@jbrowse/plugin-grid-bookmark 2.8.0 → 2.10.0

package/dist/GridBookmarkWidget/model.d.ts

@@ -1,6 +1,7 @@
 import { Instance, SnapshotIn, IMSTArray } from 'mobx-state-tree';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { Region } from '@jbrowse/core/util/types';
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 declare const LabeledRegionModel: import("mobx-state-tree").IModelType<{
     refName: import("mobx-state-tree").ISimpleType<string>;
     start: import("mobx-state-tree").ISimpleType<number>;
@@ -10,25 +11,38 @@ declare const LabeledRegionModel: import("mobx-state-tree").IModelType<{
     assemblyName: import("mobx-state-tree").ISimpleType<string>;
 } & {
     label: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
 }, {
     setRefName(newRefName: string): void;
 } & {
     setLabel(label: string): void;
+    setHighlight(color: string): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export interface IExtendedLGV extends LinearGenomeViewModel {
+    showBookmarkHighlights: boolean;
+    showBookmarkLabels: boolean;
+    toggleShowBookmarkHighlights: (arg: boolean) => {};
+    toggleShowBookmarkLabels: (arg: boolean) => {};
+}
 export interface ILabeledRegionModel extends SnapshotIn<typeof LabeledRegionModel> {
     refName: string;
     start: number;
     end: number;
     reversed: boolean;
+    highlight: string;
     assemblyName: string;
     label: string;
     setRefName: (newRefName: string) => void;
     setLabel: (label: string) => void;
+    setHighlight: (color: string) => void;
 }
 export interface IExtendedLabeledRegionModel extends ILabeledRegionModel {
     id: number;
     correspondingObj: ILabeledRegionModel;
 }
+/**
+ * #stateModel GridBookmarkWidgetModel
+ */
 export default function f(_pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     /**
      * #property
@@ -51,18 +65,37 @@ export default function f(_pluginManager: PluginManager): import("mobx-state-tre
         assemblyName: import("mobx-state-tree").ISimpleType<string>;
     } & {
         label: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     }, {
         setRefName(newRefName: string): void;
     } & {
         setLabel(label: string): void;
+        setHighlight(color: string): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>, [undefined]>;
 }, {
     selectedBookmarks: IExtendedLabeledRegionModel[];
     selectedAssembliesPre: string[] | undefined;
 } & {
+    /**
+     * #getter
+     */
     readonly bookmarkAssemblies: string[];
+    /**
+     * #getter
+     */
     readonly validAssemblies: Set<string>;
+    /**
+     * #getter
+     */
+    readonly areBookmarksHighlightedOnAllOpenViews: boolean;
+    /**
+     * #getter
+     */
+    readonly areBookmarksHighlightLabelsOnAllOpenViews: boolean;
 } & {
+    /**
+     * #getter
+     */
     readonly bookmarksWithValidAssemblies: ({
         refName: string;
         start: number;
@@ -70,10 +103,12 @@ export default function f(_pluginManager: PluginManager): import("mobx-state-tre
         reversed: boolean;
         assemblyName: string;
         label: string;
+        highlight: string;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setRefName(newRefName: string): void;
     } & {
         setLabel(label: string): void;
+        setHighlight(color: string): void;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         refName: import("mobx-state-tree").ISimpleType<string>;
         start: import("mobx-state-tree").ISimpleType<number>;
@@ -83,12 +118,17 @@ export default function f(_pluginManager: PluginManager): import("mobx-state-tre
         assemblyName: import("mobx-state-tree").ISimpleType<string>;
     } & {
         label: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     }, {
         setRefName(newRefName: string): void;
     } & {
         setLabel(label: string): void;
+        setHighlight(color: string): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>)[];
 } & {
+    /**
+     * #getter
+     */
     readonly sharedBookmarksModel: {
         sharedBookmarks: (IMSTArray<import("mobx-state-tree").IModelType<{
             refName: import("mobx-state-tree").ISimpleType<string>;
@@ -99,10 +139,12 @@ export default function f(_pluginManager: PluginManager): import("mobx-state-tre
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         } & {
             label: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         }, {
             setRefName(newRefName: string): void;
         } & {
             setLabel(label: string): void;
+            setHighlight(color: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
             refName: import("mobx-state-tree").ISimpleType<string>;
             start: import("mobx-state-tree").ISimpleType<number>;
@@ -112,10 +154,12 @@ export default function f(_pluginManager: PluginManager): import("mobx-state-tre
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         } & {
             label: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         }, {
             setRefName(newRefName: string): void;
         } & {
             setLabel(label: string): void;
