@jbrowse/product-core 5.0.0-beta.13 → 5.0.0-beta.14

package/esm/RootModel/BaseRootModel.d.ts

@@ -7,7 +7,8 @@ import type { IAnyType, Instance, SnapshotIn } from '@jbrowse/mobx-state-tree';
 /**
  * #stateModel BaseRootModel
  * #category root
- * factory function for the Base-level root model shared by all products
+ * Holds the loaded config, the session, the assembly manager and the RPC
+ * manager. Every JBrowse product's root model composes this one.
  */
 export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionModelType, assemblyConfigSchema, rpcManagerOptions, }: {
     pluginManager: PluginManager;
@@ -47,13 +48,13 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
-            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
             regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
             canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             loadedGeneticCodes: Record<string, number> | undefined;
-            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
             statusMessage: string | undefined;
             statusProgress: number | undefined;
             statusSource: string | undefined;
@@ -72,7 +73,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
             setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
         } & {
-            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
                 regions: import("@jbrowse/core/util").Region[];
                 cytobands: import("@jbrowse/core/util").Feature[];
                 geneticCodes: Record<string, number>;
@@ -103,11 +104,12 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             getCanonicalRefName2(refName: string): string;
             isValidRefName(refName: string): boolean;
         } & {
+            isCircularRefName(refName: string): boolean;
             getRefNamePosition(refName: string): number | undefined;
             getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
             getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     }, {
@@ -128,13 +130,13 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
         }> & {
             error: unknown;
             loadingP: Promise<void> | undefined;
-            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
             regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
             canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             loadedGeneticCodes: Record<string, number> | undefined;
-            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
             statusMessage: string | undefined;
             statusProgress: number | undefined;
             statusSource: string | undefined;
@@ -153,7 +155,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
             setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
         } & {
-            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
                 regions: import("@jbrowse/core/util").Region[];
                 cytobands: import("@jbrowse/core/util").Feature[];
                 geneticCodes: Record<string, number>;
@@ -184,24 +186,25 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             getCanonicalRefName2(refName: string): string;
             isValidRefName(refName: string): boolean;
         } & {
+            isCircularRefName(refName: string): boolean;
             getRefNamePosition(refName: string): number | undefined;
             getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
             getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
             configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
-            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
             regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
             canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             loadedGeneticCodes: Record<string, number> | undefined;
-            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
             statusMessage: string | undefined;
             statusProgress: number | undefined;
             statusSource: string | undefined;
@@ -220,7 +223,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
             setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
         } & {
-            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
                 regions: import("@jbrowse/core/util").Region[];
                 cytobands: import("@jbrowse/core/util").Feature[];
                 geneticCodes: Record<string, number>;
@@ -251,11 +254,12 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             getCanonicalRefName2(refName: string): string;
             isValidRefName(refName: string): boolean;
         } & {
+            isCircularRefName(refName: string): boolean;
             getRefNamePosition(refName: string): number | undefined;
             getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
             getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
         has(asmName: string): boolean;
@@ -264,13 +268,13 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
         }> & {
             error: unknown;
             loadingP: Promise<void> | undefined;
-            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
             regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
             canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             loadedGeneticCodes: Record<string, number> | undefined;
-            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
             statusMessage: string | undefined;
             statusProgress: number | undefined;
             statusSource: string | undefined;
@@ -289,7 +293,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
             setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
         } & {
-            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
                 regions: import("@jbrowse/core/util").Region[];
                 cytobands: import("@jbrowse/core/util").Feature[];
                 geneticCodes: Record<string, number>;
@@ -320,24 +324,25 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             getCanonicalRefName2(refName: string): string;
             isValidRefName(refName: string): boolean;
         } & {
+            isCircularRefName(refName: string): boolean;
             getRefNamePosition(refName: string): number | undefined;
             getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
             getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
             configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
-            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
             regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
             canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             loadedGeneticCodes: Record<string, number> | undefined;
-            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
             statusMessage: string | undefined;
             statusProgress: number | undefined;
             statusSource: string | undefined;
@@ -356,7 +361,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
             setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
         } & {
-            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
                 regions: import("@jbrowse/core/util").Region[];
                 cytobands: import("@jbrowse/core/util").Feature[];
                 geneticCodes: Record<string, number>;
@@ -387,11 +392,12 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             getCanonicalRefName2(refName: string): string;
             isValidRefName(refName: string): boolean;
         } & {
+            isCircularRefName(refName: string): boolean;
             getRefNamePosition(refName: string): number | undefined;
             getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
             getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
         readonly assemblyNamesList: string[];
@@ -406,13 +412,13 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
         }> & {
             error: unknown;
