@jbrowse/plugin-data-management 3.7.0 → 4.0.0

package/esm/HierarchicalTrackSelectorWidget/facetedModel.js

@@ -1,11 +1,11 @@
 import { readConfObject } from '@jbrowse/core/configuration';
 import { getSession, localStorageGetBoolean, localStorageGetNumber, } from '@jbrowse/core/util';
 import { getTrackName } from '@jbrowse/core/util/tracks';
+import { addDisposer, getParent, types } from '@jbrowse/mobx-state-tree';
 import { autorun, observable } from 'mobx';
-import { addDisposer, getParent, types } from 'mobx-state-tree';
-import { getRowStr } from './components/faceted/util';
-import { findNonSparseKeys, getRootKeys } from './facetedUtil';
-import { matches } from './util';
+import { getRowStr } from "./components/faceted/util.js";
+import { findNonSparseKeys, getRootKeys } from "./facetedUtil.js";
+import { matches } from "./util.js";
 const nonMetadataKeys = ['category', 'adapter', 'description'];
 export function facetedStateTreeF() {
     return types
@@ -44,6 +44,9 @@ export function facetedStateTreeF() {
         setShowFilters(f) {
             self.showFilters = f;
         },
+        setVisible(args) {
+            self.visible = args;
+        },
     }))
         .views(self => ({
         get allTrackConfigurations() {
@@ -56,18 +59,15 @@ export function facetedStateTreeF() {
             const { allTrackConfigurations, filterText } = self;
             return allTrackConfigurations
                 .filter(conf => matches(filterText, conf, session))
-                .map(track => {
-                var _a, _b;
-                return ({
-                    id: track.trackId,
-                    conf: track,
-                    name: getTrackName(track, session),
-                    category: (_a = readConfObject(track, 'category')) === null || _a === void 0 ? void 0 : _a.join(', '),
-                    adapter: (_b = readConfObject(track, 'adapter')) === null || _b === void 0 ? void 0 : _b.type,
-                    description: readConfObject(track, 'description'),
-                    metadata: readConfObject(track, 'metadata'),
-                });
-            });
+                .map(track => ({
+                id: track.trackId,
+                conf: track,
+                name: getTrackName(track, session),
+                category: readConfObject(track, 'category')?.join(', '),
+                adapter: readConfObject(track, 'adapter')?.type,
+                description: readConfObject(track, 'description'),
+                metadata: (track.metadata || {}),
+            }));
         },
     }))
         .views(self => ({
@@ -99,13 +99,24 @@ export function facetedStateTreeF() {
         },
     }))
         .actions(self => ({
-        setVisible(args) {
-            self.visible = args;
-        },
         afterAttach() {
-            addDisposer(self, autorun(() => {
-                this.setVisible(Object.fromEntries(self.fields.map(c => [c, true])));
-            }));
+            addDisposer(self, autorun(function facetedVisibleAutorun() {
+                self.setVisible(Object.fromEntries(self.fields.map(c => [c, true])));
+            }, { name: 'FacetedVisible' }));
         },
-    }));
+    }))
+        .postProcessSnapshot(snap => {
+        if (!snap) {
+            return snap;
+        }
+        const { filterText, showSparse, showFilters, showOptions, panelWidth, ...rest } = snap;
+        return {
+            ...rest,
+            ...(filterText ? { filterText } : {}),
+            ...(showSparse ? { showSparse } : {}),
+            ...(!showFilters ? { showFilters } : {}),
+            ...(showOptions ? { showOptions } : {}),
+            ...(panelWidth !== 400 ? { panelWidth } : {}),
+        };
+    });
 }

package/esm/HierarchicalTrackSelectorWidget/facetedUtil.js

@@ -1,8 +1,8 @@
 export function findNonSparseKeys(keys, rows, cb) {
-    return keys.filter(f => rows.map(r => cb(r, f)).filter(f => !!f).length > 5);
+    return keys.filter(key => rows.filter(row => cb(row, key)).length > 5);
 }
 export function getRootKeys(obj) {
     return Object.entries(obj)
         .map(([key, val]) => (typeof val === 'string' ? key : ''))
-        .filter(f => !!f);
+        .filter((f) => !!f);
 }

package/esm/HierarchicalTrackSelectorWidget/filterTracks.d.ts

@@ -7,12 +7,8 @@ export declare function filterTracks(tracks: AnyConfigurationModel[], self: {
     assemblyNames: string[];
 }): ({
     [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<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-} & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];

