@jbrowse/product-core 4.3.0 → 5.0.0-beta.1

package/esm/Session/MultipleViews.d.ts

@@ -1,1664 +1,1608 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { IBaseViewModel } from '@jbrowse/core/pluggableElementTypes';
 import type { IAnyStateTreeNode, Instance } from '@jbrowse/mobx-state-tree';
-export declare function MultipleViewsSessionMixin(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
+/**
+ * #stateModel MultipleViewsSessionMixin
+ */
+export declare function MultipleViewsSessionMixin(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
-    margin: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
-} & {
-    drawerPosition: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    focusedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    heldForMissingPlugins: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined, import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined, import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined>, [undefined]>;
+}, never>, "activeWidgets" | "drawerPosition" | "drawerWidth" | "minimized" | "widgets"> & {
+    drawerPosition: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("@jbrowse/core/util").DrawerPosition>, [undefined]>;
     drawerWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
-    widgets: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IAnyType>;
-    activeWidgets: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>>;
+    widgets: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IAnyType>, [undefined]>;
+    activeWidgets: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>>, [undefined]>;
     minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-} & {
+}, "stickyViewHeaders" | "useWorkspaces" | "views"> & {
+    /**
+     * #property
+     */
     views: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
+    /**
+     * #property
+     */
     stickyViewHeaders: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    useWorkspaces: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     * enables the tabbed/tiled workspace layout for this session. Undefined
+     * means unspecified — read `effectiveUseWorkspaces`.
+     */
+    useWorkspaces: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
 }, {
     selection: unknown;
     hovered: unknown;
+    queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>][];
+    preferencesOverrides: import("mobx").ObservableMap<string, unknown>;
 } & {
-    readonly root: {
-        jbrowse: any;
-        session: any;
-        sessionPath: string;
-        assemblyManager: {
-            assemblies: import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").IModelType<{
+    readonly root: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        jbrowse: import("@jbrowse/mobx-state-tree").IAnyType;
+        session: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IAnyType>;
+        sessionPath: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+        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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
                 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: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                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>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<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>>;
+        }, {
+            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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
                 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>;
-                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>>>;
-        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
-            readonly assemblyNameMap: Record<string, {
-                configuration: any;
-            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
-                error: unknown;
-                loadingP: Promise<void> | undefined;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
-                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
-                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                load(): Promise<void>;
             } & {
-                getConf(arg: string): any;
-                readonly lowerCaseRefNameAliases: {
-                    [k: string]: string;
-                } | undefined;
+                afterAttach(): void;
             } & {
                 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 namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-                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, }: {
-                    regions: import("@jbrowse/core/util").Region[];
-                    refNameAliases: {
-                        [x: string]: string;
-                    };
-                    cytobands: import("@jbrowse/core/util").Feature[];
-                }): 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>;
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
             } & {
-                getAdapterMapEntry(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
                 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: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
                 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: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
                 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>;
-                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;
-            readonly assemblyNamesList: any[];
-            readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
-            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-        } & {
-            waitForAssembly(assemblyName: string): Promise<({
-                configuration: any;
-            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
-                error: unknown;
-                loadingP: Promise<void> | undefined;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
-                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
-                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                load(): Promise<void>;
             } & {
-                getConf(arg: string): any;
-                readonly lowerCaseRefNameAliases: {
-                    [k: string]: string;
-                } | undefined;
+                afterAttach(): void;
             } & {
                 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 namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-                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, }: {
-                    regions: import("@jbrowse/core/util").Region[];
-                    refNameAliases: {
-                        [x: string]: string;
-                    };
-                    cytobands: import("@jbrowse/core/util").Feature[];
-                }): 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>;
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
             } & {
-                getAdapterMapEntry(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
                 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: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                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>;
-            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>;
-            isValidRefName(refName: string, assemblyName: string): boolean;
-        } & {
-            afterAttach(): void;
-            removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
-            addAssembly(configuration: any): void;
-        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<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<{
+                }, 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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