             loadingP: Promise<void> | undefined;
-            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
             regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
             canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             loadedGeneticCodes: Record<string, number> | undefined;
-            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
             statusMessage: string | undefined;
             statusProgress: number | undefined;
             statusSource: string | undefined;
@@ -431,7 +437,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
             setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
         } & {
-            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
                 regions: import("@jbrowse/core/util").Region[];
                 cytobands: import("@jbrowse/core/util").Feature[];
                 geneticCodes: Record<string, number>;
@@ -462,24 +468,25 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             getCanonicalRefName2(refName: string): string;
             isValidRefName(refName: string): boolean;
         } & {
+            isCircularRefName(refName: string): boolean;
             getRefNamePosition(refName: string): number | undefined;
             getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
             getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
             configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
-            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
             regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
             canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             loadedGeneticCodes: Record<string, number> | undefined;
-            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
             statusMessage: string | undefined;
             statusProgress: number | undefined;
             statusSource: string | undefined;
@@ -498,7 +505,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
             setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
         } & {
-            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
                 regions: import("@jbrowse/core/util").Region[];
                 cytobands: import("@jbrowse/core/util").Feature[];
                 geneticCodes: Record<string, number>;
@@ -529,11 +536,12 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             getCanonicalRefName2(refName: string): string;
             isValidRefName(refName: string): boolean;
         } & {
+            isCircularRefName(refName: string): boolean;
             getRefNamePosition(refName: string): number | undefined;
             getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
             getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
         requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
@@ -541,13 +549,13 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
         }> & {
             error: unknown;
             loadingP: Promise<void> | undefined;
-            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
             regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
             canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             loadedGeneticCodes: Record<string, number> | undefined;
-            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
             statusMessage: string | undefined;
             statusProgress: number | undefined;
             statusSource: string | undefined;
@@ -566,7 +574,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
             setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
         } & {
-            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
                 regions: import("@jbrowse/core/util").Region[];
                 cytobands: import("@jbrowse/core/util").Feature[];
                 geneticCodes: Record<string, number>;
@@ -597,24 +605,25 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             getCanonicalRefName2(refName: string): string;
             isValidRefName(refName: string): boolean;
         } & {
+            isCircularRefName(refName: string): boolean;
             getRefNamePosition(refName: string): number | undefined;
             getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
             getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
             configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
         }, {
             error: unknown;
             loadingP: Promise<void> | undefined;
-            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
             regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
             canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
             cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             loadedGeneticCodes: Record<string, number> | undefined;
-            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
             statusMessage: string | undefined;
             statusProgress: number | undefined;
             statusSource: string | undefined;
@@ -633,7 +642,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
             setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
         } & {
-            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
                 regions: import("@jbrowse/core/util").Region[];
                 cytobands: import("@jbrowse/core/util").Feature[];
                 geneticCodes: Record<string, number>;
@@ -664,16 +673,17 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             getCanonicalRefName2(refName: string): string;
             isValidRefName(refName: string): boolean;
         } & {
+            isCircularRefName(refName: string): boolean;
             getRefNamePosition(refName: string): number | undefined;
             getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
             getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
-        }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+        }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
         isValidRefName(refName: string, assemblyName: string): boolean;
     } & {
         afterAttach(): void;
@@ -701,11 +711,39 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
      * #volatile
      */
     pluginManager: PluginManager;
+    /**
+     * #volatile
+     * What has to stop the moment the host lets go of this root: everything
+     * reaching outside the tree, like an autosave autorun.
+     *
+     * Not `addDisposer`, which fires only on destroy, and destroy follows a
+     * task later, once React has let go of the views it still holds (ADR-069).
+     * Work left running in that gap acts for the outgoing session. See
+     * `detach`.
+     */
+    detachDisposers: (() => void)[];
 } & {
     /**
      * #action
      */
     setError(error: unknown): void;
+    /**
+     * #action
+     * Register something that must stop when the host detaches this root.
+     */
+    addDetachDisposer(disposer: () => void): void;
+    /**
+     * #action
+     * Called when the host releases this root. Stops the worker pool and
+     * whatever was registered with `addDetachDisposer`, and leaves the tree
+     * itself alone.
+     *
+     * The caller destroys the tree on a later task
+     * (`scheduleDetachedDestroy`), which runs the `beforeDestroy` hooks in
+     * it; plugins rely on those hooks, so the destroy cannot be skipped.
+     * ADR-069.
+     */
+    detach(): void;
     /**
      * #action
      * Sets the active session. Remaps any legacy display type names
@@ -723,6 +761,9 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
      * Starts a new session from the config's defaultSession. An `id` in it
      * (a pasted session export carries one) is dropped, since sessions are
      * autosaved by id and each new one would otherwise overwrite the last.
+     * The name carries no date: the saved-session lists show when each was
+     * used, and a dated name saved back as the default gained another date
+     * on every new session.
      */
     setDefaultSession(): void;
     /**

