@jbrowse/core 4.3.0 → 5.0.0-beta.10

package/esm/assemblyManager/assemblyManager.d.ts

@@ -1,528 +1,791 @@
-import type { Assembly } from './assembly.ts';
 import type PluginManager from '../PluginManager.ts';
 import type { AnyConfigurationModel } from '../configuration/index.ts';
 import type RpcManager from '../rpc/RpcManager.ts';
-import type { StopToken } from '../util/stopToken.ts';
+import type { StatusCallback } from '../util/progress.ts';
+import type { Assembly } from './assembly.ts';
 import type { IAnyType } from '@jbrowse/mobx-state-tree';
 type AdapterConf = Record<string, unknown>;
 export interface AssemblyBaseOpts {
-    stopToken?: StopToken;
+    signal?: AbortSignal;
     sessionId: string;
-    statusCallback?: (arg: string) => void;
+    statusCallback?: StatusCallback;
 }
+/**
+ * #stateModel AssemblyManager
+ */
 declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
+    /**
+     * #property
+     * this is automatically managed by an autorun which looks in the parent
+     * session.assemblies, session.sessionAssemblies, and
+     * session.temporaryAssemblies
+     */
     assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
         configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
     }, {
         error: unknown;
         loadingP: Promise<void> | undefined;
-        volatileRegions: import("./assembly.ts").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("./refNameMaps.ts").RefNameAliases>>;
+        regions: import("./assembly.ts").BasicRegion[] | undefined;
+        refNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
         canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
         cytobands: import("../util/simpleFeature.ts").Feature[] | undefined;
+        loadedGeneticCodes: Record<string, number> | undefined;
+        lowerCaseRefNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
+        statusMessage: string | undefined;
+        statusProgress: number | undefined;
+        statusSource: string | undefined;
+        refNameMismatches: Map<string, import("./refNameMismatch.ts").RefNameMismatch>;
     } & {
         getConf(arg: string): any;
-        readonly lowerCaseRefNameAliases: {
-            [k: string]: string;
-        } | undefined;
     } & {
-        readonly initialized: boolean;
         readonly name: string;
-        readonly regions: import("./assembly.ts").BasicRegion[] | undefined;
         readonly aliases: string[];
         readonly displayName: string;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly allRefNames: string[] | undefined;
-        readonly lowerCaseRefNames: string[] | undefined;
-        readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: RpcManager;
         readonly refNameColors: string[];
     } & {
-        readonly refNames: string[] | undefined;
+        readonly allAliases: string[];
+        hasName(name: string): boolean;
     } & {
-        getCanonicalRefName(refName: string): string | undefined;
-        getCanonicalRefName2(refName: string): string;
-        getRefNameColor(refName: string): string | undefined;
-        isValidRefName(refName: string): boolean;
-        getSeqAdapterRefName(canonicalRefName: string): string;
+        setStatus(status?: import("../util/progress.ts").RpcStatus): void;
+        setRefNameMismatch(adapterCacheKey: string, mismatch: import("./refNameMismatch.ts").RefNameMismatch): void;
     } & {
-        setLoaded({ regions, refNameAliases, cytobands, }: {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("./refNameMaps.ts").RefNameMaps & {
             regions: import("../util/index.ts").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
             cytobands: import("../util/simpleFeature.ts").Feature[];
+            geneticCodes: Record<string, number>;
         }): void;
         setError(e: unknown): void;
-        setRegions(regions: import("../util/index.ts").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("../util/simpleFeature.ts").Feature[]): void;
-        setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
         setLoadingP(p?: Promise<void>): void;
-        load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: {
-            [x: string]: unknown;
-        }, options: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<import("./assembly.ts").RefNameMap>;
+        load(): Promise<void>;
+    } & {
+        afterAttach(): void;
+    } & {
+        readonly initialized: boolean;
+        readonly allRefNames: string[] | undefined;
+        readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+        readonly rpcManager: RpcManager;
+    } & {
+        readonly refNames: string[] | undefined;
+    } & {
+        readonly refNameToIndex: Map<string, number> | undefined;
+    } & {
+        getCanonicalRefName(refName: string): string | undefined;
+        getRefNameColor(refName: string): string | undefined;
+        getRegionForRefName(refName: string): import("./assembly.ts").BasicRegion | undefined;
+        getGeneticCodeId(refName: string): number;
+        getSeqAdapterRefName(canonicalRefName: string): string;
+    } & {
+        getCanonicalRefName2(refName: string): string;
+        isValidRefName(refName: string): boolean;
+    } & {
+        getRefNamePosition(refName: string): number | undefined;
+        getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        afterCreate(): void;
+        }, options: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<import("./refNameMaps.ts").RefNameAliases>;
+        getRefNameMismatch(adapterCacheKey: string): import("./refNameMismatch.ts").RefNameMismatch | undefined;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
 }, {
-    readonly assemblyNameMap: Record<string, {
-        configuration: any;
-    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+    /**
+     * #volatile
+     * rate limiter for `get`'s `Core-handleUnrecognizedAssembly` reports, so
+     * each unknown name reaches the extension point once per session
+     */
+    unrecognizedReports: {
+        /**
+         * Report `name` via `fire`, once per session, and keep what came back.
