@jbrowse/product-core 5.0.0-beta.7 → 5.0.0-beta.9

package/esm/RootModel/menuItems.js

@@ -27,7 +27,7 @@ export function importSessionMenuItem() {
         label: 'Import session...',
         icon: PublishIcon,
         onClick: (session) => {
-            session.showWidget(session.addWidget('ImportSessionWidget', 'importSessionWidget'));
+            session.openWidget('ImportSessionWidget', 'importSessionWidget');
         },
     };
 }
@@ -58,10 +58,9 @@ export function openTrackMenuItem() {
                 session.notify('Please open a view to add a track first');
             }
             else {
-                const widget = session.addWidget('AddTrackWidget', 'addTrackWidget', {
+                session.openWidget('AddTrackWidget', 'addTrackWidget', {
                     view: firstView.id,
                 });
-                session.showWidget(widget);
                 if (session.views.length > 1) {
                     session.notify(MULTI_VIEW_WARNING);
                 }
@@ -74,8 +73,7 @@ export function openConnectionMenuItem() {
         label: 'Open connection...',
         icon: Cable,
         onClick: (session) => {
-            const widget = session.addWidget('AddConnectionWidget', 'addConnectionWidget');
-            session.showWidget(widget);
+            session.openWidget('AddConnectionWidget', 'addConnectionWidget');
         },
     };
 }
@@ -84,7 +82,7 @@ export function pluginStoreMenuItem() {
         label: 'Plugin store',
         icon: ExtensionIcon,
         onClick: (session) => {
-            session.showWidget(session.addWidget('PluginStoreWidget', 'pluginStoreWidget'));
+            session.openWidget('PluginStoreWidget', 'pluginStoreWidget');
         },
     };
 }

package/esm/Session/BaseSession.d.ts

@@ -4,6 +4,7 @@ import type PluginManager from '@jbrowse/core/PluginManager';
 import type { BaseAssemblyConfigModel } from '@jbrowse/core/assemblyManager';
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import type { AnimationMode, DialogComponentType, TrackConfigChange } from '@jbrowse/core/util';
+import type { HighlightType } from '@jbrowse/core/util/highlights';
 import type { IAnyStateTreeNode, Instance } from '@jbrowse/mobx-state-tree';
 type DoneCallback = (doneCallback: () => void) => [DialogComponentType, Record<string, unknown>];
 /**
@@ -28,22 +29,26 @@ export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelTy
     focusedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     /**
      * #property
-     * one session-wide toggle for all region highlight bands (URL/view
-     * highlights and bookmark overlays)
+     * translucent bands over genomic regions; every view draws the ones on
+     * its own assemblies
+     */
+    highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<HighlightType, HighlightType, HighlightType>>, [undefined]>;
+    /**
+     * #property
      */
     highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     /**
      * #property
      * views, tracks, displays and widgets `pruneUnbuildableNodes` took out of
      * the tree because this build has no plugin for their type, each with the
-     * anchor that puts it back. Opaque here on purpose — nothing in the
-     * session reads it, and the shape belongs to that module.
+     * anchor that puts it back. Nothing in the session reads its contents,
+     * and `pruneUnbuildableNodes` defines their structure.
      *
-     * It is a **declared property** rather than data riding along in the
-     * snapshot because MST silently drops an undeclared key: without this
-     * line the held nodes survive the prune and then vanish the moment
-     * `setSession` builds the tree, and every unit test of the prune still
-     * passes. `heldNodesSurviveTheSession.test.ts` is the canary.
+     * It is a **declared property** because MST drops undeclared snapshot
+     * keys without error. Without this declaration the held nodes survive
+     * the prune and are then discarded when `setSession` builds the tree,
+     * while every unit test of the prune still passes.
+     * `heldNodesSurviveTheSession.test.ts` tests that they survive.
      */
     heldForMissingPlugins: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<HeldNode[] | undefined, HeldNode[] | undefined, HeldNode[] | undefined>, [undefined]>;
 }, never>, {
@@ -194,15 +199,27 @@ export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelTy
     setHovered(thing: unknown): void;
     /**
      * #action
-     * toggle all region highlight bands across every view
      */
     setHighlightsVisible(arg: boolean): void;
     /**
      * #action
-     * turn highlight bands back on, so a newly made highlight or bookmark is
-     * never silently swallowed by an earlier "highlights off"
+     * an identical entry is not added twice, so a spec launched again does not
+     * stack its bands. Adding shows the bands again, since a highlight made
+     * while they are off would otherwise read as nothing happening
+     */
+    addHighlight(highlight: HighlightType): void;
+    /**
+     * #action
+     */
+    removeHighlight(highlight: HighlightType): void;
+    /**
+     * #action
+     */
+    updateHighlight(old: HighlightType, updates: Partial<HighlightType>): void;
+    /**
+     * #action
      */
-    revealHighlights(): void;
+    setHighlights(highlights: HighlightType[]): void;
     /**
      * #action
      * set a runtime user-preference override (see `getPreference`). Mutates