package/esm/RootModel/BaseRootModel.js

@@ -15,7 +15,8 @@ import { filterSessionInPlace } from '../sessionUtils.js';
 /**
  * #stateModel BaseRootModel
  * #category root
- * factory function for the Base-level root model shared by all products
+ * Holds the loaded config, the session, the assembly manager and the RPC
+ * manager. Every JBrowse product's root model composes this one.
  */
 export function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionModelType, assemblyConfigSchema, rpcManagerOptions, }) {
     return types
@@ -63,6 +64,17 @@ export function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionM
          * #volatile
          */
         pluginManager,
+        /**
+         * #volatile
+         * What has to stop the moment the host lets go of this root: everything
+         * reaching outside the tree, like an autosave autorun.
+         *
+         * Not `addDisposer`, which fires only on destroy, and destroy follows a
+         * task later, once React has let go of the views it still holds (ADR-069).
+         * Work left running in that gap acts for the outgoing session. See
+         * `detach`.
+         */
+        detachDisposers: [],
     }))
         .actions(self => ({
         /**
@@ -71,6 +83,34 @@ export function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionM
         setError(error) {
             self.error = error;
         },
+        /**
+         * #action
+         * Register something that must stop when the host detaches this root.
+         */
+        addDetachDisposer(disposer) {
+            self.detachDisposers.push(disposer);
+        },
+        /**
+         * #action
+         * Called when the host releases this root. Stops the worker pool and
+         * whatever was registered with `addDetachDisposer`, and leaves the tree
+         * itself alone.
+         *
+         * The caller destroys the tree on a later task
+         * (`scheduleDetachedDestroy`), which runs the `beforeDestroy` hooks in
+         * it; plugins rely on those hooks, so the destroy cannot be skipped.
+         * ADR-069.
+         */
+        detach() {
+            // rpcManager is a plain object on a volatile, so MST teardown never
+            // reaches it
+            self.rpcManager.destroy();
+            const disposers = self.detachDisposers;
+            self.detachDisposers = [];
+            for (const disposer of disposers) {
+                disposer();
+            }
+        },
         /**
          * #action
          * Sets the active session. Remaps any legacy display type names
@@ -142,12 +182,15 @@ export function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionM
          * Starts a new session from the config's defaultSession. An `id` in it
          * (a pasted session export carries one) is dropped, since sessions are
          * autosaved by id and each new one would otherwise overwrite the last.
+         * The name carries no date: the saved-session lists show when each was
+         * used, and a dated name saved back as the default gained another date
+         * on every new session.
          */
         setDefaultSession() {
             const { id: _id, ...defaultSession } = self.jbrowse.defaultSession;
             this.setSession({
                 ...defaultSession,
-                name: `${defaultSession.name || 'New session'} ${new Date().toLocaleString()}`,
+                name: defaultSession.name || 'New session',
             });
         },
         /**

package/esm/RootModel/HierarchicalConfig.d.ts

@@ -1,7 +1,9 @@
 /**
  * #config HierarchicalConfigSchema
  * #category root
- * generally exists on the config.json or root config as configuration.hierarchical
+ * Sets the hierarchical track selector's starting sort order, and which
+ * categories show as folders or start collapsed. Found on the root config as
+ * `configuration.hierarchical`.
  */
 export declare function HierarchicalConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     readonly sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{

package/esm/RootModel/HierarchicalConfig.js

@@ -2,7 +2,9 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration';
 /**
  * #config HierarchicalConfigSchema
  * #category root
- * generally exists on the config.json or root config as configuration.hierarchical
+ * Sets the hierarchical track selector's starting sort order, and which
+ * categories show as folders or start collapsed. Found on the root config as
+ * `configuration.hierarchical`.
  */
 export function HierarchicalConfigSchemaFactory() {
     return ConfigurationSchema('hierarchical', {

