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

package/esm/Session/Preferences.d.ts

@@ -0,0 +1,1389 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+/**
+ * #stateModel PreferencesSessionMixin
+ *
+ * loads and persists user-preference overrides (the BaseSession
+ * `preferencesOverrides` volatile) to localStorage. Compose into products that
+ * let users edit preferences (web, desktop); embedded sessions omit it and
+ * resolve preferences from `configuration.preferences` admin defaults only.
+ */
+export declare function PreferencesSessionMixin(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    focusedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType>>, [undefined]>;
+    highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    highlightLabelsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    heldForMissingPlugins: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined, import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined, import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined>, [undefined]>;
+}, never>, never>, {
+    selection: unknown;
+    hovered: unknown;
+    queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>][];
+    preferencesOverrides: import("mobx").ObservableMap<string, unknown>;
+} & {
+    readonly root: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        jbrowse: import("@jbrowse/mobx-state-tree").IAnyType;
+        session: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IAnyType>;
+        sessionPath: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+        assemblyManager: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
+            assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
+                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+            }, {
+                error: unknown;
+                loadingP: Promise<void> | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly 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 allRefNames: string[] | undefined;
+                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                readonly refNameToIndex: Map<string, number> | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+                getGeneticCodeId(refName: string): number;
+                getSeqAdapterRefName(canonicalRefName: string): string;
+            } & {
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+                getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+        }, {
+            unrecognizedReports: {
+                report(session: unknown, name: string, handlerCount: number, fire: () => unknown): void;
+                reportFor(session: unknown, name: string): {
+                    handled: boolean;
+                    claim?: Promise<void>;
+                } | undefined;
+            };
+        } & {
+            readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
+        } & {
+            getCanonicalAssemblyName(asmName: string): string | undefined;
+            getDisplayName(asmName: string): string;
+            get(asmName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<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>>;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly 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 allRefNames: string[] | undefined;
+                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                readonly refNameToIndex: Map<string, number> | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+                getGeneticCodeId(refName: string): number;
+                getSeqAdapterRefName(canonicalRefName: string): string;
+            } & {
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, 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>>;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly 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 allRefNames: string[] | undefined;
+                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                readonly refNameToIndex: Map<string, number> | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+                getGeneticCodeId(refName: string): number;
+                getSeqAdapterRefName(canonicalRefName: string): string;
+            } & {
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, 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>>;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly 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 allRefNames: string[] | undefined;
+                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                readonly refNameToIndex: Map<string, number> | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+                getGeneticCodeId(refName: string): number;
+                getSeqAdapterRefName(canonicalRefName: string): string;
+            } & {
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, 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>>;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly 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 allRefNames: string[] | undefined;
+                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                readonly refNameToIndex: Map<string, number> | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+                getGeneticCodeId(refName: string): number;
+                getSeqAdapterRefName(canonicalRefName: string): string;
+            } & {
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+                getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
+            readonly assemblyNamesList: string[];
+            readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
+            readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
+            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>>;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly 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 allRefNames: string[] | undefined;
+                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                readonly refNameToIndex: Map<string, number> | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+                getGeneticCodeId(refName: string): number;
+                getSeqAdapterRefName(canonicalRefName: string): string;
+            } & {
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, 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>>;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly 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 allRefNames: string[] | undefined;
+                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                readonly refNameToIndex: Map<string, number> | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+                getGeneticCodeId(refName: string): number;
+                getSeqAdapterRefName(canonicalRefName: string): string;
+            } & {
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, 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>>;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly 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 allRefNames: string[] | undefined;
+                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                readonly refNameToIndex: Map<string, number> | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+                getGeneticCodeId(refName: string): number;
+                getSeqAdapterRefName(canonicalRefName: string): string;
+            } & {
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, 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>>;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly 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 allRefNames: string[] | undefined;
+                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                readonly refNameToIndex: Map<string, number> | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+                getGeneticCodeId(refName: string): number;
+                getSeqAdapterRefName(canonicalRefName: string): string;
+            } & {
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, 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>, [undefined]>;
+    }> & {
+        rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        adminMode: boolean;
+        error: unknown;
+        textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
+        pluginManager: PluginManager;
+    } & {
+        setError(error: unknown): void;
+        setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
+        setDefaultSession(): void;
+        setSessionPath(path: string): void;
+        renameCurrentSession(newName: string): void;
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+        jbrowse: import("@jbrowse/mobx-state-tree").IAnyType;
+        session: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IAnyType>;
+        sessionPath: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+        assemblyManager: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
+            assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
+                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+            }, {
+                error: unknown;
+                loadingP: Promise<void> | undefined;
+                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly 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 allRefNames: string[] | undefined;
+                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                readonly refNameToIndex: Map<string, number> | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+                getGeneticCodeId(refName: string): number;
+                getSeqAdapterRefName(canonicalRefName: string): string;
+            } & {
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+                getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+        }, {
+            unrecognizedReports: {
+                report(session: unknown, name: string, handlerCount: number, fire: () => unknown): void;
+                reportFor(session: unknown, name: string): {
