@jbrowse/core 2.17.0 → 3.0.0

package/ReExports/list.js

@@ -1,16 +1,12 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-/**
- * Used by plugin build systems to determine if a module is provided by JBrowse
- * globally and thus doesn't need to be bundled. A check in ./modules.tsx makes
- * sure this is in sync with the re-exported modules.
- */
 exports.default = [
     'mobx',
     'mobx-state-tree',
     'react',
     'react/jsx-runtime',
     'react-dom',
+    'react-dom/client',
     'mobx-react',
     '@mui/x-data-grid',
     '@mui/material/utils',
@@ -62,6 +58,7 @@ exports.default = [
     '@material-ui/core/FormHelperText',
     '@material-ui/core/FormGroup',
     '@material-ui/core/Grid',
+    '@material-ui/core/Grid2',
     '@material-ui/core/Grow',
     '@material-ui/core/Icon',
     '@material-ui/core/IconButton',
@@ -171,6 +168,7 @@ exports.default = [
     '@mui/material/FormHelperText',
     '@mui/material/FormGroup',
     '@mui/material/Grid',
+    '@mui/material/Grid2',
     '@mui/material/Grow',
     '@mui/material/Icon',
     '@mui/material/IconButton',

package/ReExports/modules.d.ts

@@ -1,40 +1,43 @@
-import React from 'react';
-import * as ReactJSXRuntime from 'react/jsx-runtime';
-import * as ReactDom from 'react-dom';
-import * as mobx from 'mobx';
-import * as mst from 'mobx-state-tree';
-import * as mxreact from 'mobx-react';
+import type { LazyExoticComponent } from 'react';
+import * as React from 'react';
+import { useTheme } from '@mui/material';
 import * as MUIStyles from '@mui/material/styles';
 import * as MUIUtils from '@mui/material/utils';
 import { useGridApiContext } from '@mui/x-data-grid';
+import * as mobx from 'mobx';
+import * as mxreact from 'mobx-react';
+import * as mst from 'mobx-state-tree';
+import * as ReactJSXRuntime from 'react/jsx-runtime';
+import * as ReactDom from 'react-dom';
+import * as ReactDomClient from 'react-dom/client';
+import Plugin from '../Plugin';
+import * as Configuration from '../configuration';
 import * as BaseAdapterExports from '../data_adapters/BaseAdapter';
 import * as pluggableElementTypes from '../pluggableElementTypes';
 import * as pluggableElementTypeModels from '../pluggableElementTypes/models';
-import * as ServerSideRendererType from '../pluggableElementTypes/renderers/ServerSideRendererType';
 import * as BoxRendererType from '../pluggableElementTypes/renderers/BoxRendererType';
 import * as FeatureRendererType from '../pluggableElementTypes/renderers/FeatureRendererType';
 import * as RendererType from '../pluggableElementTypes/renderers/RendererType';
-import * as Configuration from '../configuration';
-import Plugin from '../Plugin';
+import * as ServerSideRendererType from '../pluggableElementTypes/renderers/ServerSideRendererType';
 import * as coreUi from '../ui';
 import * as coreUtil from '../util';
 import * as coreColor from '../util/color';
-import * as coreLayouts from '../util/layouts';
-import * as trackUtils from '../util/tracks';
 import * as coreIo from '../util/io';
+import * as coreLayouts from '../util/layouts';
 import * as coreMstReflection from '../util/mst-reflection';
 import * as rxjs from '../util/rxjs';
+import * as trackUtils from '../util/tracks';
 import * as mstTypes from '../util/types/mst';
 declare const libs: {
