@jbrowse/product-core 2.17.0 → 3.0.0

package/esm/Session/MultipleViews.js

@@ -1,45 +1,26 @@
-import { cast, getSnapshot, types, } from 'mobx-state-tree';
 import { readConfObject } from '@jbrowse/core/configuration';
-import { DrawerWidgetSessionMixin } from './DrawerWidgets';
-// locals
+import { cast, getSnapshot, types } from 'mobx-state-tree';
 import { BaseSessionModel, isBaseSession } from './BaseSession';
-/**
- * #stateModel MultipleViewsSessionMixin
- * composed of
- * - [BaseSessionModel](../basesessionmodel)
- * - [DrawerWidgetSessionMixin](../drawerwidgetsessionmixin)
- */
+import { DrawerWidgetSessionMixin } from './DrawerWidgets';
 export function MultipleViewsSessionMixin(pluginManager) {
     return types
         .compose(BaseSessionModel(pluginManager), DrawerWidgetSessionMixin(pluginManager))
         .props({
-        /**
-         * #property
-         */
         views: types.array(pluginManager.pluggableMstType('view', 'stateModel')),
     })
         .actions(self => ({
-        /**
-         * #action
-         */
         moveViewDown(id) {
             const idx = self.views.findIndex(v => v.id === id);
             if (idx !== -1 && idx < self.views.length - 1) {
                 self.views.splice(idx, 2, self.views[idx + 1], self.views[idx]);
             }
         },
-        /**
-         * #action
-         */
         moveViewUp(id) {
             const idx = self.views.findIndex(view => view.id === id);
             if (idx > 0) {
                 self.views.splice(idx - 1, 2, self.views[idx], self.views[idx - 1]);
             }
         },
-        /**
-         * #action
-         */
         moveViewToTop(id) {
             const idx = self.views.findIndex(view => view.id === id);
             self.views = cast([
@@ -47,9 +28,6 @@ export function MultipleViewsSessionMixin(pluginManager) {
                 ...self.views.filter(view => view.id !== id),
             ]);
         },
-        /**
-         * #action
-         */
         moveViewToBottom(id) {
             const idx = self.views.findIndex(view => view.id === id);
             self.views = cast([
@@ -57,9 +35,6 @@ export function MultipleViewsSessionMixin(pluginManager) {
                 self.views[idx],
             ]);
         },
-        /**
-         * #action
-         */
         addView(typeName, initialState = {}) {
             const typeDefinition = pluginManager.getElementType('view', typeName);
             if (!typeDefinition) {
@@ -71,9 +46,6 @@ export function MultipleViewsSessionMixin(pluginManager) {
             });
             return self.views[length - 1];
         },
-        /**
-         * #action
-         */
         removeView(view) {
             for (const [, widget] of self.activeWidgets) {
                 if (widget.view && widget.view.id === view.id) {
@@ -82,15 +54,9 @@ export function MultipleViewsSessionMixin(pluginManager) {
             }
             self.views.remove(view);
         },
-        /**
-         * #action
-         */
         addLinearGenomeViewOfAssembly(assemblyName, initialState = {}) {
             return this.addViewOfAssembly('LinearGenomeView', assemblyName, initialState);
         },
-        /**
-         * #action
-         */
         addViewOfAssembly(viewType, assemblyName, initialState = {}) {
             const asm = self.assemblies.find(s => readConfObject(s, 'name') === assemblyName);
             if (!asm) {
@@ -101,9 +67,6 @@ export function MultipleViewsSessionMixin(pluginManager) {
                 displayRegionsFromAssemblyName: readConfObject(asm, 'name'),
             });
         },
-        /**
-         * #action
-         */
         addViewFromAnotherView(viewType, otherView, initialState = {}) {
             const state = { ...initialState };
             state.displayedRegions = getSnapshot(otherView.displayedRegions);
@@ -111,7 +74,6 @@ export function MultipleViewsSessionMixin(pluginManager) {
         },
     }));
 }
-/** Type guard for SessionWithMultipleViews */
 export function isSessionWithMultipleViews(session) {
     return isBaseSession(session) && 'views' in session;
 }