-                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")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
+            readonly assemblyNamesList: string[];
+            readonly configuredAssemblyNames: Set<string>;
+            readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
+                setSubschema(slotName: string, data: Record<string, unknown>): any;
+                setSlot(slotName: string, value: unknown): void;
+            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                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>>;
-        }, {
-            readonly assemblyNameMap: Record<string, {
-                configuration: any;
-            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                }, 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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
-                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")._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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
                 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: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                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>>>;
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            isValidRefName(refName: string, assemblyName: string): boolean;
         } & {
-            getCanonicalAssemblyName(asmName: string): string | undefined;
-            getCanonicalAssemblyName2(asmName: string): string;
-            get(asmName: string): ({
-                configuration: any;
-            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+            afterAttach(): void;
+            removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
+            addAssembly(configuration: any): void;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
+    }> & {
+        rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        adminMode: boolean;
+        error: unknown;
+        textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
+        pluginManager: PluginManager;
+    } & {
+        setError(error: unknown): void;
+        setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
+        setDefaultSession(): void;
+        setSessionPath(path: string): void;
+        renameCurrentSession(newName: string): void;
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+        jbrowse: import("@jbrowse/mobx-state-tree").IAnyType;
+        session: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IAnyType>;
+        sessionPath: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+        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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
-                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")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+        }, {
+            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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
                 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: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                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;
-            readonly assemblyNamesList: any[];
-            readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
-            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+                }, 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>>>;
         } & {
-            waitForAssembly(assemblyName: string): Promise<({
-                configuration: any;
-            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+            getCanonicalAssemblyName(asmName: string): string | undefined;
+            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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
                 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: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
-                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")._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<import("@jbrowse/mobx-state-tree").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>;
-                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>;
-            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>;
-            isValidRefName(refName: string, assemblyName: string): boolean;
-        } & {
-            afterAttach(): void;
-            removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
-            addAssembly(configuration: any): void;
-        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>>;
-    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
-        rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-        adminMode: boolean;
-        error: unknown;
-        textSearchManager: import("@jbrowse/core/util").TextSearchManager;
-        pluginManager: PluginManager;
-    } & {
-        setError(error: unknown): void;
-        setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
-        setDefaultSession(): void;
-        setSessionPath(path: string): void;
-        renameCurrentSession(newName: string): void;
-    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
-        jbrowse: import("@jbrowse/mobx-state-tree").IAnyType;
-        session: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IAnyType>;
-        sessionPath: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
-        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<{
+                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: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                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;
+                }, 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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
                 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>;
-                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>>;
-        }, {
-            readonly assemblyNameMap: Record<string, {
-                configuration: any;
-            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
-                error: unknown;
-                loadingP: Promise<void> | undefined;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
-                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
-                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                load(): Promise<void>;
             } & {
-                getConf(arg: string): any;
-                readonly lowerCaseRefNameAliases: {
-                    [k: string]: string;
-                } | undefined;
+                afterAttach(): void;
             } & {
                 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 namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-                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, }: {
-                    regions: import("@jbrowse/core/util").Region[];
-                    refNameAliases: {
-                        [x: string]: string;
-                    };
-                    cytobands: import("@jbrowse/core/util").Feature[];
-                }): 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>;
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
             } & {
-                getAdapterMapEntry(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                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;
+            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: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
                 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>;
-                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>>>;
-        } & {
-            getCanonicalAssemblyName(asmName: string): string | undefined;
-            getCanonicalAssemblyName2(asmName: string): string;
