@jbrowse/plugin-data-management 2.17.0 → 2.18.0

package/esm/HierarchicalTrackSelectorWidget/model.d.ts

@@ -1,27 +1,12 @@
-import { Instance } from 'mobx-state-tree';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Instance } from 'mobx-state-tree';
 type MaybeAnyConfigurationModel = AnyConfigurationModel | undefined;
 type MaybeBoolean = boolean | undefined;
-/**
- * #stateModel HierarchicalTrackSelectorWidget
- */
 export default function stateTreeFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    /**
-     * #property
-     */
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<"HierarchicalTrackSelectorWidget">;
-    /**
-     * #property
-     */
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    /**
-     * #property
-     */
     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]>;
@@ -101,50 +86,17 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }, {
-    /**
-     * #volatile
-     */
     favorites: string[];
-    /**
-     * #volatile
-     */
     recentlyUsed: string[];
-    /**
-     * #volatile
-     */
     selection: AnyConfigurationModel[];
-    /**
-     * #volatile
-     */
     sortTrackNames: MaybeBoolean;
-    /**
-     * #volatile
-     */
     sortCategories: MaybeBoolean;
-    /**
-     * #volatile
-     */
     collapsed: import("mobx").ObservableMap<string, boolean>;
-    /**
-     * #volatile
-     */
     filterText: string;
-    /**
-     * #volatile
-     */
     recentlyUsedCounter: number;
-    /**
-     * #volatile
-     */
     favoritesCounter: number;
 } & {
-    /**
-     * #getter
-     */
     readonly shownTrackIds: Set<string>;
-    /**
-     * #getter
-     */
     readonly selectionSet: Set<{
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -156,137 +108,40 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
             } & 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>>;
-    /**
-     * #getter
-     */
     readonly favoritesSet: Set<string>;
-    /**
-     * #getter
-     */
     readonly recentlyUsedSet: Set<string>;
-    /**
-     * #getter
-     */
     readonly assemblyNames: string[];
 } & {
-    /**
-     * #action
-     */
     setSortTrackNames(val: boolean): void;
-    /**
-     * #action
-     */
     setSortCategories(val: boolean): void;
-    /**
-     * #action
-     */
     setSelection(elt: AnyConfigurationModel[]): void;
-    /**
-     * #action
-     */
     addToSelection(elt: AnyConfigurationModel[]): void;
-    /**
-     * #action
-     */
     removeFromSelection(elt: AnyConfigurationModel[]): void;
-    /**
-     * #action
-     */
     clearSelection(): void;
-    /**
-     * #action
-     */
     addToFavorites(trackId: string): void;
-    /**
-     * #action
-     */
     removeFromFavorites(trackId: string): void;
-    /**
-     * #action
-     */
     clearFavorites(): void;
-    /**
-     * #action
-     */
     setRecentlyUsedCounter(val: number): void;
-    /**
-     * #action
-     */
     setRecentlyUsed(str: string[]): void;
-    /**
-     * #action
-     */
     setFavorites(str: string[]): void;
-    /**
-     * #action
-     */
     setFavoritesCounter(val: number): void;
-    /**
-     * #action
-     */
     addToRecentlyUsed(id: string): void;
-    /**
-     * #action
-     */
     clearRecentlyUsed(): void;
-    /**
-     * #action
-     */
     setView(view: unknown): void;
-    /**
-     * #action
-     */
     toggleCategory(pathName: string): void;
-    /**
-     * #action
-     */
     setCategoryCollapsed(pathName: string, status: boolean): void;
-    /**
-     * #action
-     */
     expandAllCategories(): void;
-    /**
-     * #action
-     */
     setCollapsedCategories(str: [string, boolean][]): void;
-    /**
-     * #action
-     */
     clearFilterText(): void;
-    /**
-     * #action
-     */
     setFilterText(newText: string): void;
 } & {
-    /**
-     * #method
-     */
     isSelected(track: AnyConfigurationModel): boolean;
-    /**
-     * #method
-     */
     isFavorite(trackId: string): boolean;
-    /**
-     * #method
-     */
     isRecentlyUsed(trackId: string): boolean;
-    /**
-     * #method
-     */
     getRefSeqTrackConf(assemblyName: string): MaybeAnyConfigurationModel;
 } & {
-    /**
-     * #getter
-     */
     readonly activeSortTrackNames: any;
-    /**
-     * #getter
-     */
     readonly activeSortCategories: any;
-    /**
-     * #getter
-     * filter out tracks that don't match the current assembly/display types
-     */
     readonly configAndSessionTrackConfigurations: ({
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -298,9 +153,6 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
