
 import CircularView from '@jbrowse/plugin-circular-view';
 import ComparativeAdapters from '@jbrowse/plugin-comparative-adapters';
 import Config from '@jbrowse/plugin-config';
@@ -22,12 +23,11 @@ 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,
+    Canvas,
     LinearGenomeView,
     Alignments,
     Authentication,

package/esm/createModel.d.ts

@@ -1,17 +1,17 @@
 import PluginManager from '@jbrowse/core/PluginManager';
 import type { PluginConstructor } from '@jbrowse/core/Plugin';
-import type { Instance } from 'mobx-state-tree';
+import type { Instance } from '@jbrowse/mobx-state-tree';
 export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
     runtimePlugins: PluginConstructor[];
     makeWorkerInstance?: () => Worker;
 }): {
-    model: import("mobx-state-tree").IModelType<{
-        jbrowse: import("mobx-state-tree").IAnyType;
-        session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").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<import("mobx-state-tree").IAnyType>>;
+    model: import("@jbrowse/mobx-state-tree").IModelType<{
+        jbrowse: import("@jbrowse/mobx-state-tree").IAnyType;
+        session: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").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<import("@jbrowse/mobx-state-tree").IAnyType>>;
             }, {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
@@ -19,6 +19,7 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -42,9 +43,10 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                 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[];
@@ -59,6 +61,7 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                     [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>;
@@ -77,17 +80,18 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                     [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;
@@ -111,9 +115,10 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                 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[];
@@ -128,6 +133,7 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                     [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>;
@@ -146,8 +152,8 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                     [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<import("mobx-state-tree").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<import("@jbrowse/mobx-state-tree").IAnyType>>;
             }, {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
@@ -155,6 +161,7 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -178,9 +185,10 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                 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[];
@@ -195,6 +203,7 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                     [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>;
@@ -213,19 +222,20 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                     [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;
@@ -249,9 +259,10 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                 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[];
@@ -266,6 +277,7 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                     [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>;
@@ -284,8 +296,8 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                     [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<import("mobx-state-tree").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<import("@jbrowse/mobx-state-tree").IAnyType>>;
             }, {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
@@ -293,6 +305,7 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -316,9 +329,10 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                 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[];
@@ -333,6 +347,7 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                     [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>;
@@ -351,20 +366,21 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                     [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: import("@jbrowse/core/rpc/RpcManager").default;
         } & {
             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;
@@ -388,9 +404,10 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                 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[];
@@ -405,6 +422,7 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                     [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>;
@@ -423,8 +441,8 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                     [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<import("mobx-state-tree").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<import("@jbrowse/mobx-state-tree").IAnyType>>;
             }, {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
@@ -432,6 +450,7 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                 refNameAliases: {
                     [x: string]: string;
                 } | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
@@ -455,9 +474,10 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                 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[];
@@ -472,6 +492,7 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                     [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>;
@@ -490,21 +511,15 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
                     [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;
@@ -512,9 +527,9 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
             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<import("mobx-state-tree").IAnyType>;
+        internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
     }, {
         rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         adminMode: boolean;
@@ -523,7 +538,7 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
         pluginManager: PluginManager;
     } & {
         setError(error: unknown): void;
-        setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
+        setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
         setDefaultSession(): void;
         setSessionPath(path: string): void;
         renameCurrentSession(newName: string): void;
@@ -551,14 +566,14 @@ export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
         error: unknown;
     } & {
         afterCreate(): void;
-        setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("@jbrowse/product-core").BaseSessionType>): void;
+        setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/product-core").BaseSessionType>): void;
         setPluginsUpdated(flag: boolean): void;
         setDefaultSession(): void;
         renameCurrentSession(sessionName: string): void;
         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>;
     pluginManager: PluginManager;
 };
 export type ViewStateModel = ReturnType<typeof createModel>['model'];

package/esm/createModel.js

@@ -1,7 +1,7 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-import corePlugins from './corePlugins';
-import createRootModel from './rootModel/rootModel';
-import sessionModelFactory from './sessionModel';
+import corePlugins from "./corePlugins.js";
+import createRootModel from "./rootModel/rootModel.js";
+import sessionModelFactory from "./sessionModel/index.js";
 export default function createModel({ runtimePlugins, makeWorkerInstance = () => {
     throw new Error('no makeWorkerInstance supplied');
 }, }) {