-            get(asmName: string): ({
-                configuration: any;
-            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
-                error: unknown;
-                loadingP: Promise<void> | undefined;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
-                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
-                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                load(): Promise<void>;
             } & {
-                getConf(arg: string): any;
-                readonly lowerCaseRefNameAliases: {
-                    [k: string]: string;
-                } | undefined;
+                afterAttach(): void;
             } & {
                 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 namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-                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, }: {
-                    regions: import("@jbrowse/core/util").Region[];
-                    refNameAliases: {
-                        [x: string]: string;
-                    };
-                    cytobands: import("@jbrowse/core/util").Feature[];
-                }): 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>;
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
             } & {
-                getAdapterMapEntry(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
                 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: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                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;
-            readonly assemblyNamesList: any[];
-            readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
-            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-        } & {
-            waitForAssembly(assemblyName: string): Promise<({
-                configuration: any;
-            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                }, 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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
                 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: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                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<import("@jbrowse/mobx-state-tree").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: import("@jbrowse/core/rpc/RpcManager").default;
                 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: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                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;
@@ -1669,7 +1613,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
         rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         adminMode: boolean;
         error: unknown;
-        textSearchManager: import("@jbrowse/core/util").TextSearchManager;
+        textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
         pluginManager: PluginManager;
     } & {
         setError(error: unknown): void;
@@ -1681,63 +1625,257 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
 } & {
     readonly jbrowse: any;
     readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-    readonly configuration: {
-        [x: string]: any;
-    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+    readonly configuration: 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 adminMode: boolean;
-    readonly textSearchManager: import("@jbrowse/core/util").TextSearchManager;
+    readonly textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
+} & {
+    readonly assemblies: import("@jbrowse/core/assemblyManager").BaseAssemblyConfigModel[];
+    readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType | undefined;
+    readonly DialogProps: Record<string, unknown> | undefined;
 } & {
-    readonly assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
+    getPreferenceDefault(key: string): unknown;
+    getPreference(key: string): unknown;
+    getDisplayTypeDefault(displayType: string, slot: string): unknown;
+    getDisplayTypeDefaults(): {
+        displayType: string;
+        slot: string;
+        value: unknown;
+    }[];
+    getPreferenceChanges(): import("@jbrowse/core/util").TrackConfigChange[];
 } & {
+    readonly animationMode: import("@jbrowse/core/util").AnimationMode;
+    readonly scrollZoom: boolean;
+    readonly numberGrouping: boolean;
+} & {
+    afterAttach(): void;
     setSelection(thing: unknown): void;
     clearSelection(): void;
     setHovered(thing: unknown): void;
+    setHighlightsVisible(arg: boolean): void;
+    revealHighlights(): void;
+    setPreferenceOverride(key: string, value: unknown): void;
+    clearPreferenceOverrides(): void;
+    clearPreferenceOverride(key: string): void;
+    resetPreferenceChange(path: string[]): void;
+    setScrollZoom(flag: boolean): void;
+    setDisplayTypeDefault(displayType: string, slot: string, value: unknown): void;
+    setName(str: string): void;
+    setFocusedViewId(viewId: string | undefined): void;
+    removeActiveDialog(): void;
+    queueDialog(doneCallback: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
 } & {
-    readonly visibleWidget: any;
+    snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
+    errorDialog: import("@jbrowse/core/ui/SnackbarModel").ErrorDialogState | undefined;
 } & {
-    setDrawerPosition(arg: string): void;
-    updateDrawerWidth(drawerWidth: number): number;
-    resizeDrawer(distance: number): number;
-    addWidget(typeName: string, id: string, initialState?: {}, conf?: unknown): any;
+    readonly snackbarMessageSet: Map<string, import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
+} & {
+    notify(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction | import("@jbrowse/core/util").SnackAction[]): void;
+    notifyError(errorMessage: string, error?: unknown, extra?: unknown, action?: import("@jbrowse/core/util").SnackAction): void;
+    setErrorDialog(state: import("@jbrowse/core/ui/SnackbarModel").ErrorDialogState | undefined): void;
+    pushSnackbarMessage(message: string, level?: import("@jbrowse/core/util").NotificationLevel, actions?: import("@jbrowse/core/util").SnackAction[]): void;
+    popSnackbarMessage(): import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage | undefined;
+    removeSnackbarMessage(message: string): void;
+} & {
+    readonly visibleWidget: import("@jbrowse/core/util").Widget | undefined;
+} & {
+    poppedOut: boolean;
+} & {
+    readonly drawerVisible: boolean;
+} & {
+    setDrawerPosition(arg: import("@jbrowse/core/util").DrawerPosition): void;
+    updateDrawerWidth(drawerWidth: number, availableWidth?: number): number;
+    resizeDrawer(distance: number, availableWidth?: number): number;
+    addWidget(typeName: string, id: string, initialState?: any, conf?: unknown): any;
     showWidget(widget: any): void;
-    hasWidget(widget: any): boolean;
     hideWidget(widget: any): void;
     minimizeWidgetDrawer(): void;
     showWidgetDrawer(): void;
+    popoutWidget(): void;
+    returnWidgetToDrawer(): void;
     hideAllWidgets(): void;
     editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel | {
         trackId: string;
+    }, opts?: {
+        expandedDisplayId?: string;
     }): void;
     afterAttach(): void;
 } & {
-    moveViewDown(id: string): void;
-    moveViewUp(id: string): void;
-    moveViewToTop(id: string): void;
-    moveViewToBottom(id: string): void;
-    addView(typeName: string, initialState?: {}): any;
+    /**
+     * #getter
+     * resolved workspaces flag (never undefined): this session's value, else
+     * the user preference over the `configuration.preferences.useWorkspaces`
+     * admin default. Every consumer reads this, not the raw property — only
+     * sessions built from a snapshot or a spec `layout` set that, so the
+     * admin default is what reaches the arrivals that bypass defaultSession.