-    '@material-ui/lab/ToggleButton': React.LazyExoticComponent<import("@mui/material").ExtendButtonBase<import("@mui/material").ToggleButtonTypeMap<{}, "button">>>;
-    '@material-ui/lab/ToggleButtonGroup': React.LazyExoticComponent<typeof import("@mui/material").ToggleButtonGroup>;
-    '@material-ui/lab/Autocomplete': React.LazyExoticComponent<typeof import("@mui/material").Autocomplete>;
-    '@material-ui/lab/Alert': React.LazyExoticComponent<typeof import("@mui/material").Alert>;
+    '@material-ui/lab/ToggleButton': LazyExoticComponent<import("@mui/material").ExtendButtonBase<import("@mui/material").ToggleButtonTypeMap<{}, "button">>>;
+    '@material-ui/lab/ToggleButtonGroup': LazyExoticComponent<typeof import("@mui/material").ToggleButtonGroup>;
+    '@material-ui/lab/Autocomplete': LazyExoticComponent<typeof import("@mui/material").Autocomplete>;
+    '@material-ui/lab/Alert': LazyExoticComponent<typeof import("@mui/material").Alert>;
     '@material-ui/lab': {
-        Alert: React.LazyExoticComponent<typeof import("@mui/material").Alert>;
-        Autocomplete: React.LazyExoticComponent<typeof import("@mui/material").Autocomplete>;
-        ToggleButton: React.LazyExoticComponent<import("@mui/material").ExtendButtonBase<import("@mui/material").ToggleButtonTypeMap<{}, "button">>>;
-        ToggleButtonGroup: React.LazyExoticComponent<typeof import("@mui/material").ToggleButtonGroup>;
+        Alert: LazyExoticComponent<typeof import("@mui/material").Alert>;
+        Autocomplete: LazyExoticComponent<typeof import("@mui/material").Autocomplete>;
+        ToggleButton: LazyExoticComponent<import("@mui/material").ExtendButtonBase<import("@mui/material").ToggleButtonTypeMap<{}, "button">>>;
+        ToggleButtonGroup: LazyExoticComponent<typeof import("@mui/material").ToggleButtonGroup>;
     };
     '@jbrowse/core/Plugin': typeof Plugin;
     '@jbrowse/core/pluggableElementTypes': typeof pluggableElementTypes;
@@ -124,10 +127,11 @@ declare const libs: {
     react: typeof React;
     'react/jsx-runtime': typeof ReactJSXRuntime;
     'react-dom': typeof ReactDom;
+    'react-dom/client': typeof ReactDomClient;
     'mobx-react': typeof mxreact;
     '@mui/x-data-grid': {
         useGridApiContext: typeof useGridApiContext;
-        useGridApiRef: <Api extends import("@mui/x-data-grid").GridApiCommon = import("@mui/x-data-grid/internals").GridApiCommunity>() => React.MutableRefObject<Api>;
+        useGridApiRef: <Api extends import("@mui/x-data-grid").GridApiCommon = import("@mui/x-data-grid/internals").GridApiCommunity>() => import("@mui/x-internals/types").RefObject<Api>;
         useGridRootProps: () => import("@mui/x-data-grid/internals").DataGridProcessedProps;
     };
     '@mui/material/utils': typeof MUIUtils;
@@ -147,13 +151,13 @@ declare const libs: {
         };
     };
     '@material-ui/core': {
-        useTheme: typeof MUIStyles.useTheme;
+        useTheme: typeof useTheme;
         alpha: typeof MUIStyles.alpha;
         makeStyles: (args: any) => () => Record<string, string>;
     };
     '@mui/material': {
         alpha: typeof MUIStyles.alpha;
-        useTheme: typeof MUIStyles.useTheme;
+        useTheme: typeof useTheme;
     };
     '@mui/material/styles': {
         MUIStyles: typeof MUIStyles;

