@jbrowse/product-core 4.3.0 → 5.0.0-beta.10

package/esm/Session/SessionTracks.d.ts

@@ -1,1656 +1,1350 @@
 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;
+    source: unknown;
+}
+/**
+ * #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>>;
+    highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType>>, [undefined]>;
+    highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    highlightLabelsVisible: 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
+     * Tracks the session added, each entry the base its edits
+     * (trackConfigDeltas) diff against, as a config.json entry is for a
+     * config track.
+     */
+    sessionTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>, [undefined]>;
+    /**
+     * #property
+     * Per-track config overrides, keyed by trackId, stored as a *delta*
+     * against the base config (the sessionTracks or jbrowse.tracks entry)
+     * rather than a full copy —
+     * so a later change to an untouched field of the base still flows through
+     * (see trackConfigDelta.ts). A `null` member resets a slot the base sets.
+     * An admin's edits land here too, and reach jbrowse.tracks only through
+     * `promoteTrackConfigDeltas`. 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;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+                regions: 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 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>;
+                getRefNamePosition(refName: string): number | undefined;
+                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/core/assemblyManager/assembly").Assembly>;
+        } & {
+            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;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+                regions: 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 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 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;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                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;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+                regions: 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 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 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;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                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>>>;
-        } & {
-            getCanonicalAssemblyName(asmName: string): string | undefined;
-            getCanonicalAssemblyName2(asmName: string): string;
-            get(asmName: 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>>) | 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;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+                regions: 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 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 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;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                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;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+                regions: 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 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 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;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string;
-                }>;
-                getReverseRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string;
-                }>;
-                afterCreate(): void;
+                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+                getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
-            readonly assemblyNamesList: any[];
+            readonly assemblyNamesList: string[];
+            readonly confByName: Map<string, AnyConfigurationModel>;
             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 & {
+            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;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+                regions: 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 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 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;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                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;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+                regions: 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 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;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getCanonicalRefName2(refName: string): string;
-                getRefNameColor(refName: string): string | undefined;
-                isValidRefName(refName: string): boolean;
-                getSeqAdapterRefName(canonicalRefName: string): 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, 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 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;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string;
-                }>;
-                getReverseRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string;
-                }>;
-                afterCreate(): void;
+                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+                getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
-            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>>;
-            }, {
+            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;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+                regions: 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 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>;
+                getRefNamePosition(refName: string): number | undefined;
+                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;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+                regions: 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 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 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;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                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;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+                regions: 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 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").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
-                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
-            }, {
-                error: unknown;
-                loadingP: Promise<void> | undefined;
-                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>;
+                getRefNamePosition(refName: string): number | undefined;
+                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>>;
+        }, {
+            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/core/assemblyManager/assembly").Assembly>;
         } & {
-            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;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+                regions: 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 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").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
-                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
-            }, {
-                error: unknown;
-                loadingP: Promise<void> | undefined;
-                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>;
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string;
-                }>;
-                getReverseRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string;
-                }>;
-                afterCreate(): void;
-            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
-            getRefNameMapForAdapter(adapterConf: {
-                [x: string]: unknown;
-            }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<{
-                [x: string]: string;
-            } | undefined>;
-            getReverseRefNameMapForAdapter(adapterConf: {
-                [x: string]: unknown;
-            }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<{
-                [x: string]: string;
-            } | undefined>;
-            isValidRefName(refName: string, assemblyName: string): boolean;
-        } & {