package/esm/RootModel/InternetAccounts.d.ts

@@ -5,6 +5,8 @@ import type { Instance } from '@jbrowse/mobx-state-tree';
 /**
  * #stateModel InternetAccountsMixin
  * #category root
+ * Adds internet accounts to the root model, and finds the account that signs
+ * the request for a given file location.
  */
 export declare function InternetAccountsRootModelMixin(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
     /**

package/esm/RootModel/InternetAccounts.js

@@ -55,6 +55,8 @@ function warnScopeMismatch(internetAccountId, uri) {
 /**
  * #stateModel InternetAccountsMixin
  * #category root
+ * Adds internet accounts to the root model, and finds the account that signs
+ * the request for a given file location.
  */
 export function InternetAccountsRootModelMixin(pluginManager) {
     return types

package/esm/RootModel/PreferencesConfig.d.ts

@@ -1,10 +1,10 @@
 /**
  * #config PreferencesConfigSchema
  * #category root
- * admin/embedder defaults for user-facing preferences, found on the root config
- * as `configuration.preferences`. Individual users override these at runtime
- * (persisted to localStorage) via the session `getPreference` reader; a runtime
- * override map layered over config defaults, at app scope.
+ * Sets an admin's or embedder's defaults for user-facing preferences, found on
+ * the root config as `configuration.preferences`. Each user's runtime
+ * overrides, kept in localStorage, sit over these defaults at app scope, and
+ * the session's `getPreference` reads the result.
  */
 export declare function PreferencesConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     readonly animationMode: {

package/esm/RootModel/PreferencesConfig.js

@@ -3,10 +3,10 @@ import { types } from '@jbrowse/mobx-state-tree';
 /**
  * #config PreferencesConfigSchema
  * #category root
- * admin/embedder defaults for user-facing preferences, found on the root config
- * as `configuration.preferences`. Individual users override these at runtime
- * (persisted to localStorage) via the session `getPreference` reader; a runtime
- * override map layered over config defaults, at app scope.
+ * Sets an admin's or embedder's defaults for user-facing preferences, found on
+ * the root config as `configuration.preferences`. Each user's runtime
+ * overrides, kept in localStorage, sit over these defaults at app scope, and
+ * the session's `getPreference` reads the result.
  */
 export function PreferencesConfigSchemaFactory() {
     return ConfigurationSchema('Preferences', {

package/esm/RootModel/menuItems.d.ts

@@ -1,6 +1,5 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { MenuItem } from '@jbrowse/core/ui';
-import type { DialogComponentType } from '@jbrowse/core/util';
 interface RootWithDefaultSession {
     setDefaultSession: () => void;
 }
@@ -10,7 +9,7 @@ export declare function exportSessionMenuItem(): MenuItem;
 export declare function openTrackMenuItem(): MenuItem;
 export declare function openConnectionMenuItem(): MenuItem;
 export declare function pluginStoreMenuItem(): MenuItem;
-export declare function preferencesMenuItem(pluginManager: PluginManager, PreferencesDialog: DialogComponentType): MenuItem;
+export declare function preferencesMenuItem(pluginManager: PluginManager): MenuItem;
 interface HistoryManager {
     canUndo: boolean;
     canRedo: boolean;

package/esm/RootModel/menuItems.js

@@ -1,3 +1,4 @@
+import { lazy } from 'react';
 import { Cable } from '@jbrowse/core/ui/Icons';
 import AddIcon from '@mui/icons-material/Add';
 import ExtensionIcon from '@mui/icons-material/Extension';
@@ -8,6 +9,7 @@ import SettingsIcon from '@mui/icons-material/Settings';
 import StorageIcon from '@mui/icons-material/Storage';
 import UndoIcon from '@mui/icons-material/Undo';
 import { getShareableSessionSnapshot } from '../Session/index.js';
+const PreferencesDialog = lazy(() => import('../ui/PreferencesDialog.js'));
 // the renderer binds the active session into each onClick (see AppToolbar's
 // wrapMenuItems), so these handlers receive it as their argument
 const MULTI_VIEW_WARNING = 'This will add a track to the first view. Note: if you want to open a track in a specific view open the track selector for that view and use the add track (plus icon) in the bottom right';
@@ -84,10 +86,7 @@ export function pluginStoreMenuItem() {
         },
     };
 }
-// the dialog component differs per product, so it is passed in rather than
-// imported; typing it as DialogComponentType lets queueDialog accept it with no
-// cast (the inline call sites needed `as BaseSession` to reach queueDialog)
-export function preferencesMenuItem(pluginManager, PreferencesDialog) {
+export function preferencesMenuItem(pluginManager) {
     return {
         label: 'Preferences',
         icon: SettingsIcon,