package/esm/Session/BaseSession.js

@@ -1,10 +1,11 @@
-import { getConf } from '@jbrowse/core/configuration';
+import { readConfObject } from '@jbrowse/core/configuration';
 import SnackbarModel from '@jbrowse/core/ui/SnackbarModel';
 import { setNumberGrouping } from '@jbrowse/core/util';
 import { freezeDeep } from '@jbrowse/core/util/freezeDeep';
+import { isSameHighlight } from '@jbrowse/core/util/highlights';
 import { isFeature, unwrapFeature } from '@jbrowse/core/util/simpleFeature';
 import { ElementId } from '@jbrowse/core/util/types/mst';
-import { getParent, isStateTreeNode, types } from '@jbrowse/mobx-state-tree';
+import { cast, getParent, isStateTreeNode, types, } from '@jbrowse/mobx-state-tree';
 import { observable } from 'mobx';
 import { applyDeveloperMode } from './developerMode.js';
 function isAnimationMode(val) {
@@ -34,22 +35,26 @@ export function BaseSessionModel(_pluginManager) {
         focusedViewId: types.maybe(types.string),
         /**
          * #property
-         * one session-wide toggle for all region highlight bands (URL/view
-         * highlights and bookmark overlays)
+         * translucent bands over genomic regions; every view draws the ones on
+         * its own assemblies
+         */
+        highlights: types.stripDefault(types.array(types.frozen()), []),
+        /**
+         * #property
          */
         highlightsVisible: types.stripDefault(types.boolean, true),
         /**
          * #property
          * views, tracks, displays and widgets `pruneUnbuildableNodes` took out of
          * the tree because this build has no plugin for their type, each with the
-         * anchor that puts it back. Opaque here on purpose — nothing in the
-         * session reads it, and the shape belongs to that module.
+         * anchor that puts it back. Nothing in the session reads its contents,
+         * and `pruneUnbuildableNodes` defines their structure.
          *
-         * It is a **declared property** rather than data riding along in the
-         * snapshot because MST silently drops an undeclared key: without this
-         * line the held nodes survive the prune and then vanish the moment
-         * `setSession` builds the tree, and every unit test of the prune still
-         * passes. `heldNodesSurviveTheSession.test.ts` is the canary.
+         * It is a **declared property** because MST drops undeclared snapshot
+         * keys without error. Without this declaration the held nodes survive
+         * the prune and are then discarded when `setSession` builds the tree,
+         * while every unit test of the prune still passes.
+         * `heldNodesSurviveTheSession.test.ts` tests that they survive.
          */
         heldForMissingPlugins: types.stripDefault(types.frozen(), undefined),
     })
@@ -168,7 +173,8 @@ export function BaseSessionModel(_pluginManager) {
          * `defaultUseWorkspaces`).
          */
         getPreferenceDefault(key) {
-            return getConf(self, ['preferences', key]);
+            const { preferences } = self.configuration;
+            return preferences ? readConfObject(preferences, key) : undefined;
         },
         /**
          * #method
@@ -270,19 +276,47 @@ export function BaseSessionModel(_pluginManager) {
         },
         /**
          * #action
-         * toggle all region highlight bands across every view
          */
         setHighlightsVisible(arg) {
             self.highlightsVisible = arg;
         },
         /**
          * #action
-         * turn highlight bands back on, so a newly made highlight or bookmark is
-         * never silently swallowed by an earlier "highlights off"
+         * an identical entry is not added twice, so a spec launched again does not
+         * stack its bands. Adding shows the bands again, since a highlight made
+         * while they are off would otherwise read as nothing happening
          */
-        revealHighlights() {
+        addHighlight(highlight) {
+            if (!self.highlights.some(h => isSameHighlight(h, highlight))) {
+                self.highlights.push(highlight);
+            }
             self.highlightsVisible = true;
         },
+        /**
+         * #action
+         */
+        removeHighlight(highlight) {
+            self.highlights.remove(highlight);
+        },
+        /**
+         * #action
+         */
+        updateHighlight(old, updates) {
+            const idx = self.highlights.indexOf(old);
+            if (idx !== -1) {
+                self.highlights[idx] = { ...old, ...updates };
+                self.highlightsVisible = true;
+            }
+        },
+        /**
+         * #action
+         */
+        setHighlights(highlights) {
+            self.highlights = cast(highlights);
+            if (highlights.length) {
+                self.highlightsVisible = true;
+            }
+        },
         /**
          * #action
          * set a runtime user-preference override (see `getPreference`). Mutates