             } & 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>)[];
-    /**
-     * #getter
-     */
     readonly allTrackConfigurations: ({
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -312,9 +164,6 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
             } & 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>)[];
-    /**
-     * #getter
-     */
     readonly allTrackConfigurationTrackIdSet: Map<any, {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -327,10 +176,6 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>>;
 } & {
-    /**
-     * #getter
-     * filters out tracks that are not in the favorites group
-     */
     readonly favoriteTracks: ({
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -342,10 +187,6 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
             } & 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>)[];
-    /**
-     * #getter
-     * filters out tracks that are not in the recently used group
-     */
     readonly recentlyUsedTracks: ({
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -358,9 +199,6 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
 } & {
-    /**
-     * #getter
-     */
     readonly allTracks: {
         group: any;
         tracks: ({
@@ -378,9 +216,6 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         menuItems: never[];
     }[];
 } & {
-    /**
-     * #getter
-     */
     readonly hierarchy: {
         name: string;
         id: string;
@@ -396,18 +231,9 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         }[];
     };
 } & {
-    /**
-     * #action
-     */
     collapseSubCategories(): void;
-    /**
-     * #action
-     */
     collapseTopLevelCategories(): void;
 } & {
-    /**
-     * #getter
-     */
     readonly hasAnySubcategories: boolean;
 } & {
     afterAttach(): void;

package/esm/HierarchicalTrackSelectorWidget/model.js

@@ -1,14 +1,12 @@
-import { types, addDisposer } from 'mobx-state-tree';
-import { autorun, observable } from 'mobx';
-import { getConf, readConfObject, } from '@jbrowse/core/configuration';
+import { getConf, readConfObject } from '@jbrowse/core/configuration';
 import { dedupe, getSession, localStorageGetItem, localStorageSetItem, notEmpty, } from '@jbrowse/core/util';
 import { ElementId } from '@jbrowse/core/util/types/mst';
-// locals
+import { autorun, observable } from 'mobx';
+import { addDisposer, types } from 'mobx-state-tree';
+import { facetedStateTreeF } from './facetedModel';
 import { filterTracks } from './filterTracks';
 import { generateHierarchy } from './generateHierarchy';
 import { findSubCategories, findTopLevelCategories } from './util';
-import { facetedStateTreeF } from './facetedModel';
-// for settings that are config dependent
 function keyConfigPostFix() {
     return typeof window !== 'undefined'
         ? [
@@ -24,8 +22,6 @@ function recentlyUsedK(assemblyNames) {
         .filter(f => !!f)
         .join('-');
 }
-// this has a extra } at the end because that's how it was initially
-// released
 function favoritesK() {
     return `favoriteTracks-${keyConfigPostFix()}}`;
 }
@@ -55,185 +51,86 @@ function localStorageSetJSON(key, val) {
     }
 }
 const MAX_RECENTLY_USED = 10;
-/**
- * #stateModel HierarchicalTrackSelectorWidget
- */
 export default function stateTreeFactory(pluginManager) {
     return types
         .model('HierarchicalTrackSelectorWidget', {
-        /**
-         * #property
-         */
         id: ElementId,
-        /**
-         * #property
-         */
         type: types.literal('HierarchicalTrackSelectorWidget'),
-        /**
-         * #property
-         */
         view: types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
-        /**
-         * #property
-         */
         faceted: types.optional(facetedStateTreeF(), {}),
     })
         .volatile(() => ({
-        /**
-         * #volatile
-         */
         favorites: localStorageGetJSON(favoritesK(), []),
-        /**
-         * #volatile
-         */
         recentlyUsed: [],
-        /**
-         * #volatile
-         */
         selection: [],
-        /**
-         * #volatile
-         */
         sortTrackNames: localStorageGetJSON(sortTrackNamesK(), undefined),
-        /**
-         * #volatile
-         */
         sortCategories: localStorageGetJSON(sortCategoriesK(), undefined),
-        /**
-         * #volatile
-         */
         collapsed: observable.map(),
-        /**
-         * #volatile
-         */
         filterText: '',
-        /**
-         * #volatile
-         */
         recentlyUsedCounter: 0,
-        /**
-         * #volatile
