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

package/esm/RootModel/BaseRootModel.d.ts

@@ -530,10 +530,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
         }, 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: RpcManager;
     } & {
         settleAssemblyResolution(assemblyName: string): Promise<void>;

package/esm/RootModel/HierarchicalConfig.d.ts

@@ -5,63 +5,37 @@
  */
 export declare function HierarchicalConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     readonly sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot configuration.hierarchical.sort.trackNames
-         * start the track selector with tracks sorted alphabetically inside each
-         * category rather than in config order. Only the initial state — the
-         * selector's own "Sort track names" toggle overrides it from then on
-         */
         readonly trackNames: {
-            readonly type: "boolean";
-            readonly defaultValue: false;
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
         };
-        /**
-         * #slot configuration.hierarchical.sort.categories
-         * start the track selector with categories sorted alphabetically rather
-         * than in config order. Only the initial state — the selector's own
-         * "Sort categories" toggle overrides it from then on
-         */
         readonly categories: {
-            readonly type: "boolean";
-            readonly defaultValue: false;
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    /**
-     * #slot configuration.hierarchical.defaultFolderCategories
-     */
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
     readonly defaultFolderCategories: {
-        readonly type: "stringArray";
-        readonly description: "list of category names to display as folders by default";
-        readonly defaultValue: readonly [];
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
     };
     readonly defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot configuration.hierarchical.defaultCollapsed.categoryNames
-         * named top-level categories that start collapsed, e.g.
-         * `['ENCODE', 'RNA-seq']`. Once a user expands or collapses anything, the
-         * selector remembers their state instead
-         */
         readonly categoryNames: {
-            readonly type: "stringArray";
-            readonly defaultValue: readonly [];
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
         };
-        /**
-         * #slot configuration.hierarchical.defaultCollapsed.topLevelCategories
-         * start every top-level category collapsed, so a config with many
-         * categories opens as a short list rather than a wall of tracks
-         */
         readonly topLevelCategories: {
-            readonly type: "boolean";
-            readonly defaultValue: false;
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
         };
-        /**
-         * #slot configuration.hierarchical.defaultCollapsed.subCategories
-         * start every nested category collapsed while leaving the top level
-         * open, for deeply categorized track sets
-         */
         readonly subCategories: {
-            readonly type: "boolean";
-            readonly defaultValue: false;
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;

package/esm/RootModel/PreferencesConfig.d.ts

@@ -7,62 +7,31 @@
  * override map layered over config defaults, at app scope.
  */
 export declare function PreferencesConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot configuration.preferences.animationMode
-     * controls feature-layout animations: 'enabled' always animates (the
-     * default), 'system' respects the OS prefers-reduced-motion setting,
-     * 'disabled' never animates
-     */
     readonly animationMode: {
-        readonly model: import("@jbrowse/mobx-state-tree").ISimpleType<"disabled" | "enabled" | "system">;
-        readonly type: "stringEnum";
-        readonly defaultValue: "enabled";
+        type: "stringEnum";
+    } & {
+        model: import("@jbrowse/mobx-state-tree").ISimpleType<"disabled" | "enabled" | "system">;
+    } & {
+        defaultValue: string;
     };
-    /**
-     * #slot configuration.preferences.scrollZoom
-     * when true, scrolling the mouse wheel over a track zooms in and out
-     * without holding Ctrl. Applies globally to all wheel-zoom views.
-     */
     readonly scrollZoom: {
-        readonly type: "boolean";
-        readonly defaultValue: false;
+        type: "boolean";
+    } & {
+        defaultValue: boolean;
     };
-    /**
-     * #slot configuration.preferences.numberGrouping
-     * when true (the default), numbers are displayed with thousand separators
-     * — `chr1:1,234,567`. Turn it off to render them bare, which is what you
-     * want if you copy coordinates out of JBrowse into tools that won't accept
-     * the commas. Applies to every displayed number, and takes effect on
-     * reload.
-     */
     readonly numberGrouping: {
-        readonly type: "boolean";
-        readonly defaultValue: true;
+        type: "boolean";
+    } & {
+        defaultValue: boolean;
     };
-    /**
-     * #slot configuration.preferences.useWorkspaces
-     * when true, views open in the tabbed/tiled workspace layout rather than
-     * stacked vertically. Only the default: a session that names
-     * `useWorkspaces` itself (a shared snapshot, or a session spec carrying a
-     * `layout`) still wins, and a user's own toggle overrides it.
-     */
     readonly useWorkspaces: {
-        readonly type: "boolean";
-        readonly defaultValue: false;
+        type: "boolean";
+    } & {
+        defaultValue: boolean;
     };
-    /**
-     * #slot configuration.preferences.developerMode
-     * when true, the ordering-contract checks a display or plugin can break
-     * report themselves in the app rather than only in a development build.
-     * Off by default and deliberately not in the Preferences dialog: the
-     * messages are about code, and a reader who cannot change the code cannot
-     * act on one. Turn it on for a site that is running a plugin under
-     * development; a plugin author needs nothing here, since a plugin served
-     * from localhost arms the same channel on its own, as does
-     * `localStorage.jbrowseDeveloperMode`. Takes effect on reload.
-     */
     readonly developerMode: {
-        readonly type: "boolean";
-        readonly defaultValue: false;
+        type: "boolean";
+    } & {
+        defaultValue: boolean;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;

