@jbrowse/product-core 2.6.3 → 2.7.1

package/dist/RootModel/BaseRootModel.d.ts

@@ -48,6 +48,8 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string | undefined;
             } | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+        } & {
+            getConf(arg: string): any;
         } & {
             readonly initialized: boolean;
             readonly name: string;
@@ -70,7 +72,9 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
         } & {
             setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
             setError(e: unknown): void;
-            setRegions(regions: import("@jbrowse/core/util").Region[]): void;
+            setRegions(regions: import("@jbrowse/core/util").Region[]): void; /**
+             * #action
+             */
             setRefNameAliases(aliases: {
                 [x: string]: string | undefined;
             }, lcAliases: {
@@ -85,123 +89,124 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                 [x: string]: string | undefined;
             }>;
-            /** Type guard for checking if something is a JB root model */
             getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
                 [x: string]: string | undefined;
             }>;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }, {
-        readonly assemblyNameMap: {
-            [key: string]: ({
-                configuration: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                error: unknown;
-                loaded: boolean;
-                loadingP: Promise<void> | undefined;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                lowerCaseRefNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-            } & {
-                readonly initialized: boolean;
-                readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                readonly aliases: string[];
-                readonly displayName: string | undefined;
-                hasName(name: string): boolean;
-                readonly allAliases: string[];
-                readonly allRefNames: string[] | undefined;
-                readonly lowerCaseRefNames: string[] | undefined;
-                readonly allRefNamesWithLowerCase: string[] | undefined;
-                readonly rpcManager: RpcManager;
-                readonly refNameColors: string[];
-            } & {
-                readonly refNames: string[] | undefined;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getRefNameColor(refName: string): string | undefined;
-                isValidRefName(refName: string): boolean;
-            } & {
-                setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
-                setError(e: unknown): void;
-                setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-                setRefNameAliases(aliases: {
-                    [x: string]: string | undefined;
-                }, lcAliases: {
-                    [x: string]: string | undefined;
-                }): void;
-                setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
-                load(): Promise<void>;
-                loadPre(): Promise<void>;
-            } & {
-                getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-                getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-            } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
-            }, {
-                error: unknown;
-                loaded: boolean;
-                loadingP: Promise<void> | undefined;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                lowerCaseRefNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-            } & {
-                readonly initialized: boolean;
-                readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                readonly aliases: string[];
-                readonly displayName: string | undefined;
-                hasName(name: string): boolean;
-                readonly allAliases: string[];
-                readonly allRefNames: string[] | undefined;
-                readonly lowerCaseRefNames: string[] | undefined;
-                readonly allRefNamesWithLowerCase: string[] | undefined;
-                readonly rpcManager: RpcManager;
-                readonly refNameColors: string[];
-            } & {
-                readonly refNames: string[] | undefined;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getRefNameColor(refName: string): string | undefined;
-                isValidRefName(refName: string): boolean;
-            } & {
-                setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
-                setError(e: unknown): void;
-                setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-                setRefNameAliases(aliases: {
-                    [x: string]: string | undefined;
-                }, lcAliases: {
-                    [x: string]: string | undefined;
-                }): void;
-                setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
-                load(): Promise<void>;
-                loadPre(): Promise<void>;
-            } & {
-                getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-                getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
-        };
+        readonly assemblyNameMap: Record<string, ({
+            configuration: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            error: unknown;
+            loaded: boolean;
+            loadingP: Promise<void> | undefined;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: {
+                [x: string]: string | undefined;
+            } | undefined;
+            lowerCaseRefNameAliases: {
+                [x: string]: string | undefined;
+            } | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly initialized: boolean;
+            readonly name: string;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly aliases: string[];
+            readonly displayName: string | undefined;
+            hasName(name: string): boolean;
