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

package/esm/Session/SessionTracks.d.ts

@@ -1,1656 +1,1619 @@
 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 SessionTracksManagerSessionMixin(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
+import type { IAnyStateTreeNode, IAnyType, Instance } from '@jbrowse/mobx-state-tree';
+export interface PlainTrackConfig {
+    trackId: string;
+    [key: string]: unknown;
+}
+export interface EditableTrackConfig {
+    node: IAnyStateTreeNode;
+    delta: PlainTrackConfig | undefined;
+}
+/**
+ * #stateModel SessionTracksManagerSessionMixin
+ */
+export declare function SessionTracksManagerSessionMixin(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
-    margin: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
-} & {
-    sessionTracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
+    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>, "sessionTracks" | "trackConfigDeltas"> & {
+    /**
+     * #property
+     * User-added session tracks (no matching admin config track). A non-admin's
+     * *edits* to an existing config track are stored as deltas
+     * (trackConfigDeltas), not here.
+     */
+    sessionTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<IAnyType>, [undefined]>;
+    /**
+     * #property
+     * Per-track config overrides for a non-admin, keyed by trackId, stored as a
+     * *delta* against the admin-owned base config (jbrowse.tracks entry) rather
+     * than a full copy — so a later admin change to an untouched field still
+     * flows through (see trackConfigDelta.ts). Frozen (not a typed track array)
+     * on purpose: a typed create() would fill defaults, erasing the "unset vs
+     * default" distinction the delta merge relies on.
+     *
+     * `stripDefault` for the reason every other persisted prop beside it has
+     * it: without it the empty map is written into every snapshot and every
+     * share link, so a session that never overrode a track still ships
+     * `"trackConfigDeltas":{}`. It was the one prop added since that convention
+     * without it.
+     */
+    trackConfigDeltas: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<Record<string, PlainTrackConfig>, Record<string, PlainTrackConfig>, Record<string, PlainTrackConfig>>, [undefined]>;
 }, {
     selection: unknown;
     hovered: unknown;
+    queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>][];
+    preferencesOverrides: import("mobx").ObservableMap<string, unknown>;
 } & {
-    readonly root: {
-        jbrowse: any;
-        session: any;
-        sessionPath: string;
-        assemblyManager: {
-            assemblies: import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").IModelType<{
-                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+    readonly root: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        jbrowse: IAnyType;
+        session: import("@jbrowse/mobx-state-tree").IMaybe<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<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").IStateTreeNode<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;
-                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")._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 & {
+                }, 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<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>>;
+                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
             }, {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
             } & {
                 getConf(arg: string): any;
-                readonly lowerCaseRefNameAliases: {
-                    [k: string]: string;
-                } | undefined;
             } & {
-                readonly initialized: boolean;
                 readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly aliases: string[];
                 readonly displayName: string;
-                hasName(name: string): boolean;
-                readonly allAliases: string[];
-                readonly allRefNames: string[] | undefined;
-                readonly lowerCaseRefNames: string[] | undefined;
-                readonly allRefNamesWithLowerCase: string[] | undefined;
-                readonly rpcManager: 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<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>>;
+                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
             }, {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
             } & {
                 getConf(arg: string): any;
-                readonly lowerCaseRefNameAliases: {
-                    [k: string]: string;
-                } | undefined;
             } & {
-                readonly initialized: boolean;
                 readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly aliases: string[];
                 readonly displayName: string;
-                hasName(name: string): boolean;
-                readonly allAliases: string[];
-                readonly allRefNames: string[] | undefined;
-                readonly lowerCaseRefNames: string[] | undefined;
-                readonly allRefNamesWithLowerCase: string[] | undefined;
-                readonly rpcManager: 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<{
-                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
-            }, {
+                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+                getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
+            has(asmName: string): boolean;
+            loadingAssembly(asmNames: string[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
+            }> & {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
             } & {
                 getConf(arg: string): any;
-                readonly lowerCaseRefNameAliases: {
-                    [k: string]: string;
-                } | undefined;
             } & {
-                readonly initialized: boolean;
                 readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly aliases: string[];
                 readonly displayName: string;
-                hasName(name: string): boolean;