package/esm/Session/Connections.d.ts

@@ -111,9 +111,10 @@ export declare function ConnectionManagementSessionMixin(pluginManager: PluginMa
     pruneConnectionTrackConfig(trackId: string): void;
     /**
      * #action
-     * Lazily establish a single connection by id if it isn't already live —
-     * used when its category is expanded in the track selector. Fetches
-     * silently (no view launch / success snackbar); already-open tracks keep
+     * Lazily establish a single connection by id if it isn't already live;
+     * the track selector calls it when the connection's category is
+     * expanded. Fetches without launching a view or showing a success
+     * snackbar; already-open tracks keep
      * rendering from `connectionTrackConfigs` meanwhile. Idempotent.
      */
     hydrateConnection(connectionId: string): void;

package/esm/Session/Connections.js

@@ -189,9 +189,10 @@ export function ConnectionManagementSessionMixin(pluginManager) {
             },
             /**
              * #action
-             * Lazily establish a single connection by id if it isn't already live —
-             * used when its category is expanded in the track selector. Fetches
-             * silently (no view launch / success snackbar); already-open tracks keep
+             * Lazily establish a single connection by id if it isn't already live;
+             * the track selector calls it when the connection's category is
+             * expanded. Fetches without launching a view or showing a success
+             * snackbar; already-open tracks keep
              * rendering from `connectionTrackConfigs` meanwhile. Idempotent.
              */
             hydrateConnection(connectionId) {

package/esm/Session/DrawerWidgets.d.ts

@@ -97,6 +97,14 @@ export declare function DrawerWidgetSessionMixin(pluginManager: PluginManager):
      * #action
      */
     hideAllWidgets(): void;
+    afterAttach(): void;
+} & {
+    /**
+     * #action
+     * adds the widget, replacing one with the same id, and shows it
+     */
+    openWidget(typeName: string, id: string, initialState?: any, conf?: unknown): any;
+} & {
     /**
      * #action
      * opens a configuration editor to configure the given thing,
@@ -108,7 +116,6 @@ export declare function DrawerWidgetSessionMixin(pluginManager: PluginManager):
     }, opts?: {
         expandedDisplayId?: string;
     }): void;
-    afterAttach(): void;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
     /**
      * #property

