@jbrowse/app-core 2.6.1

package/dist/ui/App/ViewLauncher.js

@@ -0,0 +1,50 @@
+"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 (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importStar(require("react"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
+// locals
+const util_1 = require("@jbrowse/core/util");
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    selectPaper: {
+        padding: theme.spacing(4),
+    },
+}));
+const ViewLauncher = (0, mobx_react_1.observer)(({ session }) => {
+    var _a;
+    const { classes } = useStyles();
+    const { pluginManager } = (0, util_1.getEnv)(session);
+    const viewTypes = pluginManager.getElementTypeRecord('view').all();
+    const [value, setValue] = (0, react_1.useState)((_a = viewTypes[0]) === null || _a === void 0 ? void 0 : _a.name);
+    return (react_1.default.createElement(material_1.Paper, { className: classes.selectPaper },
+        react_1.default.createElement(material_1.Typography, null, "Select a view to launch"),
+        react_1.default.createElement(material_1.FormControl, { style: { margin: 2 } },
+            react_1.default.createElement(material_1.Select, { value: value, onChange: event => setValue(event.target.value) }, viewTypes.map(({ displayName, name }) => (react_1.default.createElement(material_1.MenuItem, { key: name, value: name }, displayName))))),
+        react_1.default.createElement(material_1.FormControl, { style: { margin: 2 } },
+            react_1.default.createElement(material_1.Button, { onClick: () => session.addView(value, {}), variant: "contained", color: "primary" }, "Launch view"))));
+});
+exports.default = ViewLauncher;

package/dist/ui/App/ViewMenu.d.ts

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+import React from 'react';
+import { SvgIconProps, IconButtonProps as IconButtonPropsType } from '@mui/material';
+import { IBaseViewModel } from '@jbrowse/core/pluggableElementTypes/models';
+declare const ViewMenu: ({ model, IconButtonProps, IconProps, }: {
+    model: IBaseViewModel;
+    IconButtonProps?: IconButtonPropsType | undefined;
+    IconProps: SvgIconProps;
+}) => React.JSX.Element | null;
+export default ViewMenu;

package/dist/ui/App/ViewMenu.js

@@ -0,0 +1,38 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const mobx_react_1 = require("mobx-react");
+const util_1 = require("@jbrowse/core/util");
+const CascadingMenuButton_1 = __importDefault(require("@jbrowse/core/ui/CascadingMenuButton"));
+// icons
+const Menu_1 = __importDefault(require("@mui/icons-material/Menu"));
+const ArrowDownward_1 = __importDefault(require("@mui/icons-material/ArrowDownward"));
+const ArrowUpward_1 = __importDefault(require("@mui/icons-material/ArrowUpward"));
+const ViewMenu = (0, mobx_react_1.observer)(function ({ model, IconButtonProps, IconProps, }) {
+    const { menuItems } = model;
+    const session = (0, util_1.getSession)(model);
+    const items = [
+        ...(session.views.length > 1
+            ? [
+                {
+                    label: 'Move view up',
+                    icon: ArrowUpward_1.default,
+                    onClick: () => session.moveViewUp(model.id),
+                },
+                {
+                    label: 'Move view down',
+                    icon: ArrowDownward_1.default,
+                    onClick: () => session.moveViewDown(model.id),
+                },
+            ]
+            : []),
+        // <=1.3.3 didn't use a function, so check as value also
+        ...((typeof menuItems === 'function' ? menuItems() : menuItems) || []),
+    ];
+    return items.length ? (react_1.default.createElement(CascadingMenuButton_1.default, { menuItems: items, "data-testid": "view_menu_icon" },
+        react_1.default.createElement(Menu_1.default, { ...IconProps, fontSize: "small" }))) : null;
+});
+exports.default = ViewMenu;

package/dist/ui/App/ViewPanel.d.ts

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+import React from 'react';
+import { AbstractViewModel, SessionWithDrawerWidgets } from '@jbrowse/core/util';
+import { SnackbarMessage } from '@jbrowse/core/ui/SnackbarModel';
+import { MenuItem as JBMenuItem } from '@jbrowse/core/ui/Menu';
+type AppSession = SessionWithDrawerWidgets & {
+    savedSessionNames: string[];
+    menus: {
+        label: string;
+        menuItems: JBMenuItem[];
+    }[];
+    snackbarMessages: SnackbarMessage[];
+    renameCurrentSession: (arg: string) => void;
+    popSnackbarMessage: () => unknown;
+};
+declare const ViewPanel: ({ view, session, }: {
+    view: AbstractViewModel;
+    session: AppSession;
+}) => React.JSX.Element;
+export default ViewPanel;