package/ReExports/modules.js

@@ -15,57 +15,67 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-/* eslint-disable react-refresh/only-export-components */
-// this is all the stuff that the pluginManager re-exports for plugins to use
-const react_1 = __importStar(require("react"));
-const ReactJSXRuntime = __importStar(require("react/jsx-runtime"));
-const ReactDom = __importStar(require("react-dom"));
-const mobx = __importStar(require("mobx"));
-const mst = __importStar(require("mobx-state-tree"));
-const mxreact = __importStar(require("mobx-react"));
-const mui_1 = require("tss-react/mui");
+const jsx_runtime_1 = require("react/jsx-runtime");
+const React = __importStar(require("react"));
+const react_1 = require("react");
+const material_1 = require("@mui/material");
 const MUIStyles = __importStar(require("@mui/material/styles"));
 const MUIUtils = __importStar(require("@mui/material/utils"));
-const material_1 = require("@mui/material");
 const x_data_grid_1 = require("@mui/x-data-grid");
-// material-ui lab
+const mobx = __importStar(require("mobx"));
+const mxreact = __importStar(require("mobx-react"));
+const mst = __importStar(require("mobx-state-tree"));
+const ReactJSXRuntime = __importStar(require("react/jsx-runtime"));
+const ReactDom = __importStar(require("react-dom"));
+const ReactDomClient = __importStar(require("react-dom/client"));
+const mui_1 = require("tss-react/mui");
+const Plugin_1 = __importDefault(require("../Plugin"));
+const Configuration = __importStar(require("../configuration"));
 const BaseAdapterExports = __importStar(require("../data_adapters/BaseAdapter"));
-const Base1DViewModel_1 = __importDefault(require("../util/Base1DViewModel"));
 const pluggableElementTypes = __importStar(require("../pluggableElementTypes"));
-const ViewType_1 = __importDefault(require("../pluggableElementTypes/ViewType"));
+const list_1 = __importDefault(require("./list"));
 const AdapterType_1 = __importDefault(require("../pluggableElementTypes/AdapterType"));
 const DisplayType_1 = __importDefault(require("../pluggableElementTypes/DisplayType"));
 const TrackType_1 = __importDefault(require("../pluggableElementTypes/TrackType"));
+const ViewType_1 = __importDefault(require("../pluggableElementTypes/ViewType"));
 const WidgetType_1 = __importDefault(require("../pluggableElementTypes/WidgetType"));
 const pluggableElementTypeModels = __importStar(require("../pluggableElementTypes/models"));
-const ServerSideRendererType = __importStar(require("../pluggableElementTypes/renderers/ServerSideRendererType"));
-const CircularChordRendererType_1 = __importDefault(require("../pluggableElementTypes/renderers/CircularChordRendererType"));
 const BoxRendererType = __importStar(require("../pluggableElementTypes/renderers/BoxRendererType"));
+const CircularChordRendererType_1 = __importDefault(require("../pluggableElementTypes/renderers/CircularChordRendererType"));
 const FeatureRendererType = __importStar(require("../pluggableElementTypes/renderers/FeatureRendererType"));
 const RendererType = __importStar(require("../pluggableElementTypes/renderers/RendererType"));
-const Configuration = __importStar(require("../configuration"));
-const Plugin_1 = __importDefault(require("../Plugin"));
+const ServerSideRendererType = __importStar(require("../pluggableElementTypes/renderers/ServerSideRendererType"));
 const coreUi = __importStar(require("../ui"));
 const coreUtil = __importStar(require("../util"));
+const Base1DViewModel_1 = __importDefault(require("../util/Base1DViewModel"));
 const coreColor = __importStar(require("../util/color"));
-const coreLayouts = __importStar(require("../util/layouts"));
-const trackUtils = __importStar(require("../util/tracks"));
 const coreIo = __importStar(require("../util/io"));
+const coreLayouts = __importStar(require("../util/layouts"));
 const coreMstReflection = __importStar(require("../util/mst-reflection"));
 const rxjs = __importStar(require("../util/rxjs"));
+const trackUtils = __importStar(require("../util/tracks"));
 const mstTypes = __importStar(require("../util/types/mst"));
-const list_1 = __importDefault(require("./list"));
 const Entries = {
     Accordion: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/Accordion')))),
     AccordionActions: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/AccordionActions')))),
@@ -109,6 +119,7 @@ const Entries = {
     FormHelperText: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/FormHelperText')))),
     FormGroup: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/FormGroup')))),
     Grid: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/Grid')))),