+         * `handlerCount` separates "every handler declined" from "nobody
+         * listening": the folded result is the same either way, and only the first
+         * is worth waiting out.
+         */
+        report(session: unknown, name: string, handlerCount: number, fire: () => unknown): void;
+        /** what `report` recorded for `name` under `session`, if anything */
+        reportFor(session: unknown, name: string): {
+            handled: boolean;
+            claim?: Promise<void>;
+        } | undefined;
+    };
+} & {
+    /**
+     * #getter
+     */
+    readonly assemblyNameMap: Record<string, Assembly>;
+} & {
+    /**
+     * #method
+     */
+    getCanonicalAssemblyName(asmName: string): string | undefined;
+    /**
+     * #method
+     */
+    getDisplayName(asmName: string): string;
+    /**
+     * #method
+     * The assembly `asmName` names, or undefined. Reports a name it doesn't
+     * know to `Core-handleUnrecognizedAssembly` so a plugin can go supply it,
+     * which is a side effect: a caller only asking *whether* the session has
+     * the assembly wants {@link has} instead. Each name is reported at most
+     * once per session, since a handler resolves it out of band and the
+     * assembly turning up is itself the reactive signal.
+     */
+    get(asmName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
+    }> & {
         error: unknown;
         loadingP: Promise<void> | undefined;
-        volatileRegions: import("./assembly.ts").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("./refNameMaps.ts").RefNameAliases>>;
+        regions: import("./assembly.ts").BasicRegion[] | undefined;
+        refNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
         canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
         cytobands: import("../util/simpleFeature.ts").Feature[] | undefined;
+        loadedGeneticCodes: Record<string, number> | undefined;
+        lowerCaseRefNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
+        statusMessage: string | undefined;
+        statusProgress: number | undefined;
+        statusSource: string | undefined;
+        refNameMismatches: Map<string, import("./refNameMismatch.ts").RefNameMismatch>;
     } & {
         getConf(arg: string): any;
-        readonly lowerCaseRefNameAliases: {
-            [k: string]: string;
-        } | undefined;
     } & {
-        readonly initialized: boolean;
         readonly name: string;
-        readonly regions: import("./assembly.ts").BasicRegion[] | undefined;
         readonly aliases: string[];
         readonly displayName: string;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly allRefNames: string[] | undefined;
-        readonly lowerCaseRefNames: string[] | undefined;
-        readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: RpcManager;
         readonly refNameColors: string[];
     } & {
-        readonly refNames: string[] | undefined;
+        readonly allAliases: string[];
+        hasName(name: string): boolean;
     } & {
-        getCanonicalRefName(refName: string): string | undefined;
-        getCanonicalRefName2(refName: string): string;
-        getRefNameColor(refName: string): string | undefined;
-        isValidRefName(refName: string): boolean;
-        getSeqAdapterRefName(canonicalRefName: string): string;
+        setStatus(status?: import("../util/progress.ts").RpcStatus): void;
+        setRefNameMismatch(adapterCacheKey: string, mismatch: import("./refNameMismatch.ts").RefNameMismatch): void;
     } & {
-        setLoaded({ regions, refNameAliases, cytobands, }: {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("./refNameMaps.ts").RefNameMaps & {
             regions: import("../util/index.ts").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
             cytobands: import("../util/simpleFeature.ts").Feature[];
+            geneticCodes: Record<string, number>;
         }): void;
         setError(e: unknown): void;
-        setRegions(regions: import("../util/index.ts").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("../util/simpleFeature.ts").Feature[]): void;
-        setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
         setLoadingP(p?: Promise<void>): void;
-        load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: {
-            [x: string]: unknown;
-        }, options: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<import("./assembly.ts").RefNameMap>;
+        load(): Promise<void>;
+    } & {
+        afterAttach(): void;
+    } & {
+        readonly initialized: boolean;
+        readonly allRefNames: string[] | undefined;
+        readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+        readonly rpcManager: RpcManager;
+    } & {
+        readonly refNames: string[] | undefined;
+    } & {
+        readonly refNameToIndex: Map<string, number> | undefined;
+    } & {
+        getCanonicalRefName(refName: string): string | undefined;
+        getRefNameColor(refName: string): string | undefined;
+        getRegionForRefName(refName: string): import("./assembly.ts").BasicRegion | undefined;
+        getGeneticCodeId(refName: string): number;
+        getSeqAdapterRefName(canonicalRefName: string): string;
+    } & {
+        getCanonicalRefName2(refName: string): string;