-            afterAttach(): void;
-            removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
-            addAssembly(configuration: any): void;
-        }, import("@jbrowse/mobx-state-tree")._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>>;
+                }, 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;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+                regions: 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 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 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;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                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")._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;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+                regions: 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 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 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;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                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;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+                regions: 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 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 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;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                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>>>;
+                }, 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 confByName: Map<string, AnyConfigurationModel>;
+            readonly assemblyList: AnyConfigurationModel[];
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         } & {
-            getCanonicalAssemblyName(asmName: string): string | undefined;
-            getCanonicalAssemblyName2(asmName: string): string;
-            get(asmName: string): ({
-                configuration: any;
-            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+            settleAssemblyResolution(assemblyName: string): Promise<void>;
+        } & {
+            waitForAssembly(assemblyName: string): Promise<(import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
+            }> & {
                 error: unknown;
                 loadingP: Promise<void> | undefined;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+                regions: 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 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 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;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                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;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+                regions: 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 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 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;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                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;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+                regions: 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 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 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;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                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;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string;
-                } | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+                regions: 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 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 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;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                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 +1355,11 @@ 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 +1367,275 @@ 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>);
-    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+    readonly configuration: import("@jbrowse/core/configuration").ConfigNodeProps<any> & import("@jbrowse/core/configuration").ConfigNodeActions & import("@jbrowse/core/configuration").ConfigNodeBrand<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
     readonly adminMode: boolean;
-    readonly textSearchManager: import("@jbrowse/core/util").TextSearchManager;
+    readonly textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
+} & {
+    readonly assemblies: import("@jbrowse/core/assemblyManager").BaseAssemblyConfigModel[];
+    readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType | undefined;
+    readonly DialogProps: Record<string, unknown> | undefined;
 } & {
-    readonly assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
+    getPreferenceDefault(key: string): unknown;
+    getPreference(key: string): unknown;
+    getPreferenceChanges(): import("@jbrowse/core/util").TrackConfigChange[];
 } & {
+    readonly animationMode: import("@jbrowse/core/util").AnimationMode;
+    readonly scrollZoom: boolean;
+    readonly numberGrouping: boolean;
+} & {
+    afterAttach(): void;
     setSelection(thing: unknown): void;
     clearSelection(): void;
     setHovered(thing: unknown): void;
+    setHighlightsVisible(arg: boolean): void;
+    setHighlightLabelsVisible(arg: boolean): void;
+    addHighlight(highlight: import("@jbrowse/core/util/highlights").HighlightType): void;
+    removeHighlight(highlight: import("@jbrowse/core/util/highlights").HighlightType): void;
+    updateHighlight(old: import("@jbrowse/core/util/highlights").HighlightType, updates: Partial<import("@jbrowse/core/util/highlights").HighlightType>): void;
+    setHighlights(highlights: import("@jbrowse/core/util/highlights").HighlightType[]): void;
+    setPreferenceOverride(key: string, value: unknown): void;
+    clearPreferenceOverrides(): void;
+    clearPreferenceOverride(key: string): void;
+    setScrollZoom(flag: boolean): 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;
+    removeDialog(entry: [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;
+} & {
+    afterAttach(): 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 trackBasesById: Map<string, AnyConfigurationModel>;
+    withTrackEdits(base: AnyConfigurationModel): AnyConfigurationModel;
     readonly tracks: AnyConfigurationModel[];
-    readonly assemblies: {
-        sequence: {
-            trackId: string;
-        };
-    }[];
+} & {
+    afterAttach(): void;
+} & {
+    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, 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 resolved config it mirrors, so a delta or base
+     * replaced from outside this mixin invalidates it — see
+     * `getEditableTrackConfig`.
+     */
+    editableTrackConfigs: Map<string, EditableTrackConfig>;
+} & {
+    /**
+     * #getter
+     * Each track's base by trackId: its sessionTracks entry, else its
+     * config.json entry. Rebuilt when either list changes, never on an
+     * edit.
+     */
+    readonly trackBasesById: Map<string, AnyConfigurationModel>;
+    /**
+     * #method
+     * `base` with its delta (trackConfigDeltas) merged over it, or `base`
+     * itself by identity when it has none, which keeps the hydration cache
+     * warm.
+     */
+    withTrackEdits(base: AnyConfigurationModel): AnyConfigurationModel;
+    /**
+     * #getter
+     * Session tracks first, then the config tracks, each with its edits.
+     * An edit copies the list of bases and lays each delta at its track's
+     * position, so past that copy it costs the count of edited tracks.
+     */
     readonly tracks: AnyConfigurationModel[];
+    /**
+     * #method
+     * The entry `trackId` edits over, hydrated: the one the session added
+     * it with, or its config.json entry. What a display's "is this
+     * arranged" and "reset" compare its live config against. Per-id
+     * reactive, like `getTrackById`.
+     */
+    baseTrackConfig(trackId: string): PlainTrackConfig | undefined;
+    /**
+     * #method
+     * The config node `trackId` resolves to: a live node as it stands,
+     * otherwise a private working copy of its current frozen (base+delta)
+     * config, so a shown track's in-place quick-edits (setSlot) mutate
+     * this copy and never the shared frozen base (see ADR-032). Called by
+     * TrackConfigurationReference during lazy hydration.