+     */
+    readonly effectiveUseWorkspaces: boolean;
+    /**
+     * #getter
+     * what `effectiveUseWorkspaces` becomes after `resetUseWorkspaces` — the
+     * admin default, with both this session's own value and the user's
+     * override out of the way. The Preferences reset diff needs this rather
+     * than the override map, which can't see a session-scoped value (a spec
+     * `layout`, a "move view to a tab") and so reported nothing to reset.
+     */
+    readonly defaultUseWorkspaces: boolean;
+} & {
+    /**
+     * #action
+     */
+    moveViewDown(id: string, scopeIds?: string[]): void;
+    /**
+     * #action
+     */
+    moveViewUp(id: string, scopeIds?: string[]): void;
+    /**
+     * #action
+     */
+    moveViewToTop(id: string, scopeIds?: string[]): void;
+    /**
+     * #action
+     */
+    moveViewToBottom(id: string, scopeIds?: string[]): void;
+    /**
+     * #action
+     * Put the named views into the given relative order, leaving views not
+     * named in their own slots.
+     *
+     * `session.views` is the one ordering, so this is how a channel that
+     * states an order in some other vocabulary gets it applied: a session
+     * spec's `layout` names views per panel, top to bottom, and that used to
+     * be honoured by the panel assignment array's order. Now the assignment
+     * carries membership only, so the layout says it here instead, once.
+     */
+    orderViews(ids: string[]): void;
+    /**
+     * #action
+     */
+    addView(typeName: string, initialState?: any): any;
+    /**
+     * #action
+     * swap `view` for a new view of `typeName`, in the slot it occupied.
+     *
+     * The launchers that build a view of a DIFFERENT type out of one you are
+     * already looking at — launch synteny view, read-vs-ref, split view —
+     * otherwise append, leaving the source view above the thing it produced
+     * and a stack of two views showing the same locus. This is the "replace"
+     * half of that offer, and a slot swap rather than remove-then-add so the
+     * new view lands where the reader was looking instead of at the bottom of
+     * the session.
+     *
+     * A launcher whose result is the SAME type as its source does not come
+     * here and should not: collapse introns offers "Replace current view" by
+     * navigating the view it was invoked on, which keeps the view's identity
+     * and so lets its snackbar offer an Undo. Swapping in a new node would
+     * leave nothing to undo onto.
+     *
+     * The slot is `session.views`, which is the order views render in under
+     * both layout modes (a tab's `viewIds` says which tab a view is in, not
+     * where in it), so the swap lands in place either way.
+     *
+     * WHICH panel is a separate question and this does not answer it: the
+     * new view arrives in no tab, and `homeUnassignedViews` puts it in the
+     * active panel — the same panel only when the replaced view was in the
+     * active one. In practice it is, since clicking into a view activates
+     * its panel, and the launch that offers a replace is a click on that
+     * view's own menu.