+        isValidRefName(refName: string): boolean;
+    } & {
+        getRefNamePosition(refName: string): number | undefined;
+        getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        afterCreate(): void;
+        }, options: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<import("./refNameMaps.ts").RefNameAliases>;
+        getRefNameMismatch(adapterCacheKey: string): import("./refNameMismatch.ts").RefNameMismatch | undefined;
     } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
         configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
     }, {
         error: unknown;
         loadingP: Promise<void> | undefined;
-        volatileRegions: import("./assembly.ts").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("./refNameMaps.ts").RefNameAliases>>;
+        regions: import("./assembly.ts").BasicRegion[] | undefined;
+        refNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
         canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
         cytobands: import("../util/simpleFeature.ts").Feature[] | undefined;
+        loadedGeneticCodes: Record<string, number> | undefined;
+        lowerCaseRefNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
+        statusMessage: string | undefined;
+        statusProgress: number | undefined;
+        statusSource: string | undefined;
+        refNameMismatches: Map<string, import("./refNameMismatch.ts").RefNameMismatch>;
     } & {
         getConf(arg: string): any;
-        readonly lowerCaseRefNameAliases: {
-            [k: string]: string;
-        } | undefined;
     } & {
-        readonly initialized: boolean;
         readonly name: string;
-        readonly regions: import("./assembly.ts").BasicRegion[] | undefined;
         readonly aliases: string[];
         readonly displayName: string;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly allRefNames: string[] | undefined;
-        readonly lowerCaseRefNames: string[] | undefined;
-        readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: RpcManager;
         readonly refNameColors: string[];
     } & {
-        readonly refNames: string[] | undefined;
+        readonly allAliases: string[];
+        hasName(name: string): boolean;
     } & {
-        getCanonicalRefName(refName: string): string | undefined;
-        getCanonicalRefName2(refName: string): string;
-        getRefNameColor(refName: string): string | undefined;
-        isValidRefName(refName: string): boolean;
-        getSeqAdapterRefName(canonicalRefName: string): string;
+        setStatus(status?: import("../util/progress.ts").RpcStatus): void;
+        setRefNameMismatch(adapterCacheKey: string, mismatch: import("./refNameMismatch.ts").RefNameMismatch): void;
     } & {
-        setLoaded({ regions, refNameAliases, cytobands, }: {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("./refNameMaps.ts").RefNameMaps & {
             regions: import("../util/index.ts").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
             cytobands: import("../util/simpleFeature.ts").Feature[];
+            geneticCodes: Record<string, number>;
         }): void;
         setError(e: unknown): void;
-        setRegions(regions: import("../util/index.ts").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("../util/simpleFeature.ts").Feature[]): void;
-        setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
         setLoadingP(p?: Promise<void>): void;
-        load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: {
-            [x: string]: unknown;
-        }, options: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<import("./assembly.ts").RefNameMap>;
+        load(): Promise<void>;
+    } & {
+        afterAttach(): void;
+    } & {
+        readonly initialized: boolean;
+        readonly allRefNames: string[] | undefined;
+        readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+        readonly rpcManager: RpcManager;
+    } & {
+        readonly refNames: string[] | undefined;
+    } & {
+        readonly refNameToIndex: Map<string, number> | undefined;
+    } & {
+        getCanonicalRefName(refName: string): string | undefined;
+        getRefNameColor(refName: string): string | undefined;
+        getRegionForRefName(refName: string): import("./assembly.ts").BasicRegion | undefined;
+        getGeneticCodeId(refName: string): number;
+        getSeqAdapterRefName(canonicalRefName: string): string;
+    } & {
+        getCanonicalRefName2(refName: string): string;
+        isValidRefName(refName: string): boolean;
+    } & {
+        getRefNamePosition(refName: string): number | undefined;
+        getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        afterCreate(): void;
-    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
-} & {
-    getCanonicalAssemblyName(asmName: string): string | undefined;
-    getCanonicalAssemblyName2(asmName: string): string;
-    get(asmName: string): ({
-        configuration: any;
-    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+        }, options: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<import("./refNameMaps.ts").RefNameAliases>;
+        getRefNameMismatch(adapterCacheKey: string): import("./refNameMismatch.ts").RefNameMismatch | undefined;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
