@jbrowse/product-core 2.17.0 → 3.0.0

package/esm/RootModel/FormatDetails.d.ts

@@ -1,38 +1,21 @@
-/**
- * #config FormatDetails
- * generally exists on the tracks in the config.json or as a 'session' config as
- * configuration.formatDetails
- */
 export declare function FormatDetailsConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot configuration.formatDetails.feature
-     */
     feature: {
         type: string;
         description: string;
         defaultValue: {};
         contextVariable: string[];
     };
-    /**
-     * #slot configuration.formatDetails.subfeatures
-     */
     subfeatures: {
         type: string;
         description: string;
         defaultValue: {};
         contextVariable: string[];
     };
-    /**
-     * #slot configuration.formatDetails.depth
-     */
     depth: {
         type: string;
         defaultValue: number;
         description: string;
     };
-    /**
-     * #slot configuration.formatDetails.maxDepth
-     */
     maxDepth: {
         type: string;
         defaultValue: number;

package/esm/RootModel/FormatDetails.js

@@ -1,40 +1,23 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config FormatDetails
- * generally exists on the tracks in the config.json or as a 'session' config as
- * configuration.formatDetails
- */
 export function FormatDetailsConfigSchemaFactory() {
     return ConfigurationSchema('FormatDetails', {
-        /**
-         * #slot configuration.formatDetails.feature
-         */
         feature: {
             type: 'frozen',
             description: 'adds extra fields to the feature details',
             defaultValue: {},
             contextVariable: ['feature'],
         },
-        /**
-         * #slot configuration.formatDetails.subfeatures
-         */
         subfeatures: {
             type: 'frozen',
             description: 'adds extra fields to the subfeatures of a feature',
             defaultValue: {},
             contextVariable: ['feature'],
         },
-        /**
-         * #slot configuration.formatDetails.depth
-         */
         depth: {
             type: 'number',
             defaultValue: 2,
             description: 'depth to iterate the formatDetails->subfeatures callback on subfeatures (used for example to only apply the callback to the first layer of subfeatures)',
         },
-        /**
-         * #slot configuration.formatDetails.maxDepth
-         */
         maxDepth: {
             type: 'number',
             defaultValue: 10000,

package/esm/RootModel/HierarchicalConfig.d.ts

@@ -1,42 +1,23 @@
-/**
- * #config HierarchicalConfigSchema
- * generally exists on the config.json or root config as configuration.hierarchical
- */
 export declare function HierarchicalConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot configuration.hierarchical.sort.trackNames
-         */
         trackNames: {
             type: string;
             defaultValue: boolean;
         };
-        /**
-         * #slot configuration.hierarchical.sort.categories
-         */
         categories: {
             type: string;
             defaultValue: boolean;
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot configuration.hierarchical.defaultCollapsed.categoryNames
-         */
         categoryNames: {
             type: string;
             defaultValue: never[];
         };
-        /**
-         * #slot configuration.hierarchical.defaultCollapsed.topLevelCategories
-         */
         topLevelCategories: {
             type: string;
             defaultValue: boolean;
         };
-        /**
-         * #slot configuration.hierarchical.defaultCollapsed.subCategories
-         */
         subCategories: {
             type: string;
             defaultValue: boolean;

package/esm/RootModel/HierarchicalConfig.js

@@ -1,44 +1,25 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config HierarchicalConfigSchema
- * generally exists on the config.json or root config as configuration.hierarchical
- */
 export function HierarchicalConfigSchemaFactory() {
     return ConfigurationSchema('hierarchical', {
         sort: ConfigurationSchema('hierarchicalSort', {
-            /**
-             * #slot configuration.hierarchical.sort.trackNames
-             */
             trackNames: {
                 type: 'boolean',
                 defaultValue: false,
             },
-            /**
-             * #slot configuration.hierarchical.sort.categories
-             */
             categories: {
                 type: 'boolean',
                 defaultValue: false,
             },
         }),
         defaultCollapsed: ConfigurationSchema('defaultCollapsed', {
-            /**
-             * #slot configuration.hierarchical.defaultCollapsed.categoryNames
-             */
             categoryNames: {
                 type: 'stringArray',
                 defaultValue: [],
             },
-            /**
-             * #slot configuration.hierarchical.defaultCollapsed.topLevelCategories
-             */
             topLevelCategories: {
                 type: 'boolean',
                 defaultValue: false,
             },
-            /**
-             * #slot configuration.hierarchical.defaultCollapsed.subCategories
-             */
             subCategories: {
                 type: 'boolean',
                 defaultValue: false,