package/esm/Session/ReferenceManagement.d.ts

@@ -1,34 +1,15 @@
-/** MST props, views, actions, etc related to managing connections */
-import PluginManager from '@jbrowse/core/PluginManager';
-import { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
+import type PluginManager from '@jbrowse/core/PluginManager';
 import type { BaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
+import type { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
 export interface ReferringNode {
     node: IAnyStateTreeNode;
     key: string;
 }
-/**
- * #stateModel ReferenceManagementSessionMixin
- */
 export declare function ReferenceManagementSessionMixin(_pluginManager: PluginManager): import("mobx-state-tree").IModelType<{}, {
-    /**
-     * #method
-     * See if any MST nodes currently have a types.reference to this object.
-     *
-     * @param object - object
-     * @returns An array where the first element is the node referring
-     * to the object and the second element is they property name the node is
-     * using to refer to the object
-     */
     getReferring(object: IAnyStateTreeNode): ReferringNode[];
 } & {
-    /**
-     * #action
-     */
     removeReferring(referring: ReferringNode[], track: BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-/** Session mixin MST type for a session that manages multiple views */
 export type SessionWithReferenceManagementType = ReturnType<typeof ReferenceManagementSessionMixin>;
-/** Instance of a session with MST reference management (`getReferring()`, `removeReferring()`)  */
 export type SessionWithReferenceManagement = Instance<SessionWithReferenceManagementType>;
-/** Type guard for SessionWithReferenceManagement */
 export declare function isSessionWithReferenceManagement(thing: IAnyStateTreeNode): thing is SessionWithReferenceManagement;

package/esm/Session/ReferenceManagement.js

@@ -1,24 +1,10 @@
-/** MST props, views, actions, etc related to managing connections */
 import { getContainingView, isSessionModelWithWidgets, } from '@jbrowse/core/util';
 import { getMembers, getParent, getSnapshot, getType, isModelType, isReferenceType, types, walk, } from 'mobx-state-tree';
-// locals
 import { isBaseSession } from './BaseSession';
-/**
- * #stateModel ReferenceManagementSessionMixin
- */
 export function ReferenceManagementSessionMixin(_pluginManager) {
     return types
         .model('ReferenceManagementSessionMixin', {})
         .views(self => ({
-        /**
-         * #method
-         * See if any MST nodes currently have a types.reference to this object.
-         *
-         * @param object - object
-         * @returns An array where the first element is the node referring
-         * to the object and the second element is they property name the node is
-         * using to refer to the object
-         */
         getReferring(object) {
             const refs = [];
             walk(getParent(self), node => {
@@ -35,15 +21,10 @@ export function ReferenceManagementSessionMixin(_pluginManager) {
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         removeReferring(referring, track, callbacks, dereferenceTypeCount) {
             referring.forEach(({ node }) => {
                 let dereferenced = false;
                 try {
-                    // If a view is referring to the track config, remove the track
-                    // from the view
                     const type = 'open track(s)';
                     const view = getContainingView(node);
                     callbacks.push(() => {
@@ -56,11 +37,8 @@ export function ReferenceManagementSessionMixin(_pluginManager) {
                     dereferenceTypeCount[type] += 1;
                 }
                 catch (err1) {
-                    // ignore
                 }
                 if (isSessionModelWithWidgets(self) && self.widgets.has(node.id)) {
-                    // If a configuration editor widget has the track config
-                    // open, close the widget
                     const type = 'configuration editor widget(s)';
                     if (isSessionModelWithWidgets(self)) {
                         callbacks.push(() => {
@@ -80,7 +58,6 @@ export function ReferenceManagementSessionMixin(_pluginManager) {
         },
     }));
 }
-/** Type guard for SessionWithReferenceManagement */
 export function isSessionWithReferenceManagement(thing) {
     return (isBaseSession(thing) &&
         'getReferring' in thing &&