+    /**
+     * #method
+     * Whether the session knows this assembly. Use this, not `get`, to ask
+     * only whether the assembly is present: `!has(name)` is exactly the
+     * condition under which `get` reports `name` to
+     * `Core-handleUnrecognizedAssembly`, so probing with `get` tells every
+     * installed plugin to go resolve a name that a caller supplying the
+     * assembly itself (a hub connection, MAF row navigation) is about to
+     * create.
+     */
+    has(asmName: string): boolean;
+    /**
+     * #method
+     * The first of `asmNames` that hasn't finished loading — the one a view
+     * blocked on them is waiting for, and whose `statusMessage` /
+     * `statusProgress` its spinner should show. Returns the assembly itself
+     * (a stable reference, so a consuming getter doesn't invalidate on every
+     * read) or undefined once they are all loaded.
+     */
+    loadingAssembly(asmNames: string[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
+    }> & {
         error: unknown;
         loadingP: Promise<void> | undefined;
-        volatileRegions: import("./assembly.ts").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("./refNameMaps.ts").RefNameAliases>>;
+        regions: import("./assembly.ts").BasicRegion[] | undefined;
+        refNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
         canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
         cytobands: import("../util/simpleFeature.ts").Feature[] | undefined;
+        loadedGeneticCodes: Record<string, number> | undefined;
+        lowerCaseRefNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
+        statusMessage: string | undefined;
+        statusProgress: number | undefined;
+        statusSource: string | undefined;
+        refNameMismatches: Map<string, import("./refNameMismatch.ts").RefNameMismatch>;
     } & {
         getConf(arg: string): any;
-        readonly lowerCaseRefNameAliases: {
-            [k: string]: string;
-        } | undefined;
     } & {
-        readonly initialized: boolean;
         readonly name: string;
-        readonly regions: import("./assembly.ts").BasicRegion[] | undefined;
         readonly aliases: string[];
         readonly displayName: string;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly allRefNames: string[] | undefined;
-        readonly lowerCaseRefNames: string[] | undefined;
-        readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: RpcManager;
         readonly refNameColors: string[];
     } & {
-        readonly refNames: string[] | undefined;
+        readonly allAliases: string[];
+        hasName(name: string): boolean;
     } & {
-        getCanonicalRefName(refName: string): string | undefined;
-        getCanonicalRefName2(refName: string): string;
-        getRefNameColor(refName: string): string | undefined;
-        isValidRefName(refName: string): boolean;
-        getSeqAdapterRefName(canonicalRefName: string): string;
+        setStatus(status?: import("../util/progress.ts").RpcStatus): void;
+        setRefNameMismatch(adapterCacheKey: string, mismatch: import("./refNameMismatch.ts").RefNameMismatch): void;
     } & {
-        setLoaded({ regions, refNameAliases, cytobands, }: {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("./refNameMaps.ts").RefNameMaps & {
             regions: import("../util/index.ts").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
             cytobands: import("../util/simpleFeature.ts").Feature[];
+            geneticCodes: Record<string, number>;
         }): void;
         setError(e: unknown): void;
-        setRegions(regions: import("../util/index.ts").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("../util/simpleFeature.ts").Feature[]): void;
-        setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
         setLoadingP(p?: Promise<void>): void;
-        load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: {
-            [x: string]: unknown;
-        }, options: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<import("./assembly.ts").RefNameMap>;
+        load(): Promise<void>;
+    } & {
+        afterAttach(): void;
+    } & {
+        readonly initialized: boolean;
+        readonly allRefNames: string[] | undefined;
+        readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+        readonly rpcManager: RpcManager;
+    } & {
+        readonly refNames: string[] | undefined;
+    } & {
+        readonly refNameToIndex: Map<string, number> | undefined;
+    } & {
+        getCanonicalRefName(refName: string): string | undefined;
+        getRefNameColor(refName: string): string | undefined;
+        getRegionForRefName(refName: string): import("./assembly.ts").BasicRegion | undefined;
+        getGeneticCodeId(refName: string): number;
+        getSeqAdapterRefName(canonicalRefName: string): string;
+    } & {
+        getCanonicalRefName2(refName: string): string;
+        isValidRefName(refName: string): boolean;
+    } & {
+        getRefNamePosition(refName: string): number | undefined;
+        getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        afterCreate(): void;
+        }, options: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<import("./refNameMaps.ts").RefNameAliases>;