+    Grid2: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/Grid2')))),
     Grow: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/Grow')))),
     Icon: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/Icon')))),
     IconButton: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/IconButton')))),
@@ -178,8 +189,7 @@ const Entries = {
     Typography: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/Typography')))),
 };
 const LazyMUICore = Object.fromEntries(Object.entries(Entries).map(([key, ReactComponent]) => {
-    const Component = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: null },
-        react_1.default.createElement(ReactComponent, { ...props, ref: ref }))));
+    const Component = (0, react_1.forwardRef)((props, ref) => ((0, jsx_runtime_1.jsx)(react_1.Suspense, { fallback: null, children: (0, jsx_runtime_1.jsx)(ReactComponent, { ...props, ref: ref }) })));
     Component.displayName = key;
     return [key, Component];
 }));
@@ -346,26 +356,23 @@ const DataGridEntries = {
     }))),
 };
 const LazyDataGridComponents = Object.fromEntries(Object.entries(DataGridEntries).map(([key, ReactComponent]) => {
-    const Component = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: null },
-        react_1.default.createElement(ReactComponent, { ...props, ref: ref }))));
+    const Component = (0, react_1.forwardRef)((props, ref) => ((0, jsx_runtime_1.jsx)(react_1.Suspense, { fallback: null, children: (0, jsx_runtime_1.jsx)(ReactComponent, { ...props, ref: ref }) })));
     Component.displayName = key;
     return [key, Component];
 }));
-const LazyAttributes = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: null },
-    react_1.default.createElement(Attributes, { ...props, ref: ref }))));
+const LazyAttributes = (0, react_1.forwardRef)((props, ref) => ((0, jsx_runtime_1.jsx)(react_1.Suspense, { fallback: null, children: (0, jsx_runtime_1.jsx)(Attributes, { ...props, ref: ref }) })));
 LazyAttributes.displayName = 'Attributes';
-const LazyFeatureDetails = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: null },
-    react_1.default.createElement(FeatureDetails, { ...props, ref: ref }))));
+const LazyFeatureDetails = (0, react_1.forwardRef)((props, ref) => ((0, jsx_runtime_1.jsx)(react_1.Suspense, { fallback: null, children: (0, jsx_runtime_1.jsx)(FeatureDetails, { ...props, ref: ref }) })));
 LazyFeatureDetails.displayName = 'FeatureDetails';
-const LazyBaseCard = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: null },
-    react_1.default.createElement(BaseCard, { ...props, ref: ref }))));
+const LazyBaseCard = (0, react_1.forwardRef)((props, ref) => ((0, jsx_runtime_1.jsx)(react_1.Suspense, { fallback: null, children: (0, jsx_runtime_1.jsx)(BaseCard, { ...props, ref: ref }) })));
 LazyBaseCard.displayName = 'BaseCard';
 const libs = {
     mobx,
     'mobx-state-tree': mst,
-    react: react_1.default,
+    react: React,
     'react/jsx-runtime': ReactJSXRuntime,
     'react-dom': ReactDom,
+    'react-dom/client': ReactDomClient,
     'mobx-react': mxreact,
     '@mui/x-data-grid': {
         useGridApiContext: x_data_grid_1.useGridApiContext,
@@ -373,7 +380,6 @@ const libs = {
         useGridRootProps: x_data_grid_1.useGridRootProps,
         ...LazyDataGridComponents,
     },
-    // special case so plugins can easily use @mui/icons-material; don't remove
     '@mui/material/utils': MUIUtils,
     '@material-ui/core/utils': MUIUtils,
     'tss-react/mui': { makeStyles: mui_1.makeStyles },
@@ -391,8 +397,6 @@ const libs = {
         alpha: MUIStyles.alpha,
         useTheme: MUIStyles.useTheme,
     },
-    // end special case
-    // material-ui subcomponents, should get rid of these
     '@mui/material/styles': {
         MUIStyles,
         makeStyles: (args) => {
@@ -409,7 +413,6 @@ const libs = {
     },
     ...MaterialPrefixMUI,
     ...MuiPrefixMUI,
-    // these are core in @mui/material, but used to be in @material-ui/lab
     '@material-ui/lab/ToggleButton': Entries.ToggleButton,
     '@material-ui/lab/ToggleButtonGroup': Entries.ToggleButtonGroup,
     '@material-ui/lab/Autocomplete': Entries.Autocomplete,
@@ -452,8 +455,6 @@ const libs = {
     '@jbrowse/core/data_adapters/BaseAdapter': BaseAdapterExports,
 };
 const libsList = Object.keys(libs);
-// make sure that all the items in the ReExports/list array (used by build
-// systems and such) are included here, and vice versa
 const inLibsOnly = libsList.filter(mod => !list_1.default.includes(mod));
 if (inLibsOnly.length > 0) {
     throw new Error(`The following modules are in the modules libs, but not the re-exports list: ${inLibsOnly.join(', ')}`);