+            setHighlight(color: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>>) | undefined;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         sharedBookmarks: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
@@ -127,12 +171,17 @@ export default function f(_pluginManager: PluginManager): import("mobx-state-tre
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         } & {
             label: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         }, {
             setRefName(newRefName: string): void;
         } & {
             setLabel(label: string): void;
+            setHighlight(color: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    /**
+     * #getter
+     */
     readonly allBookmarksModel: {
         sharedBookmarks: (IMSTArray<import("mobx-state-tree").IModelType<{
             refName: import("mobx-state-tree").ISimpleType<string>;
@@ -143,10 +192,12 @@ export default function f(_pluginManager: PluginManager): import("mobx-state-tre
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         } & {
             label: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         }, {
             setRefName(newRefName: string): void;
         } & {
             setLabel(label: string): void;
+            setHighlight(color: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
             refName: import("mobx-state-tree").ISimpleType<string>;
             start: import("mobx-state-tree").ISimpleType<number>;
@@ -156,10 +207,12 @@ export default function f(_pluginManager: PluginManager): import("mobx-state-tre
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         } & {
             label: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         }, {
             setRefName(newRefName: string): void;
         } & {
             setLabel(label: string): void;
+            setHighlight(color: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>>) | undefined;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         sharedBookmarks: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
@@ -171,25 +224,73 @@ export default function f(_pluginManager: PluginManager): import("mobx-state-tre
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         } & {
             label: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         }, {
             setRefName(newRefName: string): void;
         } & {
             setLabel(label: string): void;
+            setHighlight(color: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
 } & {
+    /**
+     * #action
+     */
     setSelectedAssemblies(assemblies?: string[]): void;
 } & {
+    /**
+     * #getter
+     */
     readonly selectedAssemblies: string[];
 } & {
+    /**
+     * #action
+     */
     importBookmarks(regions: Region[]): void;
+    /**
+     * #action
+     */
     addBookmark(region: Region): void;
+    /**
+     * #action
+     */
     removeBookmark(index: number): void;
+    /**
+     * #action
+     */
     updateBookmarkLabel(bookmark: IExtendedLabeledRegionModel, label: string): void;
+    /**
+     * #action
+     */
+    updateBookmarkHighlight(bookmark: IExtendedLabeledRegionModel, color: string): void;
+    /**
+     * #action
+     */
+    updateBulkBookmarkHighlights(color: string): void;
+    /**
+     * #action
+     */
     setSelectedBookmarks(bookmarks: IExtendedLabeledRegionModel[]): void;
+    /**
+     * #action
+     */
     setBookmarkedRegions(regions: IMSTArray<typeof LabeledRegionModel>): void;
+    /**
+     * #action
+     */
+    setHighlightToggle(toggle: boolean): void;
+    /**
+     * #action
+     */
+    setLabelToggle(toggle: boolean): void;
 } & {
+    /**
+     * #action
+     */
     clearAllBookmarks(): void;
+    /**
+     * #action
+     */
     clearSelectedBookmarks(): void;
 } & {
     afterAttach(): void;

package/dist/GridBookmarkWidget/model.js

@@ -7,11 +7,15 @@ const mobx_1 = require("mobx");
 const LabeledRegionModel = mobx_state_tree_1.types
     .compose(mst_1.Region, mobx_state_tree_1.types.model('Label', {
     label: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.string, ''),
+    highlight: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.string, 'rgba(247, 129, 192, 0.35)'),
 }))
     .actions(self => ({
     setLabel(label) {
         self.label = label;
     },
+    setHighlight(color) {
+        self.highlight = color;
+    },
 }));
 const SharedBookmarksModel = mobx_state_tree_1.types.model('SharedBookmarksModel', {
     sharedBookmarks: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.array(LabeledRegionModel)),
@@ -19,6 +23,9 @@ const SharedBookmarksModel = mobx_state_tree_1.types.model('SharedBookmarksModel
 const localStorageKeyF = () => typeof window !== undefined
     ? `bookmarks-${[window.location.host + window.location.pathname].join('-')}`
     : 'empty';
+/**
+ * #stateModel GridBookmarkWidgetModel
+ */
 function f(_pluginManager) {
     return mobx_state_tree_1.types
         .model('GridBookmarkModel', {
@@ -41,20 +48,46 @@ function f(_pluginManager) {
         selectedAssembliesPre: undefined,
     }))
         .views(self => ({
+        /**
+         * #getter
+         */
         get bookmarkAssemblies() {
             return [...new Set(self.bookmarks.map(r => r.assemblyName))];
         },
+        /**