+        getRefNameMismatch(adapterCacheKey: string): import("./refNameMismatch.ts").RefNameMismatch | undefined;
     } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
         configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
     }, {
         error: unknown;
         loadingP: Promise<void> | undefined;
-        volatileRegions: import("./assembly.ts").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("./refNameMaps.ts").RefNameAliases>>;
+        regions: import("./assembly.ts").BasicRegion[] | undefined;
+        refNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
         canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
         cytobands: import("../util/simpleFeature.ts").Feature[] | undefined;
+        loadedGeneticCodes: Record<string, number> | undefined;
+        lowerCaseRefNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
+        statusMessage: string | undefined;
+        statusProgress: number | undefined;
+        statusSource: string | undefined;
+        refNameMismatches: Map<string, import("./refNameMismatch.ts").RefNameMismatch>;
     } & {
         getConf(arg: string): any;
-        readonly lowerCaseRefNameAliases: {
-            [k: string]: string;
-        } | undefined;
     } & {
-        readonly initialized: boolean;
         readonly name: string;
-        readonly regions: import("./assembly.ts").BasicRegion[] | undefined;
         readonly aliases: string[];
         readonly displayName: string;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly allRefNames: string[] | undefined;
-        readonly lowerCaseRefNames: string[] | undefined;
-        readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: RpcManager;
         readonly refNameColors: string[];
     } & {
-        readonly refNames: string[] | undefined;
+        readonly allAliases: string[];
+        hasName(name: string): boolean;
     } & {
-        getCanonicalRefName(refName: string): string | undefined;
-        getCanonicalRefName2(refName: string): string;
-        getRefNameColor(refName: string): string | undefined;
-        isValidRefName(refName: string): boolean;
-        getSeqAdapterRefName(canonicalRefName: string): string;
+        setStatus(status?: import("../util/progress.ts").RpcStatus): void;
+        setRefNameMismatch(adapterCacheKey: string, mismatch: import("./refNameMismatch.ts").RefNameMismatch): void;
     } & {
-        setLoaded({ regions, refNameAliases, cytobands, }: {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("./refNameMaps.ts").RefNameMaps & {
             regions: import("../util/index.ts").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
             cytobands: import("../util/simpleFeature.ts").Feature[];
+            geneticCodes: Record<string, number>;
         }): void;
         setError(e: unknown): void;
-        setRegions(regions: import("../util/index.ts").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("../util/simpleFeature.ts").Feature[]): void;
-        setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
         setLoadingP(p?: Promise<void>): void;
-        load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: {
-            [x: string]: unknown;
-        }, options: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<import("./assembly.ts").RefNameMap>;
+        load(): Promise<void>;
+    } & {
+        afterAttach(): void;
+    } & {
+        readonly initialized: boolean;
+        readonly allRefNames: string[] | undefined;
+        readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+        readonly rpcManager: RpcManager;
+    } & {
+        readonly refNames: string[] | undefined;
+    } & {
+        readonly refNameToIndex: Map<string, number> | undefined;
+    } & {
+        getCanonicalRefName(refName: string): string | undefined;
+        getRefNameColor(refName: string): string | undefined;
+        getRegionForRefName(refName: string): import("./assembly.ts").BasicRegion | undefined;
+        getGeneticCodeId(refName: string): number;
+        getSeqAdapterRefName(canonicalRefName: string): string;
+    } & {
+        getCanonicalRefName2(refName: string): string;
+        isValidRefName(refName: string): boolean;
+    } & {
+        getRefNamePosition(refName: string): number | undefined;
+        getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        afterCreate(): void;
+        }, options: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<import("./refNameMaps.ts").RefNameAliases>;
+        getRefNameMismatch(adapterCacheKey: string): import("./refNameMismatch.ts").RefNameMismatch | undefined;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
-    readonly assemblyNamesList: any[];
+    /**
+     * #getter
+     * the canonical name of every configured assembly, read the way the
+     * afterAttach autorun names the models it builds
+     */
+    readonly assemblyNamesList: string[];
+    /**
+     * #getter
+     * Every name the *configs* answer to — each assembly's `name` and its
+     * `aliases` — mapped to its config, which exists before the assembly's
+     * model does. What {@link has} knows before the models exist, and
+     * resolved by the same precedence as `assemblyNameMap`.