package/esm/Session/DrawerWidgets.js

@@ -191,6 +191,24 @@ export function DrawerWidgetSessionMixin(pluginManager) {
             self.activeWidgets.clear();
             self.poppedOut = false;
         },
+        afterAttach() {
+            addDisposer(self, autorun(function drawerPositionAutorun() {
+                localStorageSetItem('drawerPosition', self.drawerPosition);
+            }, { name: 'DrawerPosition' }));
+        },
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         * adds the widget, replacing one with the same id, and shows it
+         */
+        openWidget(typeName, id, initialState = {}, conf) {
+            const widget = self.addWidget(typeName, id, initialState, conf);
+            self.showWidget(widget);
+            return widget;
+        },
+    }))
+        .actions(self => ({
         /**
          * #action
          * opens a configuration editor to configure the given thing,
@@ -212,16 +230,10 @@ export function DrawerWidgetSessionMixin(pluginManager) {
             else {
                 throw new Error('must pass a configuration model or frozen config with trackId to editConfiguration');
             }
-            const editor = this.addWidget('ConfigurationEditorWidget', 'configEditor', {});
+            const editor = self.openWidget('ConfigurationEditorWidget', 'configEditor');
             // Set target via action since it's now volatile
             editor.setTarget(targetConfig);
             editor.setExpandedDisplayId(opts?.expandedDisplayId);
-            this.showWidget(editor);
-        },
-        afterAttach() {
-            addDisposer(self, autorun(function drawerPositionAutorun() {
-                localStorageSetItem('drawerPosition', self.drawerPosition);
-            }, { name: 'DrawerPosition' }));
         },
     }))
         .postProcessSnapshot(snap => {

package/esm/Session/MultipleViews.d.ts

@@ -9,6 +9,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     focusedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType>>, [undefined]>;
     highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     heldForMissingPlugins: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined, import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined, import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined>, [undefined]>;
 }, never>, "activeWidgets" | "drawerPosition" | "drawerWidth" | "minimized" | "widgets"> & {
@@ -531,10 +532,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
             readonly assemblyNamesList: string[];
             readonly configuredAssemblyNames: Set<string>;
-            readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
-                setSubschema(slotName: string, data: Record<string, unknown>): any;
-                setSlot(slotName: string, value: unknown): void;
-            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+            readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
             readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         } & {
             settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -1323,10 +1321,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
             readonly assemblyNamesList: string[];
             readonly configuredAssemblyNames: Set<string>;
-            readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
-                setSubschema(slotName: string, data: Record<string, unknown>): any;
-                setSlot(slotName: string, value: unknown): void;
-            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+            readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
             readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         } & {
             settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -1626,10 +1621,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
 } & {
     readonly jbrowse: any;
     readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-    readonly configuration: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
-        setSubschema(slotName: string, data: Record<string, unknown>): any;
-        setSlot(slotName: string, value: unknown): void;
-    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+    readonly configuration: import("@jbrowse/core/configuration").ConfigNodeProps<any> & import("@jbrowse/core/configuration").ConfigNodeActions & import("@jbrowse/core/configuration").ConfigNodeBrand<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
     readonly adminMode: boolean;
     readonly textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
 } & {
@@ -1650,7 +1642,10 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
     clearSelection(): void;
     setHovered(thing: unknown): void;
     setHighlightsVisible(arg: boolean): void;
-    revealHighlights(): void;
+    addHighlight(highlight: import("@jbrowse/core/util/highlights").HighlightType): void;
+    removeHighlight(highlight: import("@jbrowse/core/util/highlights").HighlightType): void;
+    updateHighlight(old: import("@jbrowse/core/util/highlights").HighlightType, updates: Partial<import("@jbrowse/core/util/highlights").HighlightType>): void;
+    setHighlights(highlights: import("@jbrowse/core/util/highlights").HighlightType[]): void;
     setPreferenceOverride(key: string, value: unknown): void;
     clearPreferenceOverrides(): void;
     clearPreferenceOverride(key: string): void;
@@ -1691,12 +1686,15 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
     popoutWidget(): void;
     returnWidgetToDrawer(): void;
     hideAllWidgets(): void;
+    afterAttach(): void;
+} & {
+    openWidget(typeName: string, id: string, initialState?: any, conf?: unknown): any;
+} & {
     editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel | {
         trackId: string;
     }, opts?: {
         expandedDisplayId?: string;
     }): void;
-    afterAttach(): void;
 } & {
     /**
      * #getter
@@ -1856,6 +1854,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     focusedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType>>, [undefined]>;
     highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     heldForMissingPlugins: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined, import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined, import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined>, [undefined]>;
 }, never>, "activeWidgets" | "drawerPosition" | "drawerWidth" | "minimized" | "widgets"> & {

