@jbrowse/product-core 2.17.0 → 3.0.0

package/dist/Session/MultipleViews.js

@@ -2,48 +2,29 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.MultipleViewsSessionMixin = MultipleViewsSessionMixin;
 exports.isSessionWithMultipleViews = isSessionWithMultipleViews;
-const mobx_state_tree_1 = require("mobx-state-tree");
 const configuration_1 = require("@jbrowse/core/configuration");
-const DrawerWidgets_1 = require("./DrawerWidgets");
-// locals
+const mobx_state_tree_1 = require("mobx-state-tree");
 const BaseSession_1 = require("./BaseSession");
-/**
- * #stateModel MultipleViewsSessionMixin
- * composed of
- * - [BaseSessionModel](../basesessionmodel)
- * - [DrawerWidgetSessionMixin](../drawerwidgetsessionmixin)
- */
+const DrawerWidgets_1 = require("./DrawerWidgets");
 function MultipleViewsSessionMixin(pluginManager) {
     return mobx_state_tree_1.types
         .compose((0, BaseSession_1.BaseSessionModel)(pluginManager), (0, DrawerWidgets_1.DrawerWidgetSessionMixin)(pluginManager))
         .props({
-        /**
-         * #property
-         */
         views: mobx_state_tree_1.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 = (0, mobx_state_tree_1.cast)([
@@ -51,9 +32,6 @@ function MultipleViewsSessionMixin(pluginManager) {
                 ...self.views.filter(view => view.id !== id),
             ]);
         },
-        /**
-         * #action
-         */
         moveViewToBottom(id) {
             const idx = self.views.findIndex(view => view.id === id);
             self.views = (0, mobx_state_tree_1.cast)([
@@ -61,9 +39,6 @@ function MultipleViewsSessionMixin(pluginManager) {
                 self.views[idx],
             ]);
         },
-        /**
-         * #action
-         */
         addView(typeName, initialState = {}) {
             const typeDefinition = pluginManager.getElementType('view', typeName);
             if (!typeDefinition) {
@@ -75,9 +50,6 @@ 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) {
@@ -86,15 +58,9 @@ 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 => (0, configuration_1.readConfObject)(s, 'name') === assemblyName);
             if (!asm) {
@@ -105,9 +71,6 @@ function MultipleViewsSessionMixin(pluginManager) {
                 displayRegionsFromAssemblyName: (0, configuration_1.readConfObject)(asm, 'name'),
             });
         },
-        /**
-         * #action
-         */
         addViewFromAnotherView(viewType, otherView, initialState = {}) {
             const state = { ...initialState };
             state.displayedRegions = (0, mobx_state_tree_1.getSnapshot)(otherView.displayedRegions);
@@ -115,7 +78,6 @@ function MultipleViewsSessionMixin(pluginManager) {
         },
     }));
 }
-/** Type guard for SessionWithMultipleViews */
 function isSessionWithMultipleViews(session) {
     return (0, BaseSession_1.isBaseSession)(session) && 'views' in session;
 }

package/dist/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/dist/Session/ReferenceManagement.js

@@ -1,28 +1,14 @@
 "use strict";
-/** MST props, views, actions, etc related to managing connections */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.ReferenceManagementSessionMixin = ReferenceManagementSessionMixin;
 exports.isSessionWithReferenceManagement = isSessionWithReferenceManagement;
 const util_1 = require("@jbrowse/core/util");
 const mobx_state_tree_1 = require("mobx-state-tree");
-// locals
 const BaseSession_1 = require("./BaseSession");
-/**
- * #stateModel ReferenceManagementSessionMixin
- */
 function ReferenceManagementSessionMixin(_pluginManager) {
     return mobx_state_tree_1.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 = [];
             (0, mobx_state_tree_1.walk)((0, mobx_state_tree_1.getParent)(self), node => {
@@ -39,15 +25,10 @@ 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 = (0, util_1.getContainingView)(node);
                     callbacks.push(() => {
@@ -60,11 +41,8 @@ function ReferenceManagementSessionMixin(_pluginManager) {
                     dereferenceTypeCount[type] += 1;
                 }
                 catch (err1) {
-                    // ignore
                 }
                 if ((0, util_1.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 ((0, util_1.isSessionModelWithWidgets)(self)) {
                         callbacks.push(() => {
@@ -84,7 +62,6 @@ function ReferenceManagementSessionMixin(_pluginManager) {
         },
     }));
 }
-/** Type guard for SessionWithReferenceManagement */
 function isSessionWithReferenceManagement(thing) {
     return ((0, BaseSession_1.isBaseSession)(thing) &&
         'getReferring' in thing &&