package/TextSearch/BaseResults.d.ts

@@ -1,6 +1,6 @@
-import React from 'react';
-import TextSearchAdapterType from '../pluggableElementTypes/TextSearchAdapterType';
-import { SearchType } from '../data_adapters/BaseAdapter';
+import type React from 'react';
+import type { SearchType } from '../data_adapters/BaseAdapter';
+import type TextSearchAdapterType from '../pluggableElementTypes/TextSearchAdapterType';
 export interface BaseResultArgs {
     label: string;
     displayString?: string;
@@ -30,7 +30,7 @@ export default class BaseResult {
     constructor(args: BaseResultArgs);
     getLabel(): string;
     getDisplayString(): string;
-    getRenderingComponent(): React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+    getRenderingComponent(): React.ReactElement<unknown, string | React.JSXElementConstructor<any>> | undefined;
     getTrackId(): string | undefined;
     getScore(): number;
     updateScore(newScore: number): number;

package/TextSearch/TextSearchManager.d.ts

@@ -1,8 +1,8 @@
-import BaseResult from './BaseResults';
-import PluginManager from '../PluginManager';
 import QuickLRU from '../util/QuickLRU';
-import { BaseTextSearchAdapter, BaseTextSearchArgs } from '../data_adapters/BaseAdapter';
-import { AnyConfigurationModel } from '../configuration';
+import type BaseResult from './BaseResults';
+import type PluginManager from '../PluginManager';
+import type { AnyConfigurationModel } from '../configuration';
+import type { BaseTextSearchAdapter, BaseTextSearchArgs } from '../data_adapters/BaseAdapter';
 export interface SearchScope {
     includeAggregateIndexes: boolean;
     assemblyName: string;
@@ -28,18 +28,6 @@ export default class TextSearchManager {
             [x: string]: any;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>)[];
-    /**
-     * Returns list of relevant results given a search query and options
-     *
-     * @param args - search options/arguments include: search query limit of
-     * results to return, searchType...prefix | full | exact", etc.
-     */
     search(args: BaseTextSearchArgs, searchScope: SearchScope, rankFn: (results: BaseResult[]) => BaseResult[]): Promise<BaseResult[]>;
-    /**
-     * Returns array of revelevant and sorted results
-     * @param results - array of results from all text search adapters
-     * @param rankFn - function that updates results scores
-     * based on more relevance
-     */
     sortResults(results: BaseResult[], rankFn: (results: BaseResult[]) => BaseResult[]): BaseResult[];
 }

package/TextSearch/TextSearchManager.js

@@ -3,8 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const QuickLRU_1 = __importDefault(require("../util/QuickLRU"));
 const configuration_1 = require("../configuration");
+const QuickLRU_1 = __importDefault(require("../util/QuickLRU"));
 class TextSearchManager {
     constructor(pluginManager) {
         this.pluginManager = pluginManager;
@@ -53,23 +53,11 @@ class TextSearchManager {
         })
             .map(conf => conf.textSearching.textSearchAdapter);
     }
-    /**
-     * Returns list of relevant results given a search query and options
-     *
-     * @param args - search options/arguments include: search query limit of
-     * results to return, searchType...prefix | full | exact", etc.
-     */
     async search(args, searchScope, rankFn) {
         const adapters = await this.loadTextSearchAdapters(searchScope);
         const results = await Promise.all(adapters.map(a => a.searchIndex(args)));
         return this.sortResults(results.flat(), rankFn);
     }
-    /**
-     * Returns array of revelevant and sorted results
-     * @param results - array of results from all text search adapters
-     * @param rankFn - function that updates results scores
-     * based on more relevance
-     */
     sortResults(results, rankFn) {
         return rankFn(results.sort((a, b) => -b.getLabel().localeCompare(a.getLabel()))).sort((r1, r2) => r1.getScore() - r2.getScore());
     }