-                readonly 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>;
-            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<{
-                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+                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<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<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<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<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>>;
+                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
             }, {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
             } & {
                 getConf(arg: string): any;
-                readonly lowerCaseRefNameAliases: {
-                    [k: string]: string;
-                } | undefined;
             } & {
-                readonly initialized: boolean;
                 readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly aliases: string[];
                 readonly displayName: string;
-                hasName(name: string): boolean;
-                readonly allAliases: string[];
-                readonly allRefNames: string[] | undefined;
-                readonly lowerCaseRefNames: string[] | undefined;
-                readonly allRefNamesWithLowerCase: string[] | undefined;
-                readonly rpcManager: 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<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: IAnyType;
+        session: import("@jbrowse/mobx-state-tree").IMaybe<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<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<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>>;
+                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
             }, {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
             } & {
                 getConf(arg: string): any;
-                readonly lowerCaseRefNameAliases: {
-                    [k: string]: string;
-                } | undefined;
             } & {
-                readonly initialized: boolean;
                 readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly aliases: string[];
                 readonly displayName: string;
-                hasName(name: string): boolean;
-                readonly allAliases: string[];
-                readonly allRefNames: string[] | undefined;
-                readonly lowerCaseRefNames: string[] | undefined;
-                readonly allRefNamesWithLowerCase: string[] | undefined;
-                readonly rpcManager: 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<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>>;
+                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
             }, {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
             } & {
                 getConf(arg: string): any;
-                readonly lowerCaseRefNameAliases: {
-                    [k: string]: string;
-                } | undefined;
             } & {
-                readonly initialized: boolean;
                 readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly aliases: string[];
                 readonly displayName: string;
-                hasName(name: string): boolean;
+                readonly refNameColors: string[];
+            } & {
                 readonly allAliases: string[];
+                hasName(name: string): boolean;
+            } & {
+                setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+                setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+            } & {
+                setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                    regions: import("@jbrowse/core/util").Region[];
+                    cytobands: import("@jbrowse/core/util").Feature[];
+                    geneticCodes: Record<string, number>;
+                }): void;
+                setError(e: unknown): void;
+                setLoadingP(p?: Promise<void>): void;
+                loadPre(): Promise<void>;
+            } & {
+                load(): Promise<void>;
+            } & {
+                afterAttach(): void;
+            } & {
+                readonly initialized: boolean;
+                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
-                readonly lowerCaseRefNames: string[] | undefined;
-                readonly allRefNamesWithLowerCase: string[] | undefined;
+                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: 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<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<{
-                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+                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<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<{
-                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
-            }, {
+                }, 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<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>>;
+                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
             }, {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
             } & {
                 getConf(arg: string): any;
-                readonly lowerCaseRefNameAliases: {
-                    [k: string]: string;
-                } | undefined;
             } & {
-                readonly initialized: boolean;
                 readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly aliases: string[];
                 readonly displayName: string;
-                hasName(name: string): boolean;
-                readonly allAliases: string[];
-                readonly allRefNames: string[] | undefined;
-                readonly lowerCaseRefNames: string[] | undefined;
-                readonly allRefNamesWithLowerCase: string[] | undefined;
-                readonly rpcManager: 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<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>>;
+                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
             }, {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
