@jbrowse/product-core 4.2.1 → 5.0.0-beta.1

package/esm/RootModel/BaseRootModel.d.ts

@@ -2,529 +2,815 @@ import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
 import RpcManager from '@jbrowse/core/rpc/RpcManager';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager';
+import type { RpcManagerOptions } from '@jbrowse/core/rpc/RpcManager';
 import type { IAnyType, Instance, SnapshotIn } from '@jbrowse/mobx-state-tree';
-export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionModelType, assemblyConfigSchema, }: {
+/**
+ * #stateModel BaseRootModel
+ * #category root
+ * factory function for the Base-level root model shared by all products
+ */
+export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionModelType, assemblyConfigSchema, rpcManagerOptions, }: {
     pluginManager: PluginManager;
     jbrowseModelType: IAnyType;
     sessionModelType: IAnyType;
     assemblyConfigSchema: BaseAssemblyConfigSchema;
+    /**
+     * How this product drives RPC — its worker factory and default driver. Taken
+     * here rather than left to each product to redefine the `rpcManager`
+     * volatile: a redefinition shadows this one but does not stop it being
+     * constructed, so every root built two managers and threw one away.
+     */
+    rpcManagerOptions?: RpcManagerOptions;
 }): import("@jbrowse/mobx-state-tree").IModelType<{
+    /**
+     * #property
+     * `jbrowse` is a mapping of the config.json into the in-memory state
+     * tree
+     */
     jbrowse: IAnyType;
+    /**
+     * #property
+     * `session` encompasses the currently active state of the app, including
+     * views open, tracks open in those views, etc.
+     */
     session: import("@jbrowse/mobx-state-tree").IMaybe<IAnyType>;
+    /**
+     * #property
+     */
     sessionPath: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    /**
+     * #property
+     */
     assemblyManager: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
         assemblies: import("@jbrowse/mobx-state-tree").IArrayType<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>>;
             volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            refNameAliases: {
-                [x: string]: string;
-            } | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").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;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
         } & {
             getConf(arg: string): any;
-            readonly lowerCaseRefNameAliases: {
-                [k: string]: string;
-            } | undefined;
         } & {
-            readonly initialized: boolean;
             readonly name: string;
-            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             readonly aliases: string[];
             readonly displayName: string;
-            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;
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
         } & {
-            getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(refName: string): string;
-            getRefNameColor(refName: string): string | undefined;
-            isValidRefName(refName: string): boolean;
-            getSeqAdapterRefName(canonicalRefName: string): string;
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
         } & {
-            setLoaded({ regions, refNameAliases, cytobands, }: {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
                 regions: import("@jbrowse/core/util").Region[];
-                refNameAliases: {
-                    [x: string]: string;
-                };
                 cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
             }): void;
             setError(e: unknown): void;
-            setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-            setRefNameAliases(aliases: {
-                [x: string]: string;
-            }): void;
-            setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
-            load(): Promise<void>;
             loadPre(): Promise<void>;
         } & {
-            getAdapterMapEntry(adapterConf: {
-                [x: string]: unknown;
-            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: RpcManager;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                [x: string]: string;
-            }>;
-            getReverseRefNameMapForAdapter(adapterConf: {
-                [x: string]: unknown;
-            }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                [x: string]: string;
-            }>;
-            afterCreate(): void;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     }, {
-        readonly assemblyNameMap: Record<string, {
-            configuration: any;
-        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+        unrecognizedReports: {
+            report(session: unknown, name: string, handlerCount: number, fire: () => unknown): void;
+            reportFor(session: unknown, name: string): {
+                handled: boolean;
+                claim?: Promise<void>;
+            } | undefined;
+        };
+    } & {
+        readonly assemblyNameMap: Record<string, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+            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>>;
             volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            refNameAliases: {
-                [x: string]: string;
-            } | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").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;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
         } & {
             getConf(arg: string): any;
-            readonly lowerCaseRefNameAliases: {
-                [k: string]: string;
-            } | undefined;
         } & {
-            readonly initialized: boolean;
             readonly name: string;
-            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             readonly aliases: string[];
             readonly displayName: string;
-            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;
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
         } & {
-            getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(refName: string): string;
-            getRefNameColor(refName: string): string | undefined;
-            isValidRefName(refName: string): boolean;
-            getSeqAdapterRefName(canonicalRefName: string): string;
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
         } & {
-            setLoaded({ regions, refNameAliases, cytobands, }: {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
                 regions: import("@jbrowse/core/util").Region[];
-                refNameAliases: {
-                    [x: string]: string;
-                };
                 cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
             }): void;
             setError(e: unknown): void;
-            setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-            setRefNameAliases(aliases: {