package/dist/ui/App/ViewPanel.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 (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __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 });
+const react_1 = __importStar(require("react"));
+const react_error_boundary_1 = require("react-error-boundary");
+const mobx_react_1 = require("mobx-react");
+// locals
+const util_1 = require("@jbrowse/core/util");
+// ui elements
+const ErrorMessage_1 = __importDefault(require("@jbrowse/core/ui/ErrorMessage"));
+const LoadingEllipses_1 = __importDefault(require("@jbrowse/core/ui/LoadingEllipses"));
+// locals
+const ViewContainer_1 = __importDefault(require("./ViewContainer"));
+const ViewPanel = (0, mobx_react_1.observer)(function ({ view, session, }) {
+    const { pluginManager } = (0, util_1.getEnv)(session);
+    const viewType = pluginManager.getViewType(view.type);
+    if (!viewType) {
+        throw new Error(`unknown view type ${view.type}`);
+    }
+    const { ReactComponent } = viewType;
+    return (react_1.default.createElement(ViewContainer_1.default, { view: view, onClose: () => session.removeView(view), onMinimize: () => view.setMinimized(!view.minimized) }, !view.minimized ? (react_1.default.createElement(react_error_boundary_1.ErrorBoundary, { FallbackComponent: ({ error }) => react_1.default.createElement(ErrorMessage_1.default, { error: error }) },
+        react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement(LoadingEllipses_1.default, { variant: "h6" }) },
+            react_1.default.createElement(ReactComponent, { model: view, session: session })))) : (false)));
+});
+exports.default = ViewPanel;

package/dist/ui/App/index.d.ts

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+export * from './App';

package/dist/ui/App/index.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 __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);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+__exportStar(require("./App"), exports);

package/dist/ui/index.d.ts

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+export * from './App';

package/dist/ui/index.js

@@ -0,0 +1,17 @@
+"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 __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);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+__exportStar(require("./App"), exports);

package/esm/Assemblies/SessionAssembliesMixin.d.ts

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+import PluginManager from '@jbrowse/core/PluginManager';
+import { AnyConfiguration } from '@jbrowse/core/configuration';
+import { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager';
+/**
+ * #stateModel SessionAssembliesMixin
+ * #category root
+ */
+export declare function SessionAssembliesMixin(pluginManager: PluginManager, assemblyConfigSchemasType: BaseAssemblyConfigSchema): import("mobx-state-tree").IModelType<{
+    /**
+     * #property
+     */
+    sessionAssemblies: import("mobx-state-tree").IArrayType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        aliases: {
+            type: string;
+            defaultValue: never[];
+            description: string;
+        };
+        sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+        refNameColors: {
+            type: string;
+            defaultValue: never[];
+            description: string;
+        };
+        refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            adapter: import("mobx-state-tree").IAnyModelType;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            adapter: import("mobx-state-tree").IAnyModelType;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        displayName: {
+            type: string;
+            defaultValue: string;
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name">>>;
+}, {
+    /**
+     * #action
+     */
+    addSessionAssembly(conf: AnyConfiguration): {
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        aliases: {
+            type: string;
+            defaultValue: never[];
+            description: string;
+        };
+        sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+        refNameColors: {
+            type: string;
+            defaultValue: never[];
+            description: string;
+        };
+        refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            adapter: import("mobx-state-tree").IAnyModelType;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            adapter: import("mobx-state-tree").IAnyModelType;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        displayName: {
+            type: string;
+            defaultValue: string;
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name">>>;
+    /**
+     * #action
+     */
+    removeSessionAssembly(assemblyName: string): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/Assemblies/SessionAssembliesMixin.js

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+import { types } from 'mobx-state-tree';
+/**
+ * #stateModel SessionAssembliesMixin
+ * #category root
+ */
+export function SessionAssembliesMixin(pluginManager, assemblyConfigSchemasType) {
+    return types
+        .model({
+        /**
+         * #property
+         */
+        sessionAssemblies: types.array(assemblyConfigSchemasType),
+    })
+        .actions(s => {
+        const self = s;
+        return {
+            /**
+             * #action
+             */
+            addSessionAssembly(conf) {
+                const asm = self.sessionAssemblies.find(f => f.name === conf.name);
+                if (asm) {
+                    console.warn(`Assembly ${conf.name} already exists`);
+                    return asm;
+                }
+                const length = self.sessionAssemblies.push(conf);
+                return self.sessionAssemblies[length - 1];
+            },
+            /**
+             * #action
+             */
+            removeSessionAssembly(assemblyName) {
+                const elt = self.sessionAssemblies.find(a => a.name === assemblyName);
+                if (elt) {
+                    self.sessionAssemblies.remove(elt);
+                }
+            },
+        };
+    });
+}