package/esm/RootModel/InternetAccounts.d.ts

@@ -1,28 +1,12 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { UriLocation } from '@jbrowse/core/util';
-import { Instance } from 'mobx-state-tree';
-/**
- * #stateModel InternetAccountsMixin
- * #category root
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { UriLocation } from '@jbrowse/core/util';
+import type { Instance } from 'mobx-state-tree';
 export declare function InternetAccountsRootModelMixin(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    /**
-     * #property
-     */
     internetAccounts: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
 }, {
-    /**
-     * #action
-     */
     initializeInternetAccount(internetAccountConfig: AnyConfigurationModel, initialSnapshot?: {}): any;
-    /**
-     * #action
-     */
     createEphemeralInternetAccount(internetAccountId: string, initialSnapshot: Record<string, unknown>, url: string): any;
-    /**
-     * #action
-     */
     findAppropriateInternetAccount(location: UriLocation): any;
 } & {
     afterCreate(): void;

package/esm/RootModel/InternetAccounts.js

@@ -1,21 +1,11 @@
 import { autorun } from 'mobx';
 import { addDisposer, types } from 'mobx-state-tree';
-/**
- * #stateModel InternetAccountsMixin
- * #category root
- */
 export function InternetAccountsRootModelMixin(pluginManager) {
     return types
         .model({
-        /**
-         * #property
-         */
         internetAccounts: types.array(pluginManager.pluggableMstType('internet account', 'stateModel')),
     })
         .actions(self => ({
-        /**
-         * #action
-         */
         initializeInternetAccount(internetAccountConfig, initialSnapshot = {}) {
             const internetAccountType = pluginManager.getInternetAccountType(internetAccountConfig.type);
             if (!internetAccountType) {
@@ -28,16 +18,12 @@ export function InternetAccountsRootModelMixin(pluginManager) {
             });
             return self.internetAccounts[length - 1];
         },
-        /**
-         * #action
-         */
         createEphemeralInternetAccount(internetAccountId, initialSnapshot, url) {
             let hostUri;
             try {
                 hostUri = new URL(url).origin;
             }
             catch (e) {
-                // ignore
             }
             const internetAccountSplit = internetAccountId.split('-');
             const configuration = {
@@ -56,11 +42,7 @@ export function InternetAccountsRootModelMixin(pluginManager) {
             self.internetAccounts.push(internetAccount);
             return internetAccount;
         },
-        /**
-         * #action
-         */
         findAppropriateInternetAccount(location) {
-            // find the existing account selected from menu
             const selectedId = location.internetAccountId;
             if (selectedId) {
                 const selectedAccount = self.internetAccounts.find(account => {
@@ -70,14 +52,12 @@ export function InternetAccountsRootModelMixin(pluginManager) {
                     return selectedAccount;
                 }
             }
-            // if no existing account or not found, try to find working account
             for (const account of self.internetAccounts) {
                 const handleResult = account.handlesLocation(location);
                 if (handleResult) {
                     return account;
                 }
             }
-            // if still no existing account, create ephemeral config to use
             return selectedId
                 ? this.createEphemeralInternetAccount(selectedId, {}, location.uri)
                 : null;