-                [x: string]: string;
-            }): void;
-            setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
-            load(): Promise<void>;
             loadPre(): Promise<void>;
         } & {
-            getAdapterMapEntry(adapterConf: {
-                [x: string]: unknown;
-            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: RpcManager;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                [x: string]: string;
-            }>;
-            getReverseRefNameMapForAdapter(adapterConf: {
-                [x: string]: unknown;
-            }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                [x: string]: string;
-            }>;
-            afterCreate(): void;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").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>>;
             volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            refNameAliases: {
-                [x: string]: string;
-            } | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").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;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
         } & {
             getConf(arg: string): any;
-            readonly lowerCaseRefNameAliases: {
-                [k: string]: string;
-            } | undefined;
         } & {
-            readonly initialized: boolean;
             readonly name: string;
-            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             readonly aliases: string[];
             readonly displayName: string;
-            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;
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
         } & {
-            getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(refName: string): string;
-            getRefNameColor(refName: string): string | undefined;
-            isValidRefName(refName: string): boolean;
-            getSeqAdapterRefName(canonicalRefName: string): string;
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
         } & {
-            setLoaded({ regions, refNameAliases, cytobands, }: {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
                 regions: import("@jbrowse/core/util").Region[];
-                refNameAliases: {
-                    [x: string]: string;
-                };
                 cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
             }): void;
             setError(e: unknown): void;
-            setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-            setRefNameAliases(aliases: {
-                [x: string]: string;
-            }): void;
-            setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
-            load(): Promise<void>;
             loadPre(): Promise<void>;
         } & {
-            getAdapterMapEntry(adapterConf: {
-                [x: string]: unknown;
-            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: RpcManager;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                [x: string]: string;
-            }>;
-            getReverseRefNameMapForAdapter(adapterConf: {
-                [x: string]: unknown;
-            }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                [x: string]: string;
-            }>;
-            afterCreate(): void;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
     } & {
         getCanonicalAssemblyName(asmName: string): string | undefined;
-        getCanonicalAssemblyName2(asmName: string): string;
-        get(asmName: string): ({
-            configuration: any;
-        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+        getDisplayName(asmName: string): string;
+        get(asmName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+            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>>;
             volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            refNameAliases: {
-                [x: string]: string;
-            } | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").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;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
         } & {
             getConf(arg: string): any;
-            readonly lowerCaseRefNameAliases: {
-                [k: string]: string;
-            } | undefined;
         } & {
-            readonly initialized: boolean;
             readonly name: string;
-            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             readonly aliases: string[];
             readonly displayName: string;
-            hasName(name: string): boolean;
+            readonly refNameColors: string[];
+        } & {
             readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            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 & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             readonly allRefNames: string[] | undefined;
-            readonly lowerCaseRefNames: string[] | undefined;
-            readonly allRefNamesWithLowerCase: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
             readonly rpcManager: RpcManager;
-            readonly refNameColors: string[];
         } & {
             readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
         } & {
             getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(refName: string): string;
             getRefNameColor(refName: string): string | undefined;
-            isValidRefName(refName: string): boolean;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
             getSeqAdapterRefName(canonicalRefName: string): string;
         } & {
-            setLoaded({ regions, refNameAliases, cytobands, }: {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").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>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").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;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            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 & {
                 regions: import("@jbrowse/core/util").Region[];
-                refNameAliases: {
-                    [x: string]: string;
-                };
                 cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
             }): void;
             setError(e: unknown): void;
-            setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-            setRefNameAliases(aliases: {
-                [x: string]: string;
-            }): void;
-            setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
-            load(): Promise<void>;
             loadPre(): Promise<void>;
         } & {
-            getAdapterMapEntry(adapterConf: {
-                [x: string]: unknown;
-            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: RpcManager;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                [x: string]: string;
-            }>;