package/esm/Assemblies/TemporaryAssembliesMixin.d.ts

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+import PluginManager from '@jbrowse/core/PluginManager';
+import { AnyConfiguration } from '@jbrowse/core/configuration';
+/**
+ * #stateModel TemporaryAssembliesMixin
+ * #category root
+ */
+export declare function TemporaryAssembliesMixin(pluginManager: PluginManager, assemblyConfigSchemasType?: import("mobx-state-tree").IType<any, any, any>): import("mobx-state-tree").IModelType<{
+    /**
+     * #property
+     */
+    temporaryAssemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<any, any, any>>;
+}, {
+    /**
+     * #action
+     * used for read vs ref type assemblies.
+     */
+    addTemporaryAssembly(conf: AnyConfiguration): any;
+    /**
+     * #action
+     */
+    removeTemporaryAssembly(name: string): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/Assemblies/TemporaryAssembliesMixin.js

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+import { types } from 'mobx-state-tree';
+/**
+ * #stateModel TemporaryAssembliesMixin
+ * #category root
+ */
+export function TemporaryAssembliesMixin(pluginManager, assemblyConfigSchemasType = types.frozen()) {
+    return types
+        .model({
+        /**
+         * #property
+         */
+        temporaryAssemblies: types.array(assemblyConfigSchemasType),
+    })
+        .actions(s => {
+        const self = s;
+        return {
+            /**
+             * #action
+             * used for read vs ref type assemblies.
+             */
+            addTemporaryAssembly(conf) {
+                const asm = self.temporaryAssemblies.find(f => f.name === conf.name);
+                if (asm) {
+                    console.warn(`Assembly ${conf.name} was already existing`);
+                    return asm;
+                }
+                const length = self.temporaryAssemblies.push(conf);
+                return self.temporaryAssemblies[length - 1];
+            },
+            /**
+             * #action
+             */
+            removeTemporaryAssembly(name) {
+                const elt = self.temporaryAssemblies.find(a => a.name === name);
+                if (elt) {
+                    self.temporaryAssemblies.remove(elt);
+                }
+            },
+        };
+    });
+}

package/esm/Assemblies/index.d.ts

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+export * from './SessionAssembliesMixin';
+export * from './TemporaryAssembliesMixin';

package/esm/Assemblies/index.js

@@ -0,0 +1,2 @@
+export * from './SessionAssembliesMixin';
+export * from './TemporaryAssembliesMixin';

package/esm/HistoryManagement/index.d.ts

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+/**
+ * #stateModel HistoryManagementMixin
+ * #category root
+ */
+export declare function HistoryManagementMixin(): import("mobx-state-tree").IModelType<{
+    /**
+     * #property
+     * used for undo/redo
+     */
+    history: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
+        undoIdx: import("mobx-state-tree").IType<number | undefined, number, number>;
+        targetPath: import("mobx-state-tree").IType<string | undefined, string, string>;
+    }, {
+        history: unknown[];
+        notTrackingUndo: boolean;
+    } & {
+        readonly canUndo: boolean;
+        readonly canRedo: boolean;
+    } & {
+        stopTrackingUndo(): void;
+        resumeTrackingUndo(): void;
+        addUndoState(todos: unknown): void;
+        beforeDestroy(): void;
+        initialize(): void;
+        undo(): void;
+        redo(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+}, {
+    afterCreate(): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/HistoryManagement/index.js

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+import TimeTraveller from '@jbrowse/core/util/TimeTraveller';
+import { autorun } from 'mobx';
+import { addDisposer, types } from 'mobx-state-tree';
+/**
+ * #stateModel HistoryManagementMixin
+ * #category root
+ */
+export function HistoryManagementMixin() {
+    return types
+        .model({
+        /**
+         * #property
+         * used for undo/redo
+         */
+        history: types.optional(TimeTraveller, { targetPath: '../session' }),
+    })
+        .actions(self => ({
+        afterCreate() {
+            document.addEventListener('keydown', e => {
+                if (self.history.canRedo &&
+                    // ctrl+shift+z or cmd+shift+z
+                    (((e.ctrlKey || e.metaKey) && e.shiftKey && e.code === 'KeyZ') ||
+                        // ctrl+y
+                        (e.ctrlKey && !e.shiftKey && e.code === 'KeyY'))) {
+                    self.history.redo();
+                }
+                if (self.history.canUndo &&
+                    // ctrl+z or cmd+z
+                    (e.ctrlKey || e.metaKey) &&
+                    !e.shiftKey &&
+                    e.code === 'KeyZ') {
+                    self.history.undo();
+                }
+            });
+            addDisposer(self, autorun(() => {
+                const { session } = self;
+                if (session) {
+                    // we use a specific initialization routine after session is
+                    // created to get it to start tracking itself sort of related
+                    // issue here
+                    // https://github.com/mobxjs/mobx-state-tree/issues/1089#issuecomment-441207911
+                    self.history.initialize();
+                }
+            }));
+        },
+    }));
+}