+            readonly allAliases: string[];
+            readonly allRefNames: string[] | undefined;
+            readonly lowerCaseRefNames: string[] | undefined;
+            readonly allRefNamesWithLowerCase: string[] | undefined;
+            readonly rpcManager: RpcManager;
+            readonly refNameColors: string[];
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            isValidRefName(refName: string): boolean;
+        } & {
+            setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
+            setError(e: unknown): void;
+            setRegions(regions: import("@jbrowse/core/util").Region[]): void;
+            setRefNameAliases(aliases: {
+                [x: string]: string | undefined;
+            }, lcAliases: {
+                [x: string]: string | undefined;
+            }): void;
+            setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+            setLoadingP(p?: Promise<void> | undefined): void;
+            load(): Promise<void>;
+            loadPre(): Promise<void>;
+        } & {
+            getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+            getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+            getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+            configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
+        }, {
+            error: unknown;
+            loaded: boolean;
+            loadingP: Promise<void> | undefined;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: {
+                [x: string]: string | undefined;
+            } | undefined;
+            lowerCaseRefNameAliases: {
+                [x: string]: string | undefined;
+            } | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly initialized: boolean;
+            readonly name: string;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly aliases: string[];
+            readonly displayName: string | undefined;
+            hasName(name: string): boolean;
+            readonly allAliases: string[];
+            readonly allRefNames: string[] | undefined;
+            readonly lowerCaseRefNames: string[] | undefined;
+            readonly allRefNamesWithLowerCase: string[] | undefined;
+            readonly rpcManager: RpcManager;
+            readonly refNameColors: string[];
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            isValidRefName(refName: string): boolean;
+        } & {
+            setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
+            setError(e: unknown): void;
+            setRegions(regions: import("@jbrowse/core/util").Region[]): void;
+            setRefNameAliases(aliases: {
+                [x: string]: string | undefined;
+            }, lcAliases: {
+                [x: string]: string | undefined;
+            }): void;
+            setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+            setLoadingP(p?: Promise<void> | undefined): void;
+            load(): Promise<void>;
+            loadPre(): Promise<void>;
+        } & {
+            getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+            getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+            getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
     } & {
         get(asmName: string): ({
             configuration: any;
@@ -217,6 +222,8 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string | undefined;
             } | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+        } & {
+            getConf(arg: string): any;
         } & {
             readonly initialized: boolean;
             readonly name: string;
@@ -271,6 +278,8 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string | undefined;
             } | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+        } & {
+            getConf(arg: string): any;
         } & {
             readonly initialized: boolean;
             readonly name: string;
@@ -334,6 +343,8 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string | undefined;
             } | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+        } & {
+            getConf(arg: string): any;
         } & {
             readonly initialized: boolean;
             readonly name: string;
@@ -388,6 +399,8 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string | undefined;
             } | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+        } & {
+            getConf(arg: string): any;
         } & {
             readonly initialized: boolean;
             readonly name: string;
@@ -464,6 +477,8 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
              * #property
              */
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+        } & {
+            getConf(arg: string): any;
         } & {
             readonly initialized: boolean;
             readonly name: string;
@@ -476,7 +491,9 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             readonly lowerCaseRefNames: string[] | undefined;
             readonly allRefNamesWithLowerCase: string[] | undefined;
             readonly rpcManager: RpcManager;
-            readonly refNameColors: string[];
+            readonly refNameColors: string[]; /**
+             * #action
+             */
         } & {
             readonly refNames: string[] | undefined;
         } & {
@@ -524,6 +541,8 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
              * #property
              */
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+        } & {
+            getConf(arg: string): any;
         } & {
             readonly initialized: boolean;
             readonly name: string;
@@ -536,7 +555,9 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             readonly lowerCaseRefNames: string[] | undefined;
             readonly allRefNamesWithLowerCase: string[] | undefined;
             readonly rpcManager: RpcManager;
-            readonly refNameColors: string[];
+            readonly refNameColors: string[]; /**
+             * #action
+             */
         } & {
             readonly refNames: string[] | undefined;
         } & {