package/esm/RootModel/PreferencesConfig.js

@@ -37,9 +37,8 @@ export function PreferencesConfigSchemaFactory() {
         /**
          * #slot configuration.preferences.numberGrouping
          * when true (the default), numbers are displayed with thousand separators
-         * — `chr1:1,234,567`. Turn it off to render them bare, which is what you
-         * want if you copy coordinates out of JBrowse into tools that won't accept
-         * the commas. Applies to every displayed number, and takes effect on
+         * (`chr1:1,234,567`). Turn it off to display them without separators, for
+         * copying coordinates into tools that won't accept the commas. Applies to every displayed number, and takes effect on
          * reload.
          */
         numberGrouping: {

package/esm/RootModel/createConfigModel.d.ts

@@ -5,111 +5,117 @@ import type { IAnyType } from '@jbrowse/mobx-state-tree';
 declare function rootConfigurationSchema(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     readonly rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly defaultDriver: {
-            readonly type: "string";
-            readonly description: "the RPC driver to run data fetching on: MainThreadRpcDriver or WebWorkerRpcDriver. Leave empty to use the default for this application";
-            readonly defaultValue: "";
-            readonly advanced: true;
+            type: "string";
+        } & {
+            defaultValue: string;
         };
         readonly workerCount: {
-            readonly type: "number";
-            readonly description: "The number of workers to use. If 0 (the default) JBrowse will decide how many workers to use.";
-            readonly defaultValue: 0;
-            readonly advanced: true;
+            type: "number";
+        } & {
+            defaultValue: number;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
     readonly hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
             readonly trackNames: {
-                readonly type: "boolean";
-                readonly defaultValue: false;
+                type: "boolean";
+            } & {
+                defaultValue: boolean;
             };
             readonly categories: {
-                readonly type: "boolean";
-                readonly defaultValue: false;
+                type: "boolean";
+            } & {
+                defaultValue: boolean;
             };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
         readonly defaultFolderCategories: {
-            readonly type: "stringArray";
-            readonly description: "list of category names to display as folders by default";
-            readonly defaultValue: readonly [];
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
         };
         readonly defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
             readonly categoryNames: {
-                readonly type: "stringArray";
-                readonly defaultValue: readonly [];
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
             };
             readonly topLevelCategories: {
-                readonly type: "boolean";
-                readonly defaultValue: false;
+                type: "boolean";
+            } & {
+                defaultValue: boolean;
             };
             readonly subCategories: {
-                readonly type: "boolean";
-                readonly defaultValue: false;
+                type: "boolean";
+            } & {
+                defaultValue: boolean;
             };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
     readonly preferences: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly animationMode: {
-            readonly model: import("@jbrowse/mobx-state-tree").ISimpleType<"disabled" | "enabled" | "system">;
-            readonly type: "stringEnum";
-            readonly defaultValue: "enabled";
+            type: "stringEnum";
+        } & {
+            model: import("@jbrowse/mobx-state-tree").ISimpleType<"disabled" | "enabled" | "system">;
+        } & {
+            defaultValue: string;
         };
         readonly scrollZoom: {
-            readonly type: "boolean";
-            readonly defaultValue: false;
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
         };
         readonly numberGrouping: {
-            readonly type: "boolean";
-            readonly defaultValue: true;
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
         };
         readonly useWorkspaces: {
-            readonly type: "boolean";
-            readonly defaultValue: false;
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
         };
         readonly developerMode: {
-            readonly type: "boolean";
-            readonly defaultValue: false;
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
     readonly formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly feature: {
-            readonly type: "frozen";
-            readonly description: "adds extra fields to the feature details";
-            readonly defaultValue: {};
-            readonly contextVariable: ["feature"];
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
         };
         readonly subfeatures: {
-            readonly type: "frozen";
-            readonly description: "adds extra fields to the subfeatures of a feature";
-            readonly defaultValue: {};
-            readonly contextVariable: ["feature"];
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
         };
         readonly depth: {
-            readonly type: "maybeNumber";
-            readonly description: "levels of subfeature the formatDetails.subfeatures callback runs on, default 2";
+            type: "maybeNumber";
         };
         readonly maxDepth: {
-            readonly type: "maybeNumber";
-            readonly description: "hide subfeatures nested deeper than this, default no limit";
+            type: "maybeNumber";
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
     readonly formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly config: {
-            readonly type: "frozen";
-            readonly description: "formats configuration object in about dialog";
-            readonly defaultValue: {};
-            readonly contextVariable: ["config"];
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
         };
         readonly hideUris: {
-            readonly type: "boolean";
-            readonly defaultValue: false;
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
     readonly theme: {
-        readonly type: "frozen";
-        readonly defaultValue: {};
+        type: "frozen";
+    } & {
+        defaultValue: unknown;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
 /**
  * What an embedder may put in `createViewState`'s `configuration` option: every
  * root slot and sub-schema by name, values unchecked. Derived from the schema
@@ -121,120 +127,131 @@ export declare function createConfigModel(pluginManager: PluginManager, assembly
     configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
             readonly defaultDriver: {
-                readonly type: "string";
-                readonly description: "the RPC driver to run data fetching on: MainThreadRpcDriver or WebWorkerRpcDriver. Leave empty to use the default for this application";
-                readonly defaultValue: "";
-                readonly advanced: true;
+                type: "string";
+            } & {