package/esm/JBrowseConfig/index.d.ts

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+import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import { PluginDefinition } from '@jbrowse/core/PluginLoader';
+import PluginManager from '@jbrowse/core/PluginManager';
+/**
+ * #config JBrowseRootConfig
+ * #category root
+ * configuration in a config.json/file.jbrowse
+ */
+export declare function JBrowseConfigF({ pluginManager, assemblyConfigSchema, }: {
+    pluginManager: PluginManager;
+    assemblyConfigSchema: AnyConfigurationSchemaType;
+}): import("mobx-state-tree").IModelType<{
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        /**
+         * #slot configuration.rpc
+         */
+        rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            defaultDriver: {
+                type: string;
+                description: string; /**
+                 * #slot configuration.formatDetails.feature
+                 */
+                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>>;
+        /**
+         * #slot configuration.highResolutionScaling
+         */
+        highResolutionScaling: {
+            type: string;
+            defaultValue: number;
+        };
+        formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            /**
+             * #slot configuration.formatDetails.feature
+             */
+            feature: {
+                type: string;
+                description: string;
+                defaultValue: {};
+                contextVariable: string[];
+            };
+            /**
+             * #slot configuration.formatDetails.subfeatures
+             */
+            subfeatures: {
+                type: string;
+                description: string;
+                defaultValue: {};
+                contextVariable: string[];
+            };
+            /**
+             * #slot configuration.formatDetails.depth
+             */
+            depth: {
+                type: string;
+                defaultValue: number;
+                description: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            /**
+             * #slot configuration.formatAbout.config
+             */
+            config: {
+                type: string;
+                description: string;
+                defaultValue: {};
+                contextVariable: string[];
+            };
+            /**
+             * #slot configuration.formatAbout.hideUris
+             */
+            hideUris: {
+                type: string;
+                defaultValue: boolean;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        shareURL: {
+            type: string;
+            defaultValue: string;
+        };
+        /**
+         * #slot configuration.disableAnalytics
+         */
+        disableAnalytics: {
+            type: string;
+            defaultValue: boolean;
+        };
+        /**
+         * #slot configuration.theme
+         */
+        theme: {
+            type: string;
+            defaultValue: {};
+        };
+        /**
+         * #slot configuration.extraThemes
+         */
+        extraThemes: {
+            type: string;
+            defaultValue: {};
+        };
+        /**
+         * #slot configuration.logoPath
+         */
+        logoPath: {
+            type: string;
+            defaultValue: {
+                uri: string;
+                locationType: string;
+            };
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    /**
+     * #slot
+     * defines plugins of the format
+     * ```typescript
+     * type PluginDefinition=
+     *    { umdUrl: string, name:string } |
+     *    { url: string, name: string } |
+     *    { esmUrl: string } |
+     *    { cjsUrl: string } |
+     *    { umdLoc: { uri: string } } |
+     *    { esmLoc: { uri: string } } |
+     * ```
+     */
+    plugins: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<PluginDefinition, PluginDefinition, PluginDefinition>>;
+    /**
+     * #slot
+     * configuration of the assemblies in the instance, see BaseAssembly
+     */
+    assemblies: import("mobx-state-tree").IArrayType<AnyConfigurationSchemaType>;
+    /**
+     * #slot
+     * track configuration is an array of track config schemas. multiple
+     * instances of a track can exist that use the same configuration
+     */
+    tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    /**
+     * #slot
+     * configuration for internet accounts, see InternetAccounts
+     */
+    internetAccounts: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    /**
+     * #slot
+     */
+    aggregateTextSearchAdapters: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    /**
+     * #slot
+     */
+    connections: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    /**
+     * #slot
+     */
+    defaultSession: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<any, any, any>, [undefined]>;
+}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;