package/esm/Session/BaseSession.d.ts

@@ -1,122 +1,31 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-import { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import type { BaseRootModelType } from '../RootModel/BaseRootModel';
-/**
- * #stateModel BaseSessionModel
- *
- * base session shared by all JBrowse products. Be careful what you include
- * here, everything will use it.
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
 export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelType, JB_CONFIG_SCHEMA extends AnyConfigurationSchemaType>(_pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     name: import("mobx-state-tree").ISimpleType<string>;
     margin: import("mobx-state-tree").IType<number | undefined, number, number>;
 }, {
-    /**
-     * #volatile
-     * this is the globally "selected" object. can be anything. code that
-     * wants to deal with this should examine it to see what kind of thing it
-     * is.
-     */
     selection: unknown;
-    /**
-     * #volatile
-     * this is the globally "hovered" object. can be anything. code that
-     * wants to deal with this should examine it to see what kind of thing it
-     * is.
-     */
     hovered: unknown;
 } & {
-    /**
-     * #getter
-     */
     readonly root: import("mobx-state-tree").TypeOrStateTreeNodeToStateTreeNode<ROOT_MODEL_TYPE>;
 } & {
-    /**
-     * #getter
-     */
     readonly jbrowse: any;
-    /**
-     * #getter
-     */
     readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-    /**
-     * #getter
-     */
     readonly configuration: Instance<JB_CONFIG_SCHEMA>;
-    /**
-     * #getter
-     */
     readonly adminMode: boolean;
-    /**
-     * #getter
-     */
     readonly textSearchManager: import("@jbrowse/core/util").TextSearchManager;
 } & {
-    /**
-     * #getter
-     */
-    readonly assemblies: ({
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        aliases: {
-            type: string;
-            defaultValue: never[];
-            description: string;
-        };
-        sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-        refNameColors: {
-            type: string;
-            defaultValue: never[];
-            description: string;
-        };
-        refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            adapter: import("mobx-state-tree").IAnyModelType;
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-        cytobands: import("@jbrowse/core/configuration/configurationSchema" /**
-         * #getter
-         */).ConfigurationSchemaType<{
-            adapter: import("mobx-state-tree" /**
-             * #getter
-             */).IAnyModelType;
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-        displayName: {
-            type: string;
-            defaultValue: string;
-            description: string;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name">>>)[];
+    readonly assemblies: Instance<BaseAssemblyConfigSchema>[];
 } & {
-    /**
-     * #action
-     * set the global selection, i.e. the globally-selected object. can be a
-     * feature, a view, just about anything
-     */
     setSelection(thing: unknown): void;
-    /**
-     * #action
-     * clears the global selection
-     */
     clearSelection(): void;
-    /**
-     * #action
-     */
     setHovered(thing: unknown): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-/** Session mixin MST type for the most basic session */
 export type BaseSessionType = ReturnType<typeof BaseSessionModel>;
-/** Instance of the most basic possible session */
 export type BaseSession = Instance<BaseSessionType>;
-/** Type guard for BaseSession */
 export declare function isBaseSession(thing: IAnyStateTreeNode): thing is BaseSession;
-/** Type guard for whether a thing is JBrowse session */
 export declare function isSession(thing: unknown): thing is BaseSession;