+     *
+     * Cached against the resolved config it was built from, not by trackId
+     * alone. A write this mixin makes re-stamps the entry, so the copy an
+     * edit is still being typed into is never swapped out mid-keystroke;
+     * a delta or base replaced from outside — an undo's `applySnapshot` on
+     * the session, a session restore, a session track deleted and added
+     * again under its id — cannot, so the next read rebuilds the copy from
+     * what now resolves. Per-id reactive on the node rather than the
+     * config, so a display reading its config does not recompute when
+     * its own working copy is persisted. Per schema type as well, since
+     * an id re-added under another track type resolves through that
+     * type's reference.
+     */
+    getEditableTrackConfig(trackId: string, schemaType: IAnyType): AnyConfigurationModel | undefined;
+    /**
+     * #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[];
 } & {
-    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>;
+    /**
+     * #method
+     * Whether `trackId` carries an edit over its base config, which drives
+     * the "Reset track settings" item and the edited badge. Changed slots,
+     * not mere presence in trackConfigDeltas: a delta can hold only
+     * content-free display stubs, which must not read as an override.
+     */
+    isTrackOverride(trackId: string): boolean;
+    /**
+     * #getter
+     * The edited tracks `promoteTrackConfigDeltas` can write: those whose
+     * base is a config.json entry. A session track's delta has no file to
+     * go to.
+     */
+    readonly promotableTrackIds: string[];
+} & {
+    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.
+     *
+     * Returns the entry, which is the track's base: edit the track through
+     * `updateTrackConfiguration` or a display's `setConf`, not the entry.
+     */
+    addSessionTrackConf(trackConf: AnyConfiguration): AnyConfigurationModel | undefined;
+    /**
+     * #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`.
+     *
+     * **Call it only from the "Add track" workflows**, where an admin
+     * adding a track means to add it for the whole site. For a track a
+     * feature creates on the user's behalf (a search result, a computed
+     * consensus, a reconstruction's segment labels), one admin click on
+     * this publishes it to every visitor, and each later click publishes
+     * another copy, because the per-launch trackId prevents deduplication.
+     * Use `addSessionTrackConf` above 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 assembly, a MAF
+     * sample's genome, or a comparative view's synthesized pair. The
+     * Add-track widget takes its assembly from the containing view, so an
+     * admin adding a track in such a view passes a name no visitor can
+     * resolve. Publishing it would write an entry the server sends to every
+     * visitor and no visitor can draw. Adding it to the session keeps the
+     * track usable and writes no dangling entry; a snackbar names the
+     * assembly that caused the fallback.
+     *
+     * **The snackbar names the assembly and not the track**, so a batch
+     * produces one message: `pushSnackbarMessage` dedupes on the exact
+     * text, and `BulkAddTracksWorkflow` publishes in a loop. Including the
+     * track name would show one snackbar per file to an admin adding
+     * thirty. The assembly is all the admin needs to act on.
+     */
+    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): AnyConfigurationModel | undefined;
+    /**
+     * #action
+     * Persist an edited track config as a delta (trackConfigDeltas) against
+     * its base, the sessionTracks or config.json entry — only the changed
+     * slots — so the edits persist, are shared, undo and reset, while
+     * changes to untouched fields of the base still flow through. An
+     * admin's edit is a delta like anyone's: it reaches the config.json the
+     * server hands every visitor only through `promoteTrackConfigDeltas`.
+     * An opened connection track defers to the base mixin, which routes it
+     * to connectionTrackConfigs.
+     */
+    updateTrackConfiguration(trackConf: PlainTrackConfig): void;
+    /**
+     * #action
+     * Write this session's track edits into the base configs — the
+     * config.json an admin server hands every visitor — and drop the
+     * deltas they were held in. One track's, or every track's when
+     * `trackId` is omitted, of `promotableTrackIds`: a session track's
+     * edits stay in the session. An admin's alone: anyone else's base is
+     * the in-memory copy of a file they cannot write.
+     */
+    promoteTrackConfigDeltas(trackId?: string): void;
+    /**
+     * #action
+     * Drop a track's delta (trackConfigDeltas) so it reverts to its base,
+     * the sessionTracks or jbrowse.tracks entry. 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): (import("@jbrowse/core/configuration").PluggableConfigNode & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>)[] | 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;