+     */
+    readonly confByName: Map<string, AnyConfigurationModel>;
+    /**
+     * #getter
+     * combined jbrowse.assemblies, session.sessionAssemblies, and
+     * session.temporaryAssemblies
+     */
     readonly assemblyList: AnyConfigurationModel[];
     readonly rpcManager: RpcManager;
 } & {
-    waitForAssembly(assemblyName: string): Promise<({
-        configuration: any;
-    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+    /**
+     * #method
+     * Wait out whatever might still be about to supply `assemblyName`, and
+     * resolve once nothing is.
+     *
+     * Resolution is a chain of events, not a duration: a handler probes and
+     * adds a connection, the connection fetches a config, the config's
+     * assemblies land in the session. Each link is observable, so each is
+     * waited on rather than guessed at.
+     *
+     * - the handler's own promise, if it returned one, covers the part before
+     *   the session gains anything to watch (the hubs plugin's HEAD probe)
+     * - any connection still fetching could be carrying the assembly, so its
+     *   `loading` flag going false is the next event. Every loading
+     *   connection counts, not just one naming this assembly: a connection
+     *   config need not declare what it will turn out to provide, and waiting
+     *   for one connection too many costs a moment while missing one returns
+     *   the wrong answer.
+     *
+     * A handler that returned nothing gets {@link UNDECLARED_HANDLER_GRACE_MS}
+     * instead, because it left nothing to wait on.
+     */
+    settleAssemblyResolution(assemblyName: string): Promise<void>;
+} & {
+    /**
+     * #method
+     * use this method instead of assemblyManager.get(assemblyName) to get an
+     * assembly with regions loaded
+     */
+    waitForAssembly(assemblyName: string): Promise<(import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
+    }> & {
         error: unknown;
         loadingP: Promise<void> | undefined;
-        volatileRegions: import("./assembly.ts").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("./refNameMaps.ts").RefNameAliases>>;
+        regions: import("./assembly.ts").BasicRegion[] | undefined;
+        refNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
         canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
         cytobands: import("../util/simpleFeature.ts").Feature[] | undefined;
+        loadedGeneticCodes: Record<string, number> | undefined;
+        lowerCaseRefNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
+        statusMessage: string | undefined;
+        statusProgress: number | undefined;
+        statusSource: string | undefined;
+        refNameMismatches: Map<string, import("./refNameMismatch.ts").RefNameMismatch>;
     } & {
         getConf(arg: string): any;
-        readonly lowerCaseRefNameAliases: {
-            [k: string]: string;
-        } | undefined;
     } & {
-        readonly initialized: boolean;
         readonly name: string;
-        readonly regions: import("./assembly.ts").BasicRegion[] | undefined;
         readonly aliases: string[];
         readonly displayName: string;
-        hasName(name: string): boolean;
+        readonly refNameColors: string[];
+    } & {
         readonly allAliases: string[];
+        hasName(name: string): boolean;
+    } & {
+        setStatus(status?: import("../util/progress.ts").RpcStatus): void;
+        setRefNameMismatch(adapterCacheKey: string, mismatch: import("./refNameMismatch.ts").RefNameMismatch): void;
+    } & {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("./refNameMaps.ts").RefNameMaps & {
+            regions: import("../util/index.ts").Region[];
+            cytobands: import("../util/simpleFeature.ts").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 lowerCaseRefNames: string[] | undefined;
-        readonly allRefNamesWithLowerCase: string[] | undefined;
+        readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
         readonly rpcManager: RpcManager;
-        readonly refNameColors: string[];
     } & {
         readonly refNames: string[] | undefined;
+    } & {
+        readonly refNameToIndex: Map<string, number> | undefined;
     } & {
         getCanonicalRefName(refName: string): string | undefined;
-        getCanonicalRefName2(refName: string): string;
         getRefNameColor(refName: string): string | undefined;
-        isValidRefName(refName: string): boolean;
+        getRegionForRefName(refName: string): import("./assembly.ts").BasicRegion | undefined;
+        getGeneticCodeId(refName: string): number;
         getSeqAdapterRefName(canonicalRefName: string): string;