-            getReverseRefNameMapForAdapter(adapterConf: {
-                [x: string]: unknown;
-            }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                [x: string]: string;
-            }>;
-            afterCreate(): void;
-        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").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;
+        loadingAssembly(asmNames: string[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
             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>>;
             volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            refNameAliases: {
-                [x: string]: string;
-            } | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").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;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
         } & {
             getConf(arg: string): any;
-            readonly lowerCaseRefNameAliases: {
-                [k: string]: string;
-            } | undefined;
         } & {
-            readonly initialized: boolean;
             readonly name: string;
-            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             readonly aliases: string[];
             readonly displayName: string;
-            hasName(name: string): boolean;
+            readonly refNameColors: string[];
+        } & {
             readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            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 & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             readonly allRefNames: string[] | undefined;
-            readonly lowerCaseRefNames: string[] | undefined;
-            readonly allRefNamesWithLowerCase: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
             readonly rpcManager: RpcManager;
-            readonly refNameColors: string[];
         } & {
             readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
         } & {
             getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(refName: string): string;
             getRefNameColor(refName: string): string | undefined;
-            isValidRefName(refName: string): boolean;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
             getSeqAdapterRefName(canonicalRefName: string): string;
         } & {
-            setLoaded({ regions, refNameAliases, cytobands, }: {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").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>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").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;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            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 & {
                 regions: import("@jbrowse/core/util").Region[];
-                refNameAliases: {
-                    [x: string]: string;
-                };
                 cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
             }): void;
             setError(e: unknown): void;
-            setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-            setRefNameAliases(aliases: {
-                [x: string]: string;
-            }): void;
-            setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
-            load(): Promise<void>;
             loadPre(): Promise<void>;
         } & {
-            getAdapterMapEntry(adapterConf: {
-                [x: string]: unknown;
-            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: RpcManager;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                [x: string]: string;
-            }>;
-            getReverseRefNameMapForAdapter(adapterConf: {
-                [x: string]: unknown;
-            }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                [x: string]: string;
-            }>;
-            afterCreate(): void;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").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: any[];
-        readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
+        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 rpcManager: RpcManager;
     } & {
-        waitForAssembly(assemblyName: string): Promise<({
-            configuration: any;
-        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+        settleAssemblyResolution(assemblyName: string): Promise<void>;
+    } & {
+        waitForAssembly(assemblyName: string): Promise<(import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+            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>>;
             volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            refNameAliases: {
-                [x: string]: string;
-            } | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").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;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
         } & {
             getConf(arg: string): any;
-            readonly lowerCaseRefNameAliases: {
-                [k: string]: string;
-            } | undefined;
         } & {
-            readonly initialized: boolean;
             readonly name: string;
-            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             readonly aliases: string[];
             readonly displayName: string;
-            hasName(name: string): boolean;
+            readonly refNameColors: string[];
+        } & {
             readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            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 & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             readonly allRefNames: string[] | undefined;
-            readonly lowerCaseRefNames: string[] | undefined;
-            readonly allRefNamesWithLowerCase: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
             readonly rpcManager: RpcManager;
-            readonly refNameColors: string[];
         } & {
             readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
         } & {
             getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(refName: string): string;
             getRefNameColor(refName: string): string | undefined;
-            isValidRefName(refName: string): boolean;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
             getSeqAdapterRefName(canonicalRefName: string): string;
         } & {
-            setLoaded({ regions, refNameAliases, cytobands, }: {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").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>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").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;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            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 & {
                 regions: import("@jbrowse/core/util").Region[];
-                refNameAliases: {
-                    [x: string]: string;
-                };
                 cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
