@jbrowse/product-core 4.3.0 → 5.0.0-beta.2

package/esm/Session/Tracks.d.ts

@@ -1,1654 +1,1587 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfiguration, AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { IAnyStateTreeNode, Instance } from '@jbrowse/mobx-state-tree';
-export declare function TracksManagerSessionMixin(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
+/**
+ * #stateModel TracksManagerSessionMixin
+ */
+export declare function TracksManagerSessionMixin(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<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>;
-}, {
+    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>, never>, {
     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: 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>;
-                getRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string;
-                }>;
-                getReverseRefNameMapForAdapter(adapterConf: {
+                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;
-                }>;
-                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: 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: 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;
@@ -1659,7 +1592,7 @@ export declare function TracksManagerSessionMixin(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;
@@ -1671,41 +1604,162 @@ export declare function TracksManagerSessionMixin(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;
+} & {
+    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 assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
+    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;
+} & {
+    snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
+    errorDialog: import("@jbrowse/core/ui/SnackbarModel").ErrorDialogState | undefined;
+} & {
+    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;
 } & {
-    getReferring(object: IAnyStateTreeNode): import("./ReferenceManagement.ts").ReferringNode[];
+    afterAttach(): void;
 } & {
-    removeReferring(referring: import("./ReferenceManagement.ts").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
+    getReferringMultiple(trackIds: string[]): Map<string, import("./ReferenceManagement.ts").ReferringNode[]>;
 } & {
+    getReferring(trackId: string): import("./ReferenceManagement.ts").ReferringNode[];
+} & {
+    dereferenceTrack(trackId: string, referring: import("./ReferenceManagement.ts").ReferringNode[]): void;
+} & {
+    /**
+     * #getter
+     */
     readonly tracks: AnyConfigurationModel[];
-    readonly assemblies: {
-        sequence: {
-            trackId: string;
-        };
-    }[];
+} & {
+    /**
+     * #method
+     * Config for one trackId — a track, assembly sequence, or connection
+     * track — or undefined. Per-id reactive: every display resolves its
+     * config through this (via TrackConfigurationReference) and subscribes
+     * only to its own id, so one track's settings edit doesn't re-render the
+     * others.
+     */
+    getTrackById(id: string): AnyConfigurationModel | undefined;
+    /**
+     * #method
+     * Every track config the session can resolve, keyed by trackId. Prefer
+     * the per-id reactive `getTrackById(id)`: reading this whole map
+     * subscribes the caller to *every* track, so an edit to any one of them
+     * wakes it — the reason internal display config resolution moved off
+     * it. Kept for plugins that look up ids in a non-reactive context.
+     *
+     * @deprecated
+     */
     getTracksById(): Record<string, AnyConfigurationModel>;
 } & {
+    /**
+     * #action
+     * Add a track config to *this session*.
+     *
+     * This mixin's session has no separate session-track store, so the
+     * destination is the jbrowse config — which in the products that compose
+     * it (desktop) is the single user's own file rather than something a
+     * server hands other visitors, so the two scopes are the same place.
+     * Defined here anyway so that every session has it: a feature standing a
+     * track up on the user's behalf can then call one action everywhere
+     * instead of asking which mixin it landed on.
+     * `SessionTracksManagerSessionMixin` overrides it with the real
+     * session-scoped store.
+     */
+    addSessionTrackConf(trackConf: AnyConfiguration): any;
+    /**
+     * #action
+     * Add a track config wherever *this user's* catalog edits belong — the
+     * "Add track" workflows, where an admin adding a track means to add it
+     * for the whole site. `SessionTracksManagerSessionMixin` overrides it to
+     * send a non-admin's to the session instead; here there is only the one
+     * destination.
+     *
+     * Anything that is not an Add-track workflow wants
+     * `addSessionTrackConf`: a track a feature stands up on the user's behalf
+     * — a search result, a computed consensus, a reconstruction's labels — is
+     * not a catalog entry, and publishing one writes it into the config.json
+     * every visitor is served, once per click.
+     */
+    publishTrackConf(trackConf: AnyConfiguration): any;
+    /**
+     * #action
+     * Deprecated alias of `addSessionTrackConf`. Call that, or
+     * `publishTrackConf`, which say which destination they mean.
+     *
+     * @deprecated
+     *
+     * Kept because a prebuilt plugin bundle reaches this by name at runtime
+     * and cannot be recompiled — `jbrowse-plugin-protein3d` calls it, and a
+     * member lookup that stops resolving throws nothing at all
+     * (`pluginFacingSessionApi.test.ts` is the guard). It now means the
+     * session, which is the destination every such caller wanted: a track a
+     * plugin stands up for one user is not a catalog entry. Nothing in tree
+     * may call it — `no-restricted-syntax` says so.
+     *
+     * Spelled out rather than delegating through `this`, for the reason
+     * `SessionTracks.addToSession` is a plain closure: an action whose return
+     * type is inferred from a sibling's makes the pair circular.
+     */
     addTrackConf(trackConf: AnyConfiguration): any;
+    /**
+     * #action
+     * Persist edited track config back to the in-memory jbrowse config. The
+     * session-tracks mixin overrides this so a non-admin's edits become a
+     * shareable session-track override instead.
+     */
+    updateTrackConfiguration(trackConf: {
+        trackId: string;
+        [key: string]: unknown;
+    }): void;
+    /**
+     * #action
+     */
     deleteTrackConf(trackConf: AnyConfigurationModel): any;
-}, import("@jbrowse/mobx-state-tree")._NotCustomized, {
-    id: string;
-    name: string;
-    margin: number;
-} & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & import("@jbrowse/mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
+/** Session mixin MST type for a session that has tracks */
 export type SessionWithTracksType = ReturnType<typeof TracksManagerSessionMixin>;
+/** Instance of a session that has tracks */
 export type SessionWithTracks = Instance<SessionWithTracksType>;
+/** Type guard for SessionWithTracks */
 export declare function isSessionWithTracks(thing: IAnyStateTreeNode): thing is SessionWithTracks;