-         */
         favoritesCounter: 0,
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get shownTrackIds() {
             var _a, _b;
             return new Set((_b = (_a = self.view) === null || _a === void 0 ? void 0 : _a.tracks) === null || _b === void 0 ? void 0 : _b.map((t) => t.configuration.trackId));
         },
-        /**
-         * #getter
-         */
         get selectionSet() {
             return new Set(self.selection);
         },
-        /**
-         * #getter
-         */
         get favoritesSet() {
             return new Set(self.favorites);
         },
-        /**
-         * #getter
-         */
         get recentlyUsedSet() {
             return new Set(self.recentlyUsed);
         },
-        /**
-         * #getter
-         */
         get assemblyNames() {
             var _a;
             return ((_a = self.view) === null || _a === void 0 ? void 0 : _a.assemblyNames) || [];
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setSortTrackNames(val) {
             self.sortTrackNames = val;
         },
-        /**
-         * #action
-         */
         setSortCategories(val) {
             self.sortCategories = val;
         },
-        /**
-         * #action
-         */
         setSelection(elt) {
             self.selection = elt;
         },
-        /**
-         * #action
-         */
         addToSelection(elt) {
             self.selection = dedupe([...self.selection, ...elt], e => e.trackId);
         },
-        /**
-         * #action
-         */
         removeFromSelection(elt) {
             const s = new Set(elt);
             self.selection = self.selection.filter(f => !s.has(f));
         },
-        /**
-         * #action
-         */
         clearSelection() {
             self.selection = [];
         },
-        /**
-         * #action
-         */
         addToFavorites(trackId) {
             self.favoritesCounter += 1;
             self.favorites = [...self.favorites, trackId];
         },
-        /**
-         * #action
-         */
         removeFromFavorites(trackId) {
             self.favorites = self.favorites.filter(f => f !== trackId);
         },
-        /**
-         * #action
-         */
         clearFavorites() {
             self.favorites = [];
         },
-        /**
-         * #action
-         */
         setRecentlyUsedCounter(val) {
             self.recentlyUsedCounter = val;
         },
-        /**
-         * #action
-         */
         setRecentlyUsed(str) {
             self.recentlyUsed = str;
         },
-        /**
-         * #action
-         */
         setFavorites(str) {
             self.favorites = str;
         },
-        /**
-         * #action
-         */
         setFavoritesCounter(val) {
             self.favoritesCounter = val;
         },
-        /**
-         * #action
-         */
         addToRecentlyUsed(id) {
             if (!self.recentlyUsed.includes(id)) {
                 self.recentlyUsedCounter = Math.min(self.recentlyUsedCounter + 1, MAX_RECENTLY_USED);
@@ -243,77 +140,41 @@ export default function stateTreeFactory(pluginManager) {
                         : [...self.recentlyUsed, id];
             }
         },
-        /**
-         * #action
-         */
         clearRecentlyUsed() {
             self.recentlyUsed = [];
         },
-        /**
-         * #action
-         */
         setView(view) {
             self.view = view;
         },
-        /**
-         * #action
-         */
         toggleCategory(pathName) {
             self.collapsed.set(pathName, !self.collapsed.get(pathName));
         },
-        /**
-         * #action
-         */
         setCategoryCollapsed(pathName, status) {
             self.collapsed.set(pathName, status);
         },
-        /**
-         * #action
-         */
         expandAllCategories() {
             self.collapsed.clear();
         },
-        /**
-         * #action
-         */
         setCollapsedCategories(str) {
             self.collapsed.replace(str);
         },
-        /**
-         * #action
-         */
         clearFilterText() {
             self.filterText = '';
         },
-        /**
-         * #action
-         */
         setFilterText(newText) {
             self.filterText = newText;
         },
     }))
         .views(self => ({
-        /**
-         * #method
-         */
         isSelected(track) {
             return self.selectionSet.has(track);
         },
-        /**
-         * #method
-         */
         isFavorite(trackId) {
             return self.favoritesSet.has(trackId);
         },
-        /**
-         * #method