package/dist/RootModel/HierarchicalConfig.d.ts

@@ -21,21 +21,21 @@ export declare function HierarchicalConfigSchemaFactory(): import("@jbrowse/core
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         /**
-         * #slot configuration.hierarchical.defaultCollapse.categoryNames
+         * #slot configuration.hierarchical.defaultCollapsed.categoryNames
          */
         categoryNames: {
             type: string;
             defaultValue: never[];
         };
         /**
-         * #slot configuration.hierarchical.defaultCollapse.topLevelCategories
+         * #slot configuration.hierarchical.defaultCollapsed.topLevelCategories
          */
         topLevelCategories: {
             type: string;
             defaultValue: boolean;
         };
         /**
-         * #slot configuration.hierarchical.defaultCollapse.subCategories
+         * #slot configuration.hierarchical.defaultCollapsed.subCategories
          */
         subCategories: {
             type: string;

package/dist/RootModel/HierarchicalConfig.js

@@ -26,21 +26,21 @@ function HierarchicalConfigSchemaFactory() {
         }),
         defaultCollapsed: (0, configuration_1.ConfigurationSchema)('defaultCollapsed', {
             /**
-             * #slot configuration.hierarchical.defaultCollapse.categoryNames
+             * #slot configuration.hierarchical.defaultCollapsed.categoryNames
              */
             categoryNames: {
                 type: 'stringArray',
                 defaultValue: [],
             },
             /**
-             * #slot configuration.hierarchical.defaultCollapse.topLevelCategories
+             * #slot configuration.hierarchical.defaultCollapsed.topLevelCategories
              */
             topLevelCategories: {
                 type: 'boolean',
                 defaultValue: false,
             },
             /**
-             * #slot configuration.hierarchical.defaultCollapse.subCategories
+             * #slot configuration.hierarchical.defaultCollapsed.subCategories
              */
             subCategories: {
                 type: 'boolean',

package/dist/Session/BaseSession.d.ts

@@ -7,7 +7,7 @@ import type { BaseRootModelType } from '../RootModel/BaseRootModel';
  * base session shared by **all** JBrowse products. Be careful what you include
  * here, everything will use it.
  */
-export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelType, JB_CONFIG_SCHEMA extends AnyConfigurationSchemaType>(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
+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>;
@@ -52,6 +52,11 @@ export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelTy
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         aliases: {
+            /**
+             * #stateModel BaseSessionModel
+             * base session shared by **all** JBrowse products. Be careful what you include
+             * here, everything will use it.
+             */
             type: string;
             defaultValue: never[];
             description: string;
@@ -66,14 +71,16 @@ export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelTy
             adapter: import("mobx-state-tree").IAnyModelType;
         }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
         cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            adapter: import("mobx-state-tree").IAnyModelType;
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+            adapter: import("mobx-state-tree").IAnyModelType; /**
+             * #getter
+             */
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>; /**
+         * #getter
+         */
         displayName: {
             type: string;
             defaultValue: string;
-            description: string; /**
-             * #getter
-             */
+            description: string;
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name">>>)[];
 } & {

package/dist/Session/BaseSession.js

@@ -1,23 +1,20 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.isSession = exports.isBaseSession = exports.BaseSessionModel = void 0;
-const shortid_1 = __importDefault(require("shortid"));
+const nanoid_1 = require("@jbrowse/core/util/nanoid");
 const mobx_state_tree_1 = require("mobx-state-tree");
 /**
  * #stateModel BaseSessionModel
  * base session shared by **all** JBrowse products. Be careful what you include
  * here, everything will use it.
  */
-function BaseSessionModel(pluginManager) {
+function BaseSessionModel(_pluginManager) {
     return mobx_state_tree_1.types
         .model({
         /**
          * #property
          */
-        id: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.identifier, (0, shortid_1.default)()),
+        id: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.identifier, (0, nanoid_1.nanoid)()),
         /**
          * #property
          */

package/dist/Session/Connections.d.ts

@@ -1,7 +1,6 @@
 import PluginManager from '@jbrowse/core/PluginManager';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
-import { BaseConnectionConfigModel } from '@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig';
 /**
  * #stateModel ConnectionManagementSessionMixin
  */
@@ -159,7 +158,7 @@ export declare function ConnectionManagementSessionMixin(pluginManager: PluginMa
     /**
      * #action
      */
-    addConnectionConf(connectionConf: BaseConnectionConfigModel): any;
+    addConnectionConf(connectionConf: AnyConfigurationModel): any;
     /**
      * #action
      */

package/dist/Session/DialogQueue.d.ts

@@ -5,7 +5,7 @@ import { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
 /**
  * #stateModel DialogQueueSessionMixin
  */
-export declare function DialogQueueSessionMixin(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{}, {
+export declare function DialogQueueSessionMixin(_pluginManager: PluginManager): import("mobx-state-tree").IModelType<{}, {
     queueOfDialogs: [DialogComponentType, unknown][];
 } & {
     /**

package/dist/Session/DialogQueue.js

@@ -7,7 +7,7 @@ const BaseSession_1 = require("./BaseSession");
 /**
  * #stateModel DialogQueueSessionMixin
  */
-function DialogQueueSessionMixin(pluginManager) {
+function DialogQueueSessionMixin(_pluginManager) {
     return mobx_state_tree_1.types
         .model('DialogQueueSessionMixin', {})
         .volatile(() => ({