package/assemblyManager/assembly.d.ts

@@ -1,8 +1,8 @@
-import { Instance, IAnyType } from 'mobx-state-tree';
-import { BaseOptions } from '../data_adapters/BaseAdapter';
-import PluginManager from '../PluginManager';
-import { Region, Feature } from '../util';
-import RpcManager from '../rpc/RpcManager';
+import type PluginManager from '../PluginManager';
+import type { BaseOptions } from '../data_adapters/BaseAdapter';
+import type RpcManager from '../rpc/RpcManager';
+import type { Feature, Region } from '../util';
+import type { IAnyType, Instance } from 'mobx-state-tree';
 type AdapterConf = Record<string, unknown>;
 type RefNameAliases = Record<string, string>;
 export interface RefNameMap {
@@ -15,13 +15,7 @@ export interface BasicRegion {
     refName: string;
     assemblyName: string;
 }
-/**
- * #stateModel Assembly
- */
 export default function assemblyFactory(assemblyConfigType: IAnyType, pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    /**
-     * #property
-     */
     configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
 }, {
     error: unknown;
@@ -31,132 +25,43 @@ export default function assemblyFactory(assemblyConfigType: IAnyType, pluginMana
     lowerCaseRefNameAliases: RefNameAliases | undefined;
     cytobands: Feature[] | undefined;
 } & {
-    /**
-     * #method
-     */
     getConf(arg: string): any;
 } & {
-    /**
-     * #getter
-     */
     readonly initialized: boolean;
-    /**
-     * #getter
-     */
     readonly name: string;
-    /**
-     * #getter
-     */
     readonly regions: BasicRegion[] | undefined;
-    /**
-     * #getter
-     */
     readonly aliases: string[];
-    /**
-     * #getter
-     */
     readonly displayName: string | undefined;
-    /**
-     * #getter
-     */
     hasName(name: string): boolean;
-    /**
-     * #getter
-     */
     readonly allAliases: string[];
-    /**
-     * #getter
-     * note: lowerCaseRefNameAliases not included here: this allows the list
-     * of refnames to be just the "normal casing", but things like
-     * getCanonicalRefName can resolve a lower-case name if needed
-     */
     readonly allRefNames: string[] | undefined;
-    /**
-     * #getter
-     */
     readonly lowerCaseRefNames: string[] | undefined;
-    /**
-     * #getter
-     */
     readonly allRefNamesWithLowerCase: string[] | undefined;
-    /**
-     * #getter
-     */
     readonly rpcManager: RpcManager;
-    /**
-     * #getter
-     */
     readonly refNameColors: string[];
 } & {
-    /**
-     * #getter
-     */
     readonly refNames: string[] | undefined;
 } & {
-    /**
-     * #method
-     */
     getCanonicalRefName(refName: string): string | undefined;
-    /**
-     * #method
-     */
     getRefNameColor(refName: string): string | undefined;
-    /**
-     * #method
-     */
     isValidRefName(refName: string): boolean;
 } & {
-    /**
-     * #action
-     */
     setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
         regions: Region[];
         refNameAliases: RefNameAliases;
         lowerCaseRefNameAliases: RefNameAliases;
         cytobands: Feature[];
     }): void;
-    /**
-     * #action
-     */
     setError(e: unknown): void;
-    /**
-     * #action
-     */
     setRegions(regions: Region[]): void;
-    /**
-     * #action
-     */
     setRefNameAliases(aliases: RefNameAliases, lowerCaseAliases: RefNameAliases): void;
-    /**
-     * #action
-     */
     setCytobands(cytobands: Feature[]): void;
-    /**
-     * #action
-     */
     setLoadingP(p?: Promise<void>): void;
-    /**
-     * #action
-     */
     load(): Promise<void>;
-    /**
-     * #action
-     */
     loadPre(): Promise<void>;
 } & {
-    /**
-     * #method
-     */
     getAdapterMapEntry(adapterConf: AdapterConf, options: BaseOptions): Promise<RefNameMap>;
-    /**
-     * #method
-     * get Map of `canonical-name -> adapter-specific-name`
-     */
     getRefNameMapForAdapter(adapterConf: AdapterConf, opts: BaseOptions): Promise<RefNameAliases>;
-    /**
-     * #method
-     * get Map of `adapter-specific-name -> canonical-name`
-     */
     getReverseRefNameMapForAdapter(adapterConf: AdapterConf, opts: BaseOptions): Promise<RefNameAliases>;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type AssemblyModel = ReturnType<typeof assemblyFactory>;