     } & {
-        setLoaded({ regions, refNameAliases, cytobands, }: {
+        getCanonicalRefName2(refName: string): string;
+        isValidRefName(refName: string): boolean;
+    } & {
+        getRefNamePosition(refName: string): number | undefined;
+        getAliasesForRefName(refName: string): string[];
+        getRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, options: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<import("./refNameMaps.ts").RefNameAliases>;
+        getRefNameMismatch(adapterCacheKey: string): import("./refNameMismatch.ts").RefNameMismatch | undefined;
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
+    }, {
+        error: unknown;
+        loadingP: Promise<void> | undefined;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("./refNameMaps.ts").RefNameAliases>>;
+        regions: import("./assembly.ts").BasicRegion[] | undefined;
+        refNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
+        canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+        cytobands: import("../util/simpleFeature.ts").Feature[] | undefined;
+        loadedGeneticCodes: Record<string, number> | undefined;
+        lowerCaseRefNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
+        statusMessage: string | undefined;
+        statusProgress: number | undefined;
+        statusSource: string | undefined;
+        refNameMismatches: Map<string, import("./refNameMismatch.ts").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("../util/progress.ts").RpcStatus): void;
+        setRefNameMismatch(adapterCacheKey: string, mismatch: import("./refNameMismatch.ts").RefNameMismatch): void;
+    } & {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("./refNameMaps.ts").RefNameMaps & {
             regions: import("../util/index.ts").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
             cytobands: import("../util/simpleFeature.ts").Feature[];
+            geneticCodes: Record<string, number>;
         }): void;
         setError(e: unknown): void;
-        setRegions(regions: import("../util/index.ts").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("../util/simpleFeature.ts").Feature[]): void;
-        setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
         setLoadingP(p?: Promise<void>): void;
-        load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: {
-            [x: string]: unknown;
-        }, options: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<import("./assembly.ts").RefNameMap>;
+        load(): Promise<void>;
+    } & {
+        afterAttach(): void;
+    } & {
+        readonly initialized: boolean;
+        readonly allRefNames: string[] | undefined;
+        readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+        readonly rpcManager: RpcManager;
+    } & {
+        readonly refNames: string[] | undefined;
+    } & {
+        readonly refNameToIndex: Map<string, number> | undefined;
+    } & {
+        getCanonicalRefName(refName: string): string | undefined;
+        getRefNameColor(refName: string): string | undefined;
+        getRegionForRefName(refName: string): import("./assembly.ts").BasicRegion | undefined;
+        getGeneticCodeId(refName: string): number;
+        getSeqAdapterRefName(canonicalRefName: string): string;
+    } & {
+        getCanonicalRefName2(refName: string): string;
+        isValidRefName(refName: string): boolean;
+    } & {
+        getRefNamePosition(refName: string): number | undefined;
+        getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        afterCreate(): void;
-    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+        }, options: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<import("./refNameMaps.ts").RefNameAliases>;
+        getRefNameMismatch(adapterCacheKey: string): import("./refNameMismatch.ts").RefNameMismatch | undefined;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
+    /**
+     * #method
+     * {@link waitForAssembly}, but a name that cannot be resolved is an error
+     * rather than an `undefined` for the caller to interpret.
+     *
+     * Use it where a missing assembly produces a wrong result with no error.
+     * A refName map is one case: an empty map means an adapter gets queried
+     * with un-renamed refNames, finds nothing, and the track draws blank.
+     * Throwing here shows the assembly name to the user, who can add the
+     * assembly or fix the track.
+     *
+     * `waitForAssembly` returns only once every handler and connection that
+     * could supply the name has finished, so an unresolved name here is
+     * final and throwing does not race a late load.