package/esm/HierarchicalTrackSelectorWidget/filterTracks.js

@@ -1,6 +1,6 @@
 import { readConfObject } from '@jbrowse/core/configuration';
 import { getEnv, getSession, notEmpty } from '@jbrowse/core/util';
-import { hasAllOverlap, hasAnyOverlap } from './util';
+import { hasAllOverlap, hasAnyOverlap } from "./util.js";
 export function filterTracks(tracks, self) {
     const { assemblyManager } = getSession(self);
     const { pluginManager } = getEnv(self);
@@ -11,18 +11,20 @@ export function filterTracks(tracks, self) {
     const viewAssemblyNames = self.assemblyNames
         .map(a => assemblyManager.getCanonicalAssemblyName(a))
         .filter(notEmpty);
-    return tracks
-        .filter(c => {
+    const { displayTypes } = pluginManager.getViewType(view.type);
+    const viewDisplaysSet = new Set(displayTypes.map((d) => d.name));
+    return tracks.filter(c => {
         const trackConfigAssemblyNames = readConfObject(c, 'assemblyNames');
-        const trackCanonicalAssemblyNames = trackConfigAssemblyNames === null || trackConfigAssemblyNames === void 0 ? void 0 : trackConfigAssemblyNames.map(name => assemblyManager.getCanonicalAssemblyName(name)).filter(notEmpty);
-        return view.trackSelectorAnyOverlap
+        const trackCanonicalAssemblyNames = trackConfigAssemblyNames
+            ?.map(name => assemblyManager.getCanonicalAssemblyName(name))
+            .filter(notEmpty);
+        const assemblyMatch = view.trackSelectorAnyOverlap
             ? hasAnyOverlap(trackCanonicalAssemblyNames, viewAssemblyNames)
             : hasAllOverlap(trackCanonicalAssemblyNames, viewAssemblyNames);
-    })
-        .filter(c => {
-        const { displayTypes } = pluginManager.getViewType(view.type);
-        const compatDisplays = displayTypes.map(d => d.name);
-        const trackDisplays = c.displays.map((d) => d.type);
-        return hasAnyOverlap(compatDisplays, trackDisplays);
+        if (!assemblyMatch) {
+            return false;
+        }
+        const trackType = pluginManager.getTrackType(c.type);
+        return trackType.displayTypes.some(d => viewDisplaysSet.has(d.name));
     });
 }

package/esm/HierarchicalTrackSelectorWidget/generateHierarchy.d.ts

@@ -1,34 +1,8 @@
+import type { MinimalModel, TreeNode } from './types.ts';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { MenuItem } from '@jbrowse/core/ui';
-export interface TreeTrackNode {
-    name: string;
-    id: string;
-    trackId: string;
-    conf: AnyConfigurationModel;
-    checked: boolean;
-    children: TreeNode[];
-    type: 'track';
-}
-export interface TreeCategoryNode {
-    name: string;
-    id: string;
-    isOpenByDefault: boolean;
-    children: TreeNode[];
-    type: 'category';
-}
-export type TreeNode = TreeTrackNode | TreeCategoryNode;
 export declare function generateHierarchy({ model, trackConfs, extra, noCategories, menuItems, }: {
-    model: {
-        filterText: string;
-        activeSortTrackNames: boolean;
-        activeSortCategories: boolean;
-        collapsed: Map<string | number, boolean>;
-        view?: {
-            tracks: {
-                configuration: AnyConfigurationModel;
-            }[];
-        };
-    };
+    model: MinimalModel;
     noCategories?: boolean;
     menuItems?: MenuItem[];
     trackConfs: AnyConfigurationModel[];