+                defaultValue: string;
             };
             readonly workerCount: {
-                readonly type: "number";
-                readonly description: "The number of workers to use. If 0 (the default) JBrowse will decide how many workers to use.";
-                readonly defaultValue: 0;
-                readonly advanced: true;
+                type: "number";
+            } & {
+                defaultValue: number;
             };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
         readonly hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
             readonly sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                 readonly trackNames: {
-                    readonly type: "boolean";
-                    readonly defaultValue: false;
+                    type: "boolean";
+                } & {
+                    defaultValue: boolean;
                 };
                 readonly categories: {
-                    readonly type: "boolean";
-                    readonly defaultValue: false;
+                    type: "boolean";
+                } & {
+                    defaultValue: boolean;
                 };
-            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
             readonly defaultFolderCategories: {
-                readonly type: "stringArray";
-                readonly description: "list of category names to display as folders by default";
-                readonly defaultValue: readonly [];
+                type: "stringArray";
+            } & {
+                defaultValue: unknown;
             };
             readonly defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                 readonly categoryNames: {
-                    readonly type: "stringArray";
-                    readonly defaultValue: readonly [];
+                    type: "stringArray";
+                } & {
+                    defaultValue: unknown;
                 };
                 readonly topLevelCategories: {
-                    readonly type: "boolean";
-                    readonly defaultValue: false;
+                    type: "boolean";
+                } & {
+                    defaultValue: boolean;
                 };
                 readonly subCategories: {
-                    readonly type: "boolean";
-                    readonly defaultValue: false;
+                    type: "boolean";
+                } & {
+                    defaultValue: boolean;
                 };
-            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
         readonly preferences: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
             readonly animationMode: {
-                readonly model: import("@jbrowse/mobx-state-tree").ISimpleType<"disabled" | "enabled" | "system">;
-                readonly type: "stringEnum";
-                readonly defaultValue: "enabled";
+                type: "stringEnum";
+            } & {
+                model: import("@jbrowse/mobx-state-tree").ISimpleType<"disabled" | "enabled" | "system">;
+            } & {
+                defaultValue: string;
             };
             readonly scrollZoom: {
-                readonly type: "boolean";
-                readonly defaultValue: false;
+                type: "boolean";
+            } & {
+                defaultValue: boolean;
             };
             readonly numberGrouping: {
-                readonly type: "boolean";
-                readonly defaultValue: true;
+                type: "boolean";
+            } & {
+                defaultValue: boolean;
             };
             readonly useWorkspaces: {
-                readonly type: "boolean";
-                readonly defaultValue: false;
+                type: "boolean";
+            } & {
+                defaultValue: boolean;
             };
             readonly developerMode: {
-                readonly type: "boolean";
-                readonly defaultValue: false;
+                type: "boolean";
+            } & {
+                defaultValue: boolean;
             };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
         readonly formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
             readonly feature: {
-                readonly type: "frozen";
-                readonly description: "adds extra fields to the feature details";
-                readonly defaultValue: {};
-                readonly contextVariable: ["feature"];
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
             };
             readonly subfeatures: {
-                readonly type: "frozen";
-                readonly description: "adds extra fields to the subfeatures of a feature";
-                readonly defaultValue: {};
-                readonly contextVariable: ["feature"];
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
             };
             readonly depth: {
-                readonly type: "maybeNumber";
-                readonly description: "levels of subfeature the formatDetails.subfeatures callback runs on, default 2";
+                type: "maybeNumber";
             };
             readonly maxDepth: {
-                readonly type: "maybeNumber";
-                readonly description: "hide subfeatures nested deeper than this, default no limit";
+                type: "maybeNumber";
             };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
         readonly formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
             readonly config: {
-                readonly type: "frozen";
-                readonly description: "formats configuration object in about dialog";
-                readonly defaultValue: {};
-                readonly contextVariable: ["config"];
+                type: "frozen";
+            } & {
+                defaultValue: unknown;
             };
             readonly hideUris: {
-                readonly type: "boolean";
-                readonly defaultValue: false;
+                type: "boolean";
+            } & {
+                defaultValue: boolean;
             };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
         readonly theme: {
-            readonly type: "frozen";
-            readonly defaultValue: {};
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    assembly: IAnyType;
-    tracks: import("@jbrowse/mobx-state-tree").IArrayType<IAnyType>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
+    /**
+     * One genome in the ordinary case, several where the view draws them
+     * together — a circular view's synteny ribbons need both ends of an
+     * alignment on the circle. The order is the order a view lays them out
+     * in.
+     */
+    assemblies: import("@jbrowse/mobx-state-tree").IArrayType<IAnyType>;
+    tracks: import("@jbrowse/mobx-state-tree").IType<Record<string, unknown>[] | null | undefined, Record<string, unknown>[], Record<string, unknown>[]>;
     internetAccounts: import("@jbrowse/mobx-state-tree").IArrayType<IAnyType>;
     connections: import("@jbrowse/mobx-state-tree").IArrayType<IAnyType>;
     aggregateTextSearchAdapters: import("@jbrowse/mobx-state-tree").IArrayType<IAnyType>;
     plugins: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
 }, {
-    readonly assemblies: any[];
-    readonly assemblyName: string;
+    readonly assemblyNames: string[];
     readonly rpcManager: RpcManager;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export {};