package/esm/Session/Preferences.d.ts

@@ -11,6 +11,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     focusedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType>>, [undefined]>;
     highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     heldForMissingPlugins: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined, import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined, import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined>, [undefined]>;
 }, never>, never>, {
@@ -512,10 +513,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
             readonly assemblyNamesList: string[];
             readonly configuredAssemblyNames: Set<string>;
-            readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
-                setSubschema(slotName: string, data: Record<string, unknown>): any;
-                setSlot(slotName: string, value: unknown): void;
-            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+            readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
             readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         } & {
             settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -1304,10 +1302,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
             readonly assemblyNamesList: string[];
             readonly configuredAssemblyNames: Set<string>;
-            readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
-                setSubschema(slotName: string, data: Record<string, unknown>): any;
-                setSlot(slotName: string, value: unknown): void;
-            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+            readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
             readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         } & {
             settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -1607,10 +1602,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
 } & {
     readonly jbrowse: any;
     readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-    readonly configuration: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
-        setSubschema(slotName: string, data: Record<string, unknown>): any;
-        setSlot(slotName: string, value: unknown): void;
-    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+    readonly configuration: import("@jbrowse/core/configuration").ConfigNodeProps<any> & import("@jbrowse/core/configuration").ConfigNodeActions & import("@jbrowse/core/configuration").ConfigNodeBrand<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
     readonly adminMode: boolean;
     readonly textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
 } & {
@@ -1631,7 +1623,10 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
     clearSelection(): void;
     setHovered(thing: unknown): void;
     setHighlightsVisible(arg: boolean): void;
-    revealHighlights(): void;
+    addHighlight(highlight: import("@jbrowse/core/util/highlights").HighlightType): void;
+    removeHighlight(highlight: import("@jbrowse/core/util/highlights").HighlightType): void;
+    updateHighlight(old: import("@jbrowse/core/util/highlights").HighlightType, updates: Partial<import("@jbrowse/core/util/highlights").HighlightType>): void;
+    setHighlights(highlights: import("@jbrowse/core/util/highlights").HighlightType[]): void;
     setPreferenceOverride(key: string, value: unknown): void;
     clearPreferenceOverrides(): void;
     clearPreferenceOverride(key: string): void;