                 canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
             } & {
                 getConf(arg: string): any;
-                readonly lowerCaseRefNameAliases: {
-                    [k: string]: string;
-                } | undefined;
             } & {
-                readonly initialized: boolean;
                 readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly aliases: string[];
                 readonly displayName: string;
-                hasName(name: string): boolean;
-                readonly allAliases: string[];
-                readonly allRefNames: string[] | undefined;
-                readonly lowerCaseRefNames: string[] | undefined;
-                readonly allRefNamesWithLowerCase: string[] | undefined;
-                readonly rpcManager: 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;
@@ -1661,11 +1624,11 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
         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;
-        setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
+        setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<IAnyType>): void;
         setDefaultSession(): void;
         setSessionPath(path: string): void;
         renameCurrentSession(newName: string): void;
@@ -1673,48 +1636,222 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
 } & {
     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;
+} & {
+    getReferringMultiple(trackIds: string[]): Map<string, import("./ReferenceManagement.ts").ReferringNode[]>;
 } & {
-    getReferring(object: IAnyStateTreeNode): import("./ReferenceManagement.ts").ReferringNode[];
+    getReferring(trackId: string): import("./ReferenceManagement.ts").ReferringNode[];
 } & {
-    removeReferring(referring: import("./ReferenceManagement.ts").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
+    dereferenceTrack(trackId: string, referring: import("./ReferenceManagement.ts").ReferringNode[]): void;
 } & {
     readonly tracks: AnyConfigurationModel[];
-    readonly assemblies: {
-        sequence: {
-            trackId: string;
-        };
-    }[];
+} & {
+    getTrackById(id: string): AnyConfigurationModel | undefined;
     getTracksById(): Record<string, AnyConfigurationModel>;
 } & {
+    addSessionTrackConf(trackConf: AnyConfiguration): any;
+    publishTrackConf(trackConf: AnyConfiguration): any;
     addTrackConf(trackConf: AnyConfiguration): any;
+    updateTrackConfiguration(trackConf: {
+        trackId: string;
+        [key: string]: unknown;
+    }): void;
     deleteTrackConf(trackConf: AnyConfigurationModel): any;
 } & {
+    /**
+     * Per-track private working copies (non-admin), keyed by trackId. A plain
+     * Map — not observable, not persisted — mirroring the pluginManager
+     * hydration cache: it holds the live MST config node a shown track's
+     * in-place quick-edits mutate, so the shared frozen base is never touched.
+     * See
+     * [ADR-032](https://github.com/GMOD/jbrowse-components/blob/main/agent-docs/architecture-decision-records/adr-032-track-config-nodes-are-throwaway-views.md).
+     *
+     * Not evicted: it's a pure memoization cache, bounded by the count of
+     * distinct tracks shown this session (each entry a lazily-hydrated config
+     * node), holding no authoritative state — the persisted delta is the
+     * source of truth, and reset/programmatic edits keep a retained copy in
+     * sync. Retention is volatile RAM only (never serialized), so it's not
+     * worth a reference-counted prune at every track-removal path.
+     *
+     * Each entry carries the delta it mirrors, so a delta replaced from
+     * outside this mixin invalidates it — see `getEditableTrackConfig`.
+     */
+    editableTrackConfigs: Map<string, EditableTrackConfig>;
+} & {
+    /**
+     * #getter
+     * User-added session tracks first, then each admin config track with its
+     * delta (trackConfigDeltas) merged over it. A base track without a delta
+     * is returned unchanged by identity to keep the hydration cache warm.
+     */
     readonly tracks: AnyConfigurationModel[];
+    /**
+     * #method
+     * The overridden slots for `trackId` (empty when it has no delta): each
+     * changed setting's path, its base/default value and the edited value.
+     * Drives the "view changes" dialog opened from the edited badge.
+     */
+    getTrackConfigChanges(trackId: string): import("@jbrowse/core/util").TrackConfigChange[];
+    /**
+     * #method
+     * A non-admin's private working copy of a track config, created on first
+     * access from the current frozen (base+delta) value and cached by
+     * trackId, so a shown track's in-place quick-edits (setSlot) mutate this
+     * copy and never the shared frozen base node (see ADR-032). Undefined in
+     * admin mode — there the base jbrowse.tracks entry is edited in place.
+     * Called by TrackConfigurationReference during lazy hydration.
+     *
+     * Cached against the delta it was built from, not by trackId alone. A
+     * delta this mixin wrote re-stamps the entry, so the copy an edit is
+     * still being typed into is never swapped out mid-keystroke; a delta
+     * replaced from outside — an undo's `applySnapshot` on the session, a
+     * session restore — cannot, so the next read rebuilds the copy from the
+     * delta that now exists. Reading `trackConfigDeltas` here is also what
+     * makes an undo re-resolve the reference at all: the resolver's caller
+     * is already subscribed to it through `getTrackById`.
+     */
+    getEditableTrackConfig(trackId: string, frozenConfig: unknown, schemaType: IAnyType): IAnyStateTreeNode | undefined;
 } & {
-    addTrackConf(trackConf: AnyConfiguration): any;
-    deleteTrackConf(trackConf: AnyConfigurationModel): any;
-}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-    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>;
+    afterAttach(): void;
 } & {
-    sessionTracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
-}>>;
+    /**
+     * #action
+     * Add a track config to *this session*: it lands in `sessionTracks`,
+     * travels with the session when it is saved or shared, and never
+     * reaches the config.json the server hands every visitor.