+         * #getter
+         */
         get validAssemblies() {
             const { assemblyManager } = (0, util_1.getSession)(self);
             return new Set(this.bookmarkAssemblies.filter(a => assemblyManager.get(a)));
         },
+        /**
+         * #getter
+         */
+        get areBookmarksHighlightedOnAllOpenViews() {
+            const { views } = (0, util_1.getSession)(self);
+            return views.every(v => 'showBookmarkHighlights' in v ? v.showBookmarkHighlights : true);
+        },
+        /**
+         * #getter
+         */
+        get areBookmarksHighlightLabelsOnAllOpenViews() {
+            const { views } = (0, util_1.getSession)(self);
+            return views.every(v => 'showBookmarkLabels' in v ? v.showBookmarkLabels : true);
+        },
     }))
         .views(self => ({
+        /**
+         * #getter
+         */
         get bookmarksWithValidAssemblies() {
             return self.bookmarks.filter(e => self.validAssemblies.has(e.assemblyName));
         },
     }))
         .views(self => ({
+        /**
+         * #getter
+         */
         get sharedBookmarksModel() {
             // requires cloning bookmarks with JSON.stringify/parse to avoid duplicate
             // reference to same object in the same state tree, will otherwise error
@@ -63,6 +96,9 @@ function f(_pluginManager) {
                 sharedBookmarks: JSON.parse(JSON.stringify(self.selectedBookmarks)),
             });
         },
+        /**
+         * #getter
+         */
         get allBookmarksModel() {
             // requires cloning bookmarks with JSON.stringify/parse to avoid duplicate
             // reference to same object in the same state tree, will otherwise error
@@ -73,44 +109,102 @@ function f(_pluginManager) {
         },
     }))
         .actions(self => ({
+        /**
+         * #action
+         */
         setSelectedAssemblies(assemblies) {
             self.selectedAssembliesPre = assemblies;
         },
     }))
         .views(self => ({
+        /**
+         * #getter
+         */
         get selectedAssemblies() {
             var _a, _b;
             return ((_b = (_a = self.selectedAssembliesPre) === null || _a === void 0 ? void 0 : _a.filter(f => self.validAssemblies.has(f))) !== null && _b !== void 0 ? _b : [...self.validAssemblies]);
         },
     }))
         .actions(self => ({
+        /**
+         * #action
+         */
         importBookmarks(regions) {
             self.bookmarks = (0, mobx_state_tree_1.cast)([...self.bookmarks, ...regions]);
         },
+        /**
+         * #action
+         */
         addBookmark(region) {
             self.bookmarks.push(region);
         },
+        /**
+         * #action
+         */
         removeBookmark(index) {
             self.bookmarks.splice(index, 1);
         },
+        /**
+         * #action
+         */
         updateBookmarkLabel(bookmark, label) {
             bookmark.correspondingObj.setLabel(label);
         },
+        /**
+         * #action
+         */
+        updateBookmarkHighlight(bookmark, color) {
+            bookmark.correspondingObj.setHighlight(color);
+        },
+        /**
+         * #action
+         */
+        updateBulkBookmarkHighlights(color) {
+            self.selectedBookmarks.forEach(bookmark => this.updateBookmarkHighlight(bookmark, color));
+        },
+        /**
+         * #action
+         */
         setSelectedBookmarks(bookmarks) {
             self.selectedBookmarks = bookmarks;
         },
+        /**
+         * #action
+         */
         setBookmarkedRegions(regions) {
             self.bookmarks = (0, mobx_state_tree_1.cast)(regions);
         },
+        /**
+         * #action
+         */
+        setHighlightToggle(toggle) {
+            const { views } = (0, util_1.getSession)(self);
+            views.forEach(view => {
+                var _a;
+                (_a = view.toggleShowBookmarkHighlights) === null || _a === void 0 ? void 0 : _a.call(view, toggle);
+            });
+        },
+        /**
+         * #action
+         */
+        setLabelToggle(toggle) {
+            const { views } = (0, util_1.getSession)(self);
+            views.forEach(view => {
+                var _a;
+                (_a = view.toggleShowBookmarkLabels) === null || _a === void 0 ? void 0 : _a.call(view, toggle);
+            });
+        },
     }))
         .actions(self => ({
+        /**
+         * #action
+         */
         clearAllBookmarks() {
-            for (const bookmark of self.bookmarks) {
-                if (self.validAssemblies.has(bookmark.assemblyName)) {
-                    self.bookmarks.remove(bookmark);
-                }
-            }
+            self.setBookmarkedRegions(self.bookmarks.filter(bookmark => !self.validAssemblies.has(bookmark.assemblyName)));
         },
+        /**
+         * #action
+         */
         clearSelectedBookmarks() {
             for (const bookmark of self.selectedBookmarks) {
                 self.bookmarks.remove(bookmark.correspondingObj);
@@ -121,6 +215,16 @@ function f(_pluginManager) {
         .actions(self => ({
         afterAttach() {
             const key = localStorageKeyF();