package/esm/Session/SessionTracks.d.ts

@@ -16,6 +16,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     focusedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType>>, [undefined]>;
     highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     heldForMissingPlugins: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined, import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined, import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined>, [undefined]>;
 }, never>, never>, "sessionTracks" | "trackConfigDeltas"> & {
@@ -31,9 +32,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
      * Per-track config overrides for a non-admin, keyed by trackId, stored as a
      * *delta* against the admin-owned base config (jbrowse.tracks entry) rather
      * than a full copy — so a later admin change to an untouched field still
-     * flows through (see trackConfigDelta.ts). Frozen (not a typed track array)
-     * on purpose: a typed create() would fill defaults, erasing the "unset vs
-     * default" distinction the delta merge relies on.
+     * flows through (see trackConfigDelta.ts). A `null` member resets a slot
+     * the base sets. Frozen (not a typed track array) on purpose: a typed
+     * create() would fill defaults, erasing the "unset vs default"
+     * distinction the delta merge relies on.
      *
      * `stripDefault` for the reason every other persisted prop beside it has
      * it: without it the empty map is written into every snapshot and every
@@ -541,10 +543,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
             readonly assemblyNamesList: string[];
             readonly configuredAssemblyNames: Set<string>;
-            readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
-                setSubschema(slotName: string, data: Record<string, unknown>): any;
-                setSlot(slotName: string, value: unknown): void;
-            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+            readonly assemblyList: AnyConfigurationModel[];
             readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         } & {
             settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -1333,10 +1332,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
             readonly assemblyNamesList: string[];
             readonly configuredAssemblyNames: Set<string>;
-            readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
-                setSubschema(slotName: string, data: Record<string, unknown>): any;
-                setSlot(slotName: string, value: unknown): void;
-            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+            readonly assemblyList: AnyConfigurationModel[];
             readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         } & {
             settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -1636,10 +1632,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
 } & {
     readonly jbrowse: any;
     readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-    readonly configuration: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
-        setSubschema(slotName: string, data: Record<string, unknown>): any;
-        setSlot(slotName: string, value: unknown): void;
-    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+    readonly configuration: import("@jbrowse/core/configuration").ConfigNodeProps<any> & import("@jbrowse/core/configuration").ConfigNodeActions & import("@jbrowse/core/configuration").ConfigNodeBrand<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
     readonly adminMode: boolean;
     readonly textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
 } & {
@@ -1660,7 +1653,10 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
     clearSelection(): void;
     setHovered(thing: unknown): void;
     setHighlightsVisible(arg: boolean): void;
-    revealHighlights(): void;
+    addHighlight(highlight: import("@jbrowse/core/util/highlights").HighlightType): void;
+    removeHighlight(highlight: import("@jbrowse/core/util/highlights").HighlightType): void;
+    updateHighlight(old: import("@jbrowse/core/util/highlights").HighlightType, updates: Partial<import("@jbrowse/core/util/highlights").HighlightType>): void;
+    setHighlights(highlights: import("@jbrowse/core/util/highlights").HighlightType[]): void;
     setPreferenceOverride(key: string, value: unknown): void;
     clearPreferenceOverrides(): void;
     clearPreferenceOverride(key: string): void;
@@ -1783,31 +1779,29 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
      * config.json every visitor is served; everyone else's goes to
      * `sessionTracks`.
      *
-     * **Only the "Add track" workflows.** Those are where an admin adding a
-     * track means to add it for the whole site. A track a feature stands up
-     * on the user's behalf — a search result, a computed consensus, a
-     * reconstruction's segment labels — is not a catalog entry, and one
-     * admin click on this publishes it to every visitor, again on the next
-     * click, with a per-launch trackId that defeats the dedupe.
-     * `addSessionTrackConf` above is the destination for those.
+     * **Call it only from the "Add track" workflows**, where an admin
+     * adding a track means to add it for the whole site. For a track a
+     * feature creates on the user's behalf (a search result, a computed
+     * consensus, a reconstruction's segment labels), one admin click on
+     * this publishes it to every visitor, and each later click publishes
+     * another copy, because the per-launch trackId prevents deduplication.
+     * Use `addSessionTrackConf` above for those.
      *
      * An admin's track still goes to the session when it names an assembly
-     * the config.json does not carry — a session spec's, a MAF sample's own
-     * genome, a comparative view's synthesized pair. The Add-track widget
-     * takes its assembly from the containing view, so an admin adding a
-     * track while looking at one of those arrives here with a name no
-     * visitor can resolve, and publishing it writes an entry the server
-     * hands everyone and nobody can draw. The session is the one
-     * destination where that track works, so the click keeps working and
-     * the dangling entry is never written; a snackbar says which assembly
-     * moved it.
+     * the config.json does not carry: a session spec's assembly, a MAF
+     * sample's genome, or a comparative view's synthesized pair. The
+     * Add-track widget takes its assembly from the containing view, so an
+     * admin adding a track in such a view passes a name no visitor can
+     * resolve. Publishing it would write an entry the server sends to every
+     * visitor and no visitor can draw. Adding it to the session keeps the
+     * track usable and writes no dangling entry; a snackbar names the
+     * assembly that caused the fallback.
      *
-     * **The snackbar names the assembly and not the track**, which is what
-     * lets a batch collapse to one message: `pushSnackbarMessage` dedupes on
-     * the exact text, and `BulkAddTracksWorkflow` publishes in a loop, so
-     * interpolating the track name stacked one identical-but-for-a-name
-     * toast per file over an admin adding thirty. The assembly is the whole
-     * of what an admin has to act on anyway.
+     * **The snackbar names the assembly and not the track**, so a batch
+     * produces one message: `pushSnackbarMessage` dedupes on the exact
+     * text, and `BulkAddTracksWorkflow` publishes in a loop. Including the
+     * track name would show one snackbar per file to an admin adding
+     * thirty. The assembly is all the admin needs to act on.
      */
     publishTrackConf(trackConf: AnyConfiguration): any;
     /**