package/esm/RootModel/createConfigModel.js

@@ -1,5 +1,6 @@
 import { ConfigurationSchema, FormatAboutConfigSchemaFactory, FormatDetailsConfigSchemaFactory, readConfObject, } from '@jbrowse/core/configuration';
 import RpcManager from '@jbrowse/core/rpc/RpcManager';
+import { expandLooseSearchIndex } from '@jbrowse/core/util/expandLooseSearchIndex';
 import { expandLooseTrackConfig } from '@jbrowse/core/util/tracks';
 import { getParent, types } from '@jbrowse/mobx-state-tree';
 import { HierarchicalConfigSchemaFactory } from './HierarchicalConfig.js';
@@ -22,32 +23,43 @@ export function createConfigModel(pluginManager, assemblyConfigSchemasType) {
     return (types
         .model('Configuration', {
         configuration: rootConfigurationSchema(),
-        assembly: assemblyConfigSchemasType,
-        tracks: types.array(pluginManager.pluggableConfigSchemaType('track')),
+        /**
+         * One genome in the ordinary case, several where the view draws them
+         * together — a circular view's synteny ribbons need both ends of an
+         * alignment on the circle. The order is the order a view lays them out
+         * in.
+         */
+        assemblies: types.array(assemblyConfigSchemasType),
+        tracks: types.frozen([]),
         internetAccounts: types.array(pluginManager.pluggableConfigSchemaType('internet account')),
         connections: types.array(pluginManager.pluggableConfigSchemaType('connection')),
         aggregateTextSearchAdapters: types.array(pluginManager.pluggableConfigSchemaType('text search adapter')),
         plugins: types.frozen(),
     })
-        // The one assembly is what every loose `{ trackId, uri }` track is on, so
-        // a snapshot need not repeat its name per track.
+        // The first assembly is what every loose `{ trackId, uri }` track is on,
+        // so a snapshot need not repeat its name per track.
         .preProcessSnapshot((snap) => {
-        const tracks = snap?.tracks;
-        const assemblyName = snap?.assembly
-            ?.name;
-        return Array.isArray(tracks)
+        const { tracks, aggregateTextSearchAdapters: indexes } = snap ?? {};
+        const assemblyName = snap?.assemblies?.[0]?.name;
+        return snap
             ? {
                 ...snap,
-                tracks: tracks.map(t => expandLooseTrackConfig(t, pluginManager, assemblyName)),
+                ...(Array.isArray(tracks)
+                    ? {
+                        tracks: tracks.map(t => expandLooseTrackConfig(t, pluginManager, assemblyName)),
+                    }
+                    : {}),
+                ...(Array.isArray(indexes)
+                    ? {
+                        aggregateTextSearchAdapters: indexes.map(i => expandLooseSearchIndex(i, assemblyName ? [assemblyName] : undefined)),
+                    }
+                    : {}),
             }
             : snap;
     })
         .views(self => ({
-        get assemblies() {
-            return [self.assembly];
-        },
-        get assemblyName() {
-            return readConfObject(self.assembly, 'name');
+        get assemblyNames() {
+            return self.assemblies.map(a => readConfObject(a, 'name'));
         },
         get rpcManager() {
             return getParent(self).rpcManager;