package/esm/HierarchicalTrackSelectorWidget/generateHierarchy.js

@@ -1,87 +1,62 @@
 import { readConfObject } from '@jbrowse/core/configuration';
 import { getSession } from '@jbrowse/core/util';
 import { getTrackName } from '@jbrowse/core/util/tracks';
-import { matches } from './util';
-function sortConfs(confs, sortNames, sortCategories) {
-    const ret = confs.map(c => {
-        var _a, _b, _c;
-        return [
-            c,
-            readConfObject(c, 'name'),
-            ((_a = readConfObject(c, 'category')) === null || _a === void 0 ? void 0 : _a[0]) || '',
-            ((_b = readConfObject(c, 'category')) === null || _b === void 0 ? void 0 : _b[1]) || '',
-            ((_c = readConfObject(c, 'category')) === null || _c === void 0 ? void 0 : _c[2]) || '',
-        ];
-    });
-    if (sortNames) {
-        ret.sort((a, b) => a[1].localeCompare(b[1]));
-    }
-    if (sortCategories) {
-        ret.sort((a, b) => {
-            if (a[2] !== b[2]) {
-                return a[2].localeCompare(b[2]);
-            }
-            else if (a[3] !== b[3]) {
-                return a[3].localeCompare(b[3]);
-            }
-            else if (a[4] !== b[4]) {
-                return a[4].localeCompare(b[4]);
-            }
-            return 0;
-        });
-    }
-    return ret.map(a => a[0]);
-}
+import { sortConfs } from "./sortUtils.js";
+import { matches } from "./util.js";
 export function generateHierarchy({ model, trackConfs, extra, noCategories, menuItems, }) {
     const hierarchy = { children: [] };
-    const { collapsed, filterText, activeSortTrackNames, activeSortCategories, view, } = model;
-    if (!view) {
-        return [];
-    }
+    const { filterText, activeSortTrackNames, activeSortCategories } = model;
     const session = getSession(model);
-    const viewTracks = view.tracks;
     const confs = trackConfs.filter(conf => matches(filterText, conf, session));
+    const leafCounts = new Map();
+    const categoryMaps = new Map();
     for (const conf of sortConfs(confs, activeSortTrackNames, activeSortCategories)) {
-        const categories = [...(readConfObject(conf, 'category') || [])];
-        if (conf.trackId.endsWith('sessionTrack')) {
-            categories.unshift(' Session tracks');
-        }
+        const isSessionTrack = conf.trackId.endsWith('sessionTrack');
+        const baseCategories = readConfObject(conf, 'category') ?? [];
+        const categories = isSessionTrack
+            ? [' Session tracks', ...baseCategories]
+            : baseCategories;
         let currLevel = hierarchy;
+        let nestingLevel = 0;
         if (!noCategories) {
-            for (let i = 0; i < categories.length; i++) {
-                const category = categories[i];
-                const ret = currLevel.children.find(c => c.name === category);
-                const id = [extra, categories.slice(0, i + 1).join(',')]
-                    .filter(f => !!f)
-                    .join('-');
-                if (!ret) {
-                    const n = {
+            let categoryPath = '';
+            for (const [i, category_] of categories.entries()) {
+                const category = category_;
+                categoryPath = categoryPath ? `${categoryPath},${category}` : category;
+                let categoryMap = categoryMaps.get(currLevel);
+                if (!categoryMap) {
+                    categoryMap = new Map();
+                    categoryMaps.set(currLevel, categoryMap);
+                }
+                let existing = categoryMap.get(category);
+                if (!existing) {
+                    const id = extra ? `${extra}-${categoryPath}` : categoryPath;
+                    existing = {
                         children: [],
                         name: category,
                         id,
-                        isOpenByDefault: !collapsed.get(id),
+                        nestingLevel: i + 1,
                         menuItems,
                         type: 'category',
                     };
-                    currLevel.children.push(n);
-                    currLevel = n;
-                }
-                else {
-                    currLevel = ret;
+                    currLevel.children.push(existing);
+                    categoryMap.set(category, existing);
                 }
+                currLevel = existing;
+                nestingLevel = i + 1;
             }
         }
-        const r = currLevel.children.findIndex(elt => elt.children.length);
-        const idx = r === -1 ? currLevel.children.length : r;
-        currLevel.children.splice(idx, 0, {
-            id: [extra, conf.trackId].filter(f => !!f).join(','),
+        const leafCount = leafCounts.get(currLevel) ?? 0;
+        currLevel.children.splice(leafCount, 0, {
+            id: extra ? `${extra},${conf.trackId}` : conf.trackId,
             trackId: conf.trackId,
             name: getTrackName(conf, session),
             conf,
-            checked: viewTracks.some(f => f.configuration === conf),
             children: [],
+            nestingLevel: nestingLevel + 1,
             type: 'track',
         });
+        leafCounts.set(currLevel, leafCount + 1);
     }
     return hierarchy.children;
 }

package/esm/HierarchicalTrackSelectorWidget/index.d.ts

@@ -1,4 +1,4 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 export default function HierarchicalTrackSelectorWidgetF(pluginManager: PluginManager): void;
-export { type HierarchicalTrackSelectorModel, default as stateModelFactory, } from './model';
-export { default as configSchema } from './configSchema';
+export { type HierarchicalTrackSelectorModel, default as stateModelFactory, } from './model.ts';
+export { default as configSchema } from './configSchema.ts';