package/esm/Session/BaseSession.js

@@ -1,120 +1,58 @@
-import { getParent, isStateTreeNode, types, } from 'mobx-state-tree';
 import { ElementId } from '@jbrowse/core/util/types/mst';
-/**
- * #stateModel BaseSessionModel
- *
- * base session shared by all JBrowse products. Be careful what you include
- * here, everything will use it.
- */
+import { getParent, isStateTreeNode, types } from 'mobx-state-tree';
 export function BaseSessionModel(_pluginManager) {
     return types
         .model({
-        /**
-         * #property
-         */
         id: ElementId,
-        /**
-         * #property
-         */
         name: types.string,
-        /**
-         * #property
-         */
         margin: 0,
     })
         .volatile(() => ({
-        /**
-         * #volatile
-         * this is the globally "selected" object. can be anything. code that
-         * wants to deal with this should examine it to see what kind of thing it
-         * is.
-         */
         selection: undefined,
-        /**
-         * #volatile
-         * this is the globally "hovered" object. can be anything. code that
-         * wants to deal with this should examine it to see what kind of thing it
-         * is.
-         */
         hovered: undefined,
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get root() {
             return getParent(self);
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get jbrowse() {
             return self.root.jbrowse;
         },
-        /**
-         * #getter
-         */
         get rpcManager() {
             return self.root.rpcManager;
         },
-        /**
-         * #getter
-         */
         get configuration() {
             return this.jbrowse.configuration;
         },
-        /**
-         * #getter
-         */
         get adminMode() {
             return self.root.adminMode;
         },
-        /**
-         * #getter
-         */
         get textSearchManager() {
             return self.root.textSearchManager;
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get assemblies() {
             return self.jbrowse.assemblies;
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         * set the global selection, i.e. the globally-selected object. can be a
-         * feature, a view, just about anything
-         */
         setSelection(thing) {
             self.selection = thing;
         },
-        /**
-         * #action
-         * clears the global selection
-         */
         clearSelection() {
             self.selection = undefined;
         },
-        /**
-         * #action
-         */
         setHovered(thing) {
             self.hovered = thing;
         },
     }));
 }
-/** Type guard for BaseSession */
 export function isBaseSession(thing) {
     return 'id' in thing && 'name' in thing && 'root' in thing;
 }
-/** Type guard for whether a thing is JBrowse session */
 export function isSession(thing) {
     return isStateTreeNode(thing) && isBaseSession(thing);
 }

package/esm/Session/Connections.d.ts

@@ -1,13 +1,8 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
-/**
- * #stateModel ConnectionManagementSessionMixin
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BaseConnectionConfigModel } from '@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig';
+import type { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
 export declare function ConnectionManagementSessionMixin(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    /**
-     * #property
-     */
     connectionInstances: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
         name: import("mobx-state-tree").ISimpleType<string>;
         tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
@@ -53,35 +48,8 @@ export declare function ConnectionManagementSessionMixin(pluginManager: PluginMa
         clear(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
 }, {
-    /**
-     * #getter
-     */
-    readonly connections: ({
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & 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/configurationSchema").ConfigurationSchemaType<{
-        name: {
-            type: string;
-            defaultValue: string;
-            description: string;
-        };
-        assemblyNames: {
-            type: string;
-            defaultValue: never[];
-            description: string;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>)[];
+    readonly connections: BaseConnectionConfigModel[];
 } & {
-    /**
-     * #action
-     */
     makeConnection(configuration: AnyConfigurationModel, initialSnapshot?: {}): ({
         name: string;
         tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
@@ -179,31 +147,12 @@ export declare function ConnectionManagementSessionMixin(pluginManager: PluginMa
         setTrackConfs(trackConfs: AnyConfigurationModel[]): void;
         clear(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
-    /**
-     * #action
-     */
     prepareToBreakConnection(configuration: AnyConfigurationModel): (Record<string, number> | (() => void))[] | undefined;
-    /**
-     * #action
-     */
     breakConnection(configuration: AnyConfigurationModel): void;
-    /**
-     * #action
-     */
     deleteConnection(configuration: AnyConfigurationModel): any;
-    /**
-     * #action
-     */
     addConnectionConf(connectionConf: AnyConfigurationModel): any;
-    /**
-     * #action
-     */
     clearConnections(): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-/** Session mixin MST type for a session that has connections */
 export type SessionWithConnectionsType = ReturnType<typeof ConnectionManagementSessionMixin>;
-/** Instance of a session that has connections: `connectionInstances`,
- * `makeConnection()`, etc. */
 export type SessionWithConnections = Instance<SessionWithConnectionsType>;
-/** Type guard for SessionWithConnections */
 export declare function isSessionWithConnections(session: IAnyStateTreeNode): session is SessionWithConnections;