+            function handler(e) {
+                if (e.key === key) {
+                    const localStorage = JSON.parse((0, util_1.localStorageGetItem)(key) || '[]');
+                    self.setBookmarkedRegions(localStorage);
+                }
+            }
+            window.addEventListener('storage', handler);
+            (0, mobx_state_tree_1.addDisposer)(self, () => {
+                window.removeEventListener('storage', handler);
+            });
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
                 (0, util_1.localStorageSetItem)(key, JSON.stringify(self.bookmarks));
             }));

package/dist/index.js

@@ -8,6 +8,8 @@ const util_1 = require("@jbrowse/core/util");
 // icons
 const Bookmark_1 = __importDefault(require("@mui/icons-material/Bookmark"));
 const Bookmarks_1 = __importDefault(require("@mui/icons-material/Bookmarks"));
+const Highlight_1 = __importDefault(require("@mui/icons-material/Highlight"));
+const Label_1 = __importDefault(require("@mui/icons-material/Label"));
 const GridBookmarkWidget_1 = __importDefault(require("./GridBookmarkWidget"));
 class default_1 extends Plugin_1.default {
     constructor() {
@@ -21,7 +23,33 @@ class default_1 extends Plugin_1.default {
                 const { stateModel } = pluggableElement;
                 const lgv = stateModel;
                 const newStateModel = lgv
+                    .props({
+                    /**
+                     * #property
+                     * show the bookmark highlights on this track
+                     */
+                    showBookmarkHighlights: true,
+                    /**
+                     * #property
+                     * show the bookmark labels on this track
+                     */
+                    showBookmarkLabels: true,
+                })
                     .actions(self => ({
+                    /**
+                     * #action
+                     */
+                    toggleShowBookmarkHighlights(toggle) {
+                        self.showBookmarkHighlights =
+                            toggle !== undefined ? toggle : !self.showBookmarkHighlights;
+                    },
+                    /**
+                     * #action
+                     */
+                    toggleShowBookmarkLabels(toggle) {
+                        self.showBookmarkLabels =
+                            toggle !== undefined ? toggle : !self.showBookmarkLabels;
+                    },
                     activateBookmarkWidget() {
                         const session = (0, util_1.getSession)(self);
                         if ((0, util_1.isSessionModelWithWidgets)(session)) {
@@ -64,14 +92,34 @@ class default_1 extends Plugin_1.default {
                                 ...superMenuItems(),
                                 { type: 'divider' },
                                 {
-                                    label: 'Open bookmark widget',
+                                    label: 'Bookmarks',
                                     icon: Bookmarks_1.default,
-                                    onClick: () => self.activateBookmarkWidget(),
-                                },
-                                {
-                                    label: 'Bookmark current region',
-                                    icon: Bookmark_1.default,
-                                    onClick: () => self.bookmarkCurrentRegion(),
+                                    subMenu: [
+                                        {
+                                            label: 'Open bookmark widget',
+                                            icon: Bookmarks_1.default,
+                                            onClick: () => self.activateBookmarkWidget(),
+                                        },
+                                        {
+                                            label: 'Bookmark current region',
+                                            icon: Bookmark_1.default,
+                                            onClick: () => self.bookmarkCurrentRegion(),
+                                        },
+                                        {
+                                            label: 'Toggle bookmark highlights',
+                                            icon: Highlight_1.default,
+                                            type: 'checkbox',
+                                            checked: self.showBookmarkHighlights,
+                                            onClick: () => self.toggleShowBookmarkHighlights(),
+                                        },
+                                        {
+                                            label: 'Toggle bookmark labels',
+                                            icon: Label_1.default,
+                                            type: 'checkbox',
+                                            checked: self.showBookmarkLabels,
+                                            onClick: () => self.toggleShowBookmarkLabels(),
+                                        },
+                                    ],
                                 },
                             ];
                         },