package/esm/HierarchicalTrackSelectorWidget/index.js

@@ -1,7 +1,7 @@
 import { lazy } from 'react';
 import { WidgetType } from '@jbrowse/core/pluggableElementTypes';
-import configSchema from './configSchema';
-import stateModelFactory from './model';
+import configSchema from "./configSchema.js";
+import stateModelFactory from "./model.js";
 export default function HierarchicalTrackSelectorWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => {
         return new WidgetType({
@@ -9,9 +9,9 @@ export default function HierarchicalTrackSelectorWidgetF(pluginManager) {
             heading: 'Available tracks',
             configSchema,
             stateModel: stateModelFactory(pluginManager),
-            ReactComponent: lazy(() => import('./components/HierarchicalTrackSelector')),
+            ReactComponent: lazy(() => import("./components/HierarchicalTrackSelector.js")),
         });
     });
 }
-export { default as stateModelFactory, } from './model';
-export { default as configSchema } from './configSchema';
+export { default as stateModelFactory, } from "./model.js";
+export { default as configSchema } from "./configSchema.js";

package/esm/HierarchicalTrackSelectorWidget/model.d.ts

@@ -1,19 +1,21 @@
+import type { TreeNode } from './types.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Instance } from '@jbrowse/mobx-state-tree';
 import type { GridRowId } from '@mui/x-data-grid';
-import type { Instance } from 'mobx-state-tree';
 type MaybeAnyConfigurationModel = AnyConfigurationModel | undefined;
 type MaybeBoolean = boolean | undefined;
-export default function stateTreeFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<"HierarchicalTrackSelectorWidget">;
-    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    faceted: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
-        filterText: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-        showSparse: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        showFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        showOptions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        panelWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+export declare function getItemHeight(item: TreeNode): 40 | 22;
+export default function stateTreeFactory(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"HierarchicalTrackSelectorWidget">;
+    view: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+    faceted: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
+        filterText: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+        showSparse: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        showFilters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        showOptions: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        panelWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     }, {
         visible: Record<string, boolean>;
         useShoppingCart: boolean;
@@ -26,32 +28,25 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         setShowSparse(f: boolean): void;
         setShowOptions(f: boolean): void;
         setShowFilters(f: boolean): void;
+        setVisible(args: Record<string, boolean>): void;
     } & {
         readonly allTrackConfigurations: ({
             [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<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
     } & {
         readonly rows: {
             readonly id: string;
             readonly conf: {
                 [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<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-                } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
             readonly name: string;
             readonly category: string;
             readonly adapter: string;
@@ -67,15 +62,11 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
             readonly id: string;
             readonly conf: {
                 [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<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-                } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
             readonly name: string;
             readonly category: string;
             readonly adapter: string;
@@ -83,9 +74,14 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
             readonly metadata: Record<string, unknown>;
         }[];
     } & {
-        setVisible(args: Record<string, boolean>): void;
         afterAttach(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        filterText: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+        showSparse: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        showFilters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        showOptions: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        panelWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    }>>, [undefined]>;
 }, {
     favorites: string[];
     recentlyUsed: GridRowId[];
@@ -100,15 +96,11 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     readonly shownTrackIds: Set<string>;
     readonly selectionSet: Set<{
         [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<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>>;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>>;
     readonly favoritesSet: Set<string>;
     readonly recentlyUsedSet: Set<GridRowId>;
     readonly assemblyNames: string[];
@@ -145,74 +137,50 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     readonly activeSortCategories: any;
     readonly configAndSessionTrackConfigurations: ({
         [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<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
     readonly allTrackConfigurations: ({
         [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<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
     readonly allTrackConfigurationTrackIdSet: Map<any, {
         [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<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>>;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>>;
 } & {
     readonly favoriteTracks: ({
         [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<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
     readonly recentlyUsedTracks: ({
         [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<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
 } & {
     readonly allTracks: {
         group: any;
         tracks: ({
             [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<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
         noCategories: boolean;
         menuItems: never[];
     }[];
@@ -220,17 +188,29 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     readonly hierarchy: {
         name: string;
         id: string;
-        isOpenByDefault: boolean;
         type: "category";
         children: {
             name: any;
             id: any;
             type: "category";
-            isOpenByDefault: boolean;
             menuItems: never[];
-            children: import("./generateHierarchy").TreeNode[];
+            nestingLevel: number;
+            children: TreeNode[];
         }[];
     };
+} & {
+    readonly flattenedItems: TreeNode[];
+    readonly flattenedItemOffsets: {
+        cumulativeHeight: number;
+        offsets: number[];
+    };
+} & {
+    itemOffsets(height: number, scrollTop: number): {
+        startIndex: number;
+        endIndex: number;
+        totalHeight: number;
+        itemOffsets: number[];
+    };
 } & {
     collapseSubCategories(): void;
     collapseTopLevelCategories(): void;
@@ -238,7 +218,7 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     readonly hasAnySubcategories: boolean;
 } & {
     afterAttach(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export type HierarchicalTrackSelectorStateModel = ReturnType<typeof stateTreeFactory>;
 export type HierarchicalTrackSelectorModel = Instance<HierarchicalTrackSelectorStateModel>;
 export {};