-         */
         isRecentlyUsed(trackId) {
             return self.recentlyUsedSet.has(trackId);
         },
-        /**
-         * #method
-         */
         getRefSeqTrackConf(assemblyName) {
             const { assemblyManager } = getSession(self);
             const assembly = assemblyManager.get(assemblyName);
@@ -330,33 +191,20 @@ export default function stateTreeFactory(pluginManager) {
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get activeSortTrackNames() {
             var _a;
             return ((_a = self.sortTrackNames) !== null && _a !== void 0 ? _a : getConf(getSession(self), ['hierarchical', 'sort', 'trackNames']));
         },
-        /**
-         * #getter
-         */
         get activeSortCategories() {
             var _a;
             return ((_a = self.sortCategories) !== null && _a !== void 0 ? _a : getConf(getSession(self), ['hierarchical', 'sort', 'categories']));
         },
-        /**
-         * #getter
-         * filter out tracks that don't match the current assembly/display types
-         */
         get configAndSessionTrackConfigurations() {
             return [
                 ...self.assemblyNames.map(a => self.getRefSeqTrackConf(a)),
                 ...filterTracks(getSession(self).tracks, self),
             ].filter(notEmpty);
         },
-        /**
-         * #getter
-         */
         get allTrackConfigurations() {
             const { connectionInstances = [] } = getSession(self);
             return [
@@ -364,27 +212,16 @@ export default function stateTreeFactory(pluginManager) {
                 ...connectionInstances.flatMap(c => c.tracks),
             ];
         },
-        /**
-         * #getter
-         */
         get allTrackConfigurationTrackIdSet() {
             return new Map(this.allTrackConfigurations.map(t => [t.trackId, t]));
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         * filters out tracks that are not in the favorites group
-         */
         get favoriteTracks() {
             return self.favorites
                 .filter(t => self.allTrackConfigurationTrackIdSet.has(t))
                 .map(t => self.allTrackConfigurationTrackIdSet.get(t));
         },
-        /**
-         * #getter
-         * filters out tracks that are not in the recently used group
-         */
         get recentlyUsedTracks() {
             return self.recentlyUsed
                 .filter(t => self.allTrackConfigurationTrackIdSet.has(t))
@@ -392,9 +229,6 @@ export default function stateTreeFactory(pluginManager) {
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get allTracks() {
             const { connectionInstances = [] } = getSession(self);
             return [
@@ -414,9 +248,6 @@ export default function stateTreeFactory(pluginManager) {
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get hierarchy() {
             return {
                 name: 'Root',
@@ -440,9 +271,6 @@ export default function stateTreeFactory(pluginManager) {
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         collapseSubCategories() {
             const paths = [];
             findSubCategories(self.hierarchy.children, paths);
@@ -450,9 +278,6 @@ export default function stateTreeFactory(pluginManager) {
                 self.setCategoryCollapsed(path, true);
             }
         },
-        /**
-         * #action
-         */
         collapseTopLevelCategories() {
             const paths = [];
             for (const trackGroups of self.hierarchy.children) {
@@ -466,16 +291,12 @@ export default function stateTreeFactory(pluginManager) {
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get hasAnySubcategories() {
             return self.allTracks.some(group => group.tracks.some(t => { var _a; return ((_a = readConfObject(t, 'category')) === null || _a === void 0 ? void 0 : _a.length) > 1; }));
         },
     }))
         .actions(self => ({
         afterAttach() {
-            // this should be the first autorun to properly initialize
             addDisposer(self, autorun(() => {
                 const { assemblyNames, view } = self;
                 self.setRecentlyUsed(localStorageGetJSON(recentlyUsedK(assemblyNames), []));
@@ -500,7 +321,6 @@ export default function stateTreeFactory(pluginManager) {
                     }
                 }
             }));
-            // this should be the second autorun
             addDisposer(self, autorun(() => {
                 const { sortTrackNames, sortCategories, favorites, recentlyUsed, assemblyNames, collapsed, view, } = self;
                 localStorageSetJSON(recentlyUsedK(assemblyNames), recentlyUsed);