+                    handled: boolean;
+                    claim?: Promise<void>;
+                } | undefined;
+            };
+        } & {
+            readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
+        } & {
+            getCanonicalAssemblyName(asmName: string): string | undefined;
+            getDisplayName(asmName: string): string;
+            get(asmName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<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>>;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly 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 allRefNames: string[] | undefined;
+                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                readonly refNameToIndex: Map<string, number> | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+                getGeneticCodeId(refName: string): number;
+                getSeqAdapterRefName(canonicalRefName: string): string;
+            } & {
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, 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>>;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly 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 allRefNames: string[] | undefined;
+                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                readonly refNameToIndex: Map<string, number> | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+                getGeneticCodeId(refName: string): number;
+                getSeqAdapterRefName(canonicalRefName: string): string;
+            } & {
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, 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>>;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly 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 allRefNames: string[] | undefined;
+                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                readonly refNameToIndex: Map<string, number> | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+                getGeneticCodeId(refName: string): number;
+                getSeqAdapterRefName(canonicalRefName: string): string;
+            } & {
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, 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>>;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly 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 allRefNames: string[] | undefined;
+                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                readonly refNameToIndex: Map<string, number> | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+                getGeneticCodeId(refName: string): number;
+                getSeqAdapterRefName(canonicalRefName: string): string;
+            } & {
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
+                getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
+            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
+            readonly assemblyNamesList: string[];
+            readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
+            readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
+            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>>;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly 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 allRefNames: string[] | undefined;
+                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                readonly refNameToIndex: Map<string, number> | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+                getGeneticCodeId(refName: string): number;
+                getSeqAdapterRefName(canonicalRefName: string): string;
+            } & {
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, 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>>;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly 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 allRefNames: string[] | undefined;
+                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                readonly refNameToIndex: Map<string, number> | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+                getGeneticCodeId(refName: string): number;
+                getSeqAdapterRefName(canonicalRefName: string): string;
+            } & {
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, 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>>;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly 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 allRefNames: string[] | undefined;
+                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                readonly refNameToIndex: Map<string, number> | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+                getGeneticCodeId(refName: string): number;
+                getSeqAdapterRefName(canonicalRefName: string): string;
+            } & {
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, 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>>;
+                regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+                loadedGeneticCodes: Record<string, number> | undefined;
+                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
+                statusMessage: string | undefined;
+                statusProgress: number | undefined;
+                statusSource: string | undefined;
+                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly 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 allRefNames: string[] | undefined;
+                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                readonly refNameToIndex: Map<string, number> | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
+                getGeneticCodeId(refName: string): number;
+                getSeqAdapterRefName(canonicalRefName: string): string;
+            } & {
+                getCanonicalRefName2(refName: string): string;
+                isValidRefName(refName: string): boolean;
+            } & {
+                getRefNamePosition(refName: string): number | undefined;
+                getAliasesForRefName(refName: string): string[];
+                getRefNameMapForAdapter(adapterConf: {
+                    [x: string]: unknown;
+                }, 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>, [undefined]>;
+    }, {
+        rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+        adminMode: boolean;
+        error: unknown;
+        textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
+        pluginManager: PluginManager;
+    } & {
+        setError(error: unknown): void;
+        setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
+        setDefaultSession(): void;
+        setSessionPath(path: string): void;
+        renameCurrentSession(newName: string): void;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+} & {
+    readonly jbrowse: any;
+    readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+    readonly configuration: import("@jbrowse/core/configuration").ConfigNodeProps<any> & import("@jbrowse/core/configuration").ConfigNodeActions & import("@jbrowse/core/configuration").ConfigNodeBrand<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+    readonly adminMode: boolean;
+    readonly textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
+} & {
+    readonly assemblies: import("@jbrowse/core/assemblyManager").BaseAssemblyConfigModel[];
+    readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType | undefined;
+    readonly DialogProps: Record<string, unknown> | undefined;
+} & {
+    getPreferenceDefault(key: string): unknown;
+    getPreference(key: string): unknown;
+    getPreferenceChanges(): import("@jbrowse/core/util").TrackConfigChange[];
+} & {
+    readonly animationMode: import("@jbrowse/core/util").AnimationMode;
+    readonly scrollZoom: boolean;
+    readonly numberGrouping: boolean;
+} & {
+    afterAttach(): void;
+    setSelection(thing: unknown): void;
+    clearSelection(): void;
+    setHovered(thing: unknown): void;
+    setHighlightsVisible(arg: boolean): void;
+    setHighlightLabelsVisible(arg: boolean): void;
+    addHighlight(highlight: import("@jbrowse/core/util/highlights").HighlightType): void;
+    removeHighlight(highlight: import("@jbrowse/core/util/highlights").HighlightType): void;
+    updateHighlight(old: import("@jbrowse/core/util/highlights").HighlightType, updates: Partial<import("@jbrowse/core/util/highlights").HighlightType>): void;
+    setHighlights(highlights: import("@jbrowse/core/util/highlights").HighlightType[]): void;
+    setPreferenceOverride(key: string, value: unknown): void;
+    clearPreferenceOverrides(): void;
+    clearPreferenceOverride(key: string): void;
+    setScrollZoom(flag: boolean): void;
+    setName(str: string): void;
+    setFocusedViewId(viewId: string | undefined): void;
+    removeActiveDialog(): void;
+    queueDialog(doneCallback: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
+    removeDialog(entry: [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
+} & {
+    snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
+    errorDialog: import("@jbrowse/core/ui/SnackbarModel").ErrorDialogState | undefined;
+} & {
+    readonly snackbarMessageSet: Map<string, import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
+} & {
+    notify(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction | import("@jbrowse/core/util").SnackAction[]): void;
+    notifyError(errorMessage: string, error?: unknown, extra?: unknown, action?: import("@jbrowse/core/util").SnackAction): void;
+    setErrorDialog(state: import("@jbrowse/core/ui/SnackbarModel").ErrorDialogState | undefined): void;
+    pushSnackbarMessage(message: string, level?: import("@jbrowse/core/util").NotificationLevel, actions?: import("@jbrowse/core/util").SnackAction[]): void;
+    popSnackbarMessage(): import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage | undefined;
+    removeSnackbarMessage(message: string): void;
+} & {
+    afterAttach(): void;
+} & {
+    afterAttach(): void;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;