             }): void;
             setError(e: unknown): void;
-            setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-            setRefNameAliases(aliases: {
-                [x: string]: string;
-            }): void;
-            setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
-            load(): Promise<void>;
             loadPre(): Promise<void>;
         } & {
-            getAdapterMapEntry(adapterConf: {
-                [x: string]: unknown;
-            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: RpcManager;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                [x: string]: string;
-            }>;
-            getReverseRefNameMapForAdapter(adapterConf: {
-                [x: string]: unknown;
-            }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                [x: string]: string;
-            }>;
-            afterCreate(): void;
-        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").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<{
             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>>;
             volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            refNameAliases: {
-                [x: string]: string;
-            } | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").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;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
         } & {
             getConf(arg: string): any;
-            readonly lowerCaseRefNameAliases: {
-                [k: string]: string;
-            } | undefined;
         } & {
-            readonly initialized: boolean;
             readonly name: string;
-            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             readonly aliases: string[];
             readonly displayName: string;
-            hasName(name: string): boolean;
+            readonly refNameColors: string[];
+        } & {
             readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            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 & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             readonly allRefNames: string[] | undefined;
-            readonly lowerCaseRefNames: string[] | undefined;
-            readonly allRefNamesWithLowerCase: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
             readonly rpcManager: RpcManager;
-            readonly refNameColors: string[];
         } & {
             readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
         } & {
             getCanonicalRefName(refName: string): string | undefined;
-            getCanonicalRefName2(refName: string): string;
             getRefNameColor(refName: string): string | undefined;
-            isValidRefName(refName: string): boolean;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
             getSeqAdapterRefName(canonicalRefName: string): string;
         } & {
-            setLoaded({ regions, refNameAliases, cytobands, }: {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").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>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").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;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            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 & {
                 regions: import("@jbrowse/core/util").Region[];
-                refNameAliases: {
-                    [x: string]: string;
-                };
                 cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
             }): void;
             setError(e: unknown): void;
-            setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-            setRefNameAliases(aliases: {
-                [x: string]: string;
-            }): void;
-            setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-            setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
             setLoadingP(p?: Promise<void>): void;
-            load(): Promise<void>;
             loadPre(): Promise<void>;
         } & {
-            getAdapterMapEntry(adapterConf: {
-                [x: string]: unknown;
-            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: RpcManager;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
-            }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                [x: string]: string;
-            }>;
-            getReverseRefNameMapForAdapter(adapterConf: {
-                [x: string]: unknown;
-            }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                [x: string]: string;
-            }>;
-            afterCreate(): void;
-        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").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<{
-            [x: string]: string;
-        } | undefined>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<{
-            [x: string]: string;
-        } | undefined>;
+        }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
         isValidRefName(refName: string, assemblyName: string): boolean;
     } & {
         afterAttach(): void;
@@ -532,18 +818,57 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
         addAssembly(configuration: any): void;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
 }, {
+    /**
+     * #volatile
+     */
     rpcManager: RpcManager;
+    /**
+     * #volatile
+     */
     adminMode: boolean;
+    /**
+     * #volatile
+     */
     error: unknown;
+    /**
+     * #volatile
+     */
     textSearchManager: TextSearchManager;
+    /**
+     * #volatile
+     */
     pluginManager: PluginManager;
 } & {
+    /**
+     * #action
+     */
     setError(error: unknown): void;
+    /**
+     * #action
+     * Sets the active session. Remaps any legacy display type names
+     * (e.g. LinearPileupDisplay → LinearAlignmentsDisplay), drops nodes whose
+     * pluggable type this build has no plugin for (see
+     * `pruneUnbuildableNodes`), then walks the resulting MST tree to drop open
+     * tracks whose config can't hydrate so shared sessions still load when
+     * referencing tracks that no longer exist. Both kinds of drop are surfaced
+     * to the user via a snackbar. If filtering throws, the previous session is
+     * restored.
+     */
     setSession(sessionSnapshot?: SnapshotIn<IAnyType>): void;
+    /**
+     * #action
+     */
     setDefaultSession(): void;
+    /**
+     * #action
+     */
     setSessionPath(path: string): void;
+    /**
+     * #action
+     */
     renameCurrentSession(newName: string): void;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export type BaseRootModelType = ReturnType<typeof BaseRootModelFactory>;
 export type BaseRootModel = Instance<BaseRootModelType>;
-export declare function isRootModel(thing: unknown): thing is BaseRootModelType;
+/** Type guard for checking if something is a JB root model */
+export declare function isRootModel(thing: unknown): thing is BaseRootModel;