+     *
+     * **The default destination.** Everything that is not an Add-track
+     * workflow wants this one, whoever is looking — a session spec's
+     * `sessionTracks`, a URL's `&sessionTracks=`, and every track a feature
+     * stands up on the user's behalf. Mirrors `addSessionConnectionConf` in
+     * the connections mixins.
+     */
+    addSessionTrackConf(trackConf: AnyConfiguration): any;
+    /**
+     * #action
+     * Publish a track config to the shared catalog if this user can, and
+     * fall back to their session if they cannot: an admin's goes to
+     * `jbrowse.tracks`, which the admin server writes back into the
+     * config.json every visitor is served; everyone else's goes to
+     * `sessionTracks`.
+     *
+     * **Only the "Add track" workflows.** Those are where an admin adding a
+     * track means to add it for the whole site. A track a feature stands up
+     * on the user's behalf — a search result, a computed consensus, a
+     * reconstruction's segment labels — is not a catalog entry, and one
+     * admin click on this publishes it to every visitor, again on the next
+     * click, with a per-launch trackId that defeats the dedupe.
+     * `addSessionTrackConf` above is the destination for those.
+     *
+     * An admin's track still goes to the session when it names an assembly
+     * the config.json does not carry — a session spec's, a MAF sample's own
+     * genome, a comparative view's synthesized pair. The Add-track widget
+     * takes its assembly from the containing view, so an admin adding a
+     * track while looking at one of those arrives here with a name no
+     * visitor can resolve, and publishing it writes an entry the server
+     * hands everyone and nobody can draw. The session is the one
+     * destination where that track works, so the click keeps working and
+     * the dangling entry is never written; a snackbar says which assembly
+     * moved it.
+     *
+     * **The snackbar names the assembly and not the track**, which is what
+     * lets a batch collapse to one message: `pushSnackbarMessage` dedupes on
+     * the exact text, and `BulkAddTracksWorkflow` publishes in a loop, so
+     * interpolating the track name stacked one identical-but-for-a-name
+     * toast per file over an admin adding thirty. The assembly is the whole
+     * of what an admin has to act on anyway.
+     */
+    publishTrackConf(trackConf: AnyConfiguration): any;
+    /**
+     * #action
+     * Deprecated alias of `addSessionTrackConf`. Call that, or
+     * `publishTrackConf`.
+     *
+     * @deprecated
+     *
+     * The session-scoped add under its old name, for the prebuilt plugin
+     * bundles that reach it by name at runtime. See the base mixin's copy
+     * for why it survives and why it now means the session; nothing in tree
+     * may call it.
+     */
+    addTrackConf(trackConf: AnyConfiguration): any;
+    /**
+     * #action
+     * Persist a non-admin's edited track config as a delta (trackConfigDeltas)
+     * against the admin-owned base — only the changed slots — so the edits
+     * persist and are shared while admin changes to untouched fields still
+     * flow through. A user-added session track (no base) is edited in place.
+     * Everything else (admin edits, opened connection tracks) defers to the
+     * base mixin, which routes connection tracks to connectionTrackConfigs and
+     * the rest to the jbrowse config.
+     */
+    updateTrackConfiguration(trackConf: PlainTrackConfig): void;
+    /**
+     * #action
+     * Drop a non-admin's delta (trackConfigDeltas) so the track reverts to
+     * its admin config (jbrowse.tracks) default. Unlike deleteTrackConf this
+     * does not dereference the track from open views — the base config
+     * re-resolves in place, so an open track stays open and simply reverts.
+     */
+    resetTrackConfiguration(trackId: string): void;
+    /**
+     * #action
+     */
+    deleteTrackConf(trackConf: AnyConfigurationModel): any[] | undefined;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
+/** Session mixin MST type for a session that has `sessionTracks` */
 export type SessionWithSessionTracksType = ReturnType<typeof SessionTracksManagerSessionMixin>;
+/** Instance of a session that has `sessionTracks` */
 export type SessionWithSessionTracks = Instance<SessionWithSessionTracksType>;
-export declare function isSessionWithSessionTracks(thing: IAnyStateTreeNode): thing is SessionWithSessionTracks;