+     */
+    replaceView(view: IBaseViewModel, typeName: string, initialState?: any): any;
+    /**
+     * #action
+     */
     removeView(view: IBaseViewModel): void;
+    /**
+     * #action
+     * Take out every view the given session snapshot will not keep, before
+     * a whole-tree `applySnapshot` destroys it where it stands.
+     *
+     * Undo and redo are `applySnapshot` on the session
+     * (`core/util/TimeTraveller`, which calls this), and every view carries
+     * an `ElementId` — so MST reconciles by identifier and destroys what the
+     * target lacks, inside the action, with the components still mounted.
+     * Measured on a redo across a closed view, with the restored view
+     * repainted first: 4 liveliness reads of its display before this, 0
+     * after.
+     *
+     * A view that is present but has changed `type` is destroyed by that
+     * same reconciliation (`areSame` runs the type's `is()` before its id
+     * check), so identity here is the pair, not the id.
+     *
+     * **Views, and deliberately not what is under them.** A track or a
+     * display the snapshot drops is still destroyed in place, and that is
+     * not this door being worse than the others: `hideTrackGeneric` is a
+     * plain `tracks.remove` and measures louder (5 reads to undo's 4).
+     * Detaching one would be worse than the destroy it replaced — a
+     * detached display is a LIVE root, and `getContainingView` walks
+     * parents and throws when the walk finds no view, where a dead node
+     * only warns. At or above the view is the only place that walk still
+     * lands, which is why ADR-069's rule stops there.
+     */
+    takeOutViewsMissingFrom(snapshot: unknown): void;
+    /**
+     * #action
+     */
     setStickyViewHeaders(sticky: boolean): void;
+    /**
+     * #action
+     * set the workspaces layout for this session only, leaving the user's
+     * personal default untouched. For session-scoped intent — a spec
+     * carrying a `layout`, or an ad-hoc "move view to a tab/split" — where
+     * rewriting the visitor's global preference would be a surprise. The
+     * user-facing default toggle is `setUseWorkspacesPreference`.
+     */
     setUseWorkspaces(useWorkspaces: boolean): void;
+    /**
+     * #action
+     * the user-facing workspaces toggle: applies to this session and
+     * becomes their default for sessions that don't specify one. Persisted
+     * only here, on an explicit toggle — an autorun mirroring the resolved
+     * value would bake the admin default into every visitor's localStorage
+     * on first load, so a later admin change could never reach them.
+     */
+    setUseWorkspacesPreference(useWorkspaces: boolean): void;
+    /**
+     * #action
+     * drop both this session's explicit value and the user's override so
+     * workspaces falls back to the admin default
+     */
+    resetUseWorkspaces(): void;
     afterAttach(): void;
-}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<Omit<Omit<Omit<{
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
-    margin: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
-} & {
-    drawerPosition: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    focusedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    heldForMissingPlugins: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined, import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined, import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined>, [undefined]>;
+}, never>, "activeWidgets" | "drawerPosition" | "drawerWidth" | "minimized" | "widgets"> & {
+    drawerPosition: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("@jbrowse/core/util").DrawerPosition>, [undefined]>;
     drawerWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
-    widgets: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IAnyType>;
-    activeWidgets: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>>;
+    widgets: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IAnyType>, [undefined]>;
+    activeWidgets: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>>, [undefined]>;
     minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-} & {
+}, "stickyViewHeaders" | "useWorkspaces" | "views"> & {
+    /**
+     * #property
+     */
     views: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
+    /**
+     * #property
+     */
     stickyViewHeaders: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    useWorkspaces: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     * enables the tabbed/tiled workspace layout for this session. Undefined
+     * means unspecified — read `effectiveUseWorkspaces`.
+     */
+    useWorkspaces: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
 }>>;
+/** Session mixin MST type for a session that manages multiple views */
 export type SessionWithMultipleViewsType = ReturnType<typeof MultipleViewsSessionMixin>;
+/** Instance of a session with multiple views */
 export type SessionWithMultipleViews = Instance<SessionWithMultipleViewsType>;
+/** Type guard for SessionWithMultipleViews */
 export declare function isSessionWithMultipleViews(session: IAnyStateTreeNode): session is SessionWithMultipleViews;