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

package/esm/AppSession/AppSessionMixin.d.ts

@@ -0,0 +1,1598 @@
+import type { AppRootModel } from './AppRootModel.ts';
+import type PluginManager from '@jbrowse/core/PluginManager';
+/**
+ * #stateModel AppSessionMixin
+ *
+ * Session getters shared by the "app" products (desktop + web) that simply
+ * delegate to the root model — `version`, `history`, `menus`,
+ * `assemblyManager` — plus `renameCurrentSession`. Centralized here so the
+ * products compose one mixin instead of re-declaring (and diverging on) the
+ * same root delegations. The root must satisfy {@link AppRootModel}.
+ */
+export declare function AppSessionMixin(_pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{}, {
+    /**
+     * #getter
+     */
+    readonly root: AppRootModel;
+} & {
+    /**
+     * #getter
+     */
+    readonly version: string;
+    /**
+     * #getter
+     */
+    readonly gitCommit: string | undefined;
+    /**
+     * #getter
+     */
+    readonly history: {
+        canUndo: boolean;
+        canRedo: boolean;
+        undo(): void;
+        redo(): void;
+    } | undefined;
+    /**
+     * #getter
+     */
+    readonly assemblyManager: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }, {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    }> & {
+        unrecognizedReports: {
+            report(session: unknown, name: string, handlerCount: number, fire: () => unknown): void;
+            reportFor(session: unknown, name: string): {
+                handled: boolean;
+                claim?: Promise<void>;
+            } | undefined;
+        };
+    } & {
+        readonly assemblyNameMap: Record<string, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }> & {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }, {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
+    } & {
+        getCanonicalAssemblyName(asmName: string): string | undefined;
+        getDisplayName(asmName: string): string;
+        get(asmName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }> & {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }, {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
+        has(asmName: string): boolean;
+        loadingAssembly(asmNames: string[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }> & {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }, {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
+        readonly assemblyNamesList: string[];
+        readonly configuredAssemblyNames: Set<string>;
+        readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
+            setSubschema(slotName: string, data: Record<string, unknown>): any;
+            setSlot(slotName: string, value: unknown): void;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+        readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+    } & {
+        settleAssemblyResolution(assemblyName: string): Promise<void>;
+    } & {
+        waitForAssembly(assemblyName: string): Promise<(import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }> & {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }, {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
+        requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }> & {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }, {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        }, import("@jbrowse/mobx-state-tree")._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;
+    } & {
+        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").IModelType<{
+        assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }, {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    }, {
+        unrecognizedReports: {
+            report(session: unknown, name: string, handlerCount: number, fire: () => unknown): void;
+            reportFor(session: unknown, name: string): {
+                handled: boolean;
+                claim?: Promise<void>;
+            } | undefined;
+        };
+    } & {
+        readonly assemblyNameMap: Record<string, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }> & {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }, {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
+    } & {
+        getCanonicalAssemblyName(asmName: string): string | undefined;
+        getDisplayName(asmName: string): string;
+        get(asmName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }> & {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }, {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
+        has(asmName: string): boolean;
+        loadingAssembly(asmNames: string[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }> & {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }, {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
+        readonly assemblyNamesList: string[];
+        readonly configuredAssemblyNames: Set<string>;
+        readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
+            setSubschema(slotName: string, data: Record<string, unknown>): any;
+            setSlot(slotName: string, value: unknown): void;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+        readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+    } & {
+        settleAssemblyResolution(assemblyName: string): Promise<void>;
+    } & {
+        waitForAssembly(assemblyName: string): Promise<(import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }> & {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }, {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
+        requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }> & {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+        }, {
+            error: unknown;
+            loadingP: Promise<void> | undefined;
+            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            loadedGeneticCodes: Record<string, number> | undefined;
+            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+            statusMessage: string | undefined;
+            statusProgress: number | undefined;
+            statusSource: string | undefined;
+            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+        } & {
+            getConf(arg: string): any;
+        } & {
+            readonly name: string;
+            readonly aliases: string[];
+            readonly displayName: string;
+            readonly refNameColors: string[];
+        } & {
+            readonly allAliases: string[];
+            hasName(name: string): boolean;
+        } & {
+            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
+            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
+        } & {
+            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
+                regions: import("@jbrowse/core/util").Region[];
+                cytobands: import("@jbrowse/core/util").Feature[];
+                geneticCodes: Record<string, number>;
+            }): void;
+            setError(e: unknown): void;
+            setLoadingP(p?: Promise<void>): void;
+            loadPre(): Promise<void>;
+        } & {
+            load(): Promise<void>;
+        } & {
+            afterAttach(): void;
+        } & {
+            readonly initialized: boolean;
+            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            readonly allRefNames: string[] | undefined;
+            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+            readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        } & {
+            readonly refNames: string[] | undefined;
+        } & {
+            readonly refNameToIndex: Map<string, number> | undefined;
+        } & {
+            getCanonicalRefName(refName: string): string | undefined;
+            getRefNameColor(refName: string): string | undefined;
+            getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+            getGeneticCodeId(refName: string): number;
+            getSeqAdapterRefName(canonicalRefName: string): string;
+        } & {
+            getCanonicalRefName2(refName: string): string;
+            isValidRefName(refName: string): boolean;
+        } & {
+            getAliasesForRefName(refName: string): string[];
+            getRefNameMapForAdapter(adapterConf: {
+                [x: string]: unknown;
+            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+        }, import("@jbrowse/mobx-state-tree")._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;
+    } & {
+        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>>;
+    /**
+     * #method
+     */
+    menus(): import("../menus.ts").Menu[];
+} & {
+    /**
+     * #action
+     */
+    renameCurrentSession(sessionName: string): void;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;