+     */
+    requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
         configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
-    }, {
+    }> & {
         error: unknown;
         loadingP: Promise<void> | undefined;
-        volatileRegions: import("./assembly.ts").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("./refNameMaps.ts").RefNameAliases>>;
+        regions: import("./assembly.ts").BasicRegion[] | undefined;
+        refNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
         canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
         cytobands: import("../util/simpleFeature.ts").Feature[] | undefined;
+        loadedGeneticCodes: Record<string, number> | undefined;
+        lowerCaseRefNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
+        statusMessage: string | undefined;
+        statusProgress: number | undefined;
+        statusSource: string | undefined;
+        refNameMismatches: Map<string, import("./refNameMismatch.ts").RefNameMismatch>;
     } & {
         getConf(arg: string): any;
-        readonly lowerCaseRefNameAliases: {
-            [k: string]: string;
-        } | undefined;
     } & {
-        readonly initialized: boolean;
         readonly name: string;
-        readonly regions: import("./assembly.ts").BasicRegion[] | undefined;
         readonly aliases: string[];
         readonly displayName: string;
-        hasName(name: string): boolean;
+        readonly refNameColors: string[];
+    } & {
         readonly allAliases: string[];
+        hasName(name: string): boolean;
+    } & {
+        setStatus(status?: import("../util/progress.ts").RpcStatus): void;
+        setRefNameMismatch(adapterCacheKey: string, mismatch: import("./refNameMismatch.ts").RefNameMismatch): void;
+    } & {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("./refNameMaps.ts").RefNameMaps & {
+            regions: import("../util/index.ts").Region[];
+            cytobands: import("../util/simpleFeature.ts").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 lowerCaseRefNames: string[] | undefined;
-        readonly allRefNamesWithLowerCase: string[] | undefined;
+        readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
         readonly rpcManager: RpcManager;
-        readonly refNameColors: string[];
     } & {
         readonly refNames: string[] | undefined;
+    } & {
+        readonly refNameToIndex: Map<string, number> | undefined;
     } & {
         getCanonicalRefName(refName: string): string | undefined;
-        getCanonicalRefName2(refName: string): string;
         getRefNameColor(refName: string): string | undefined;
-        isValidRefName(refName: string): boolean;
+        getRegionForRefName(refName: string): import("./assembly.ts").BasicRegion | undefined;
+        getGeneticCodeId(refName: string): number;
         getSeqAdapterRefName(canonicalRefName: string): string;
     } & {
-        setLoaded({ regions, refNameAliases, cytobands, }: {
+        getCanonicalRefName2(refName: string): string;
+        isValidRefName(refName: string): boolean;
+    } & {
+        getRefNamePosition(refName: string): number | undefined;
+        getAliasesForRefName(refName: string): string[];
+        getRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, options: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<import("./refNameMaps.ts").RefNameAliases>;
+        getRefNameMismatch(adapterCacheKey: string): import("./refNameMismatch.ts").RefNameMismatch | undefined;
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
+    }, {
+        error: unknown;
+        loadingP: Promise<void> | undefined;
+        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("./refNameMaps.ts").RefNameAliases>>;
+        regions: import("./assembly.ts").BasicRegion[] | undefined;
+        refNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
+        canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
+        cytobands: import("../util/simpleFeature.ts").Feature[] | undefined;
+        loadedGeneticCodes: Record<string, number> | undefined;
+        lowerCaseRefNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
+        statusMessage: string | undefined;
+        statusProgress: number | undefined;
+        statusSource: string | undefined;
+        refNameMismatches: Map<string, import("./refNameMismatch.ts").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("../util/progress.ts").RpcStatus): void;
+        setRefNameMismatch(adapterCacheKey: string, mismatch: import("./refNameMismatch.ts").RefNameMismatch): void;
+    } & {
+        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("./refNameMaps.ts").RefNameMaps & {
             regions: import("../util/index.ts").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
             cytobands: import("../util/simpleFeature.ts").Feature[];
+            geneticCodes: Record<string, number>;
         }): void;
         setError(e: unknown): void;
-        setRegions(regions: import("../util/index.ts").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("../util/simpleFeature.ts").Feature[]): void;
-        setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
         setLoadingP(p?: Promise<void>): void;
-        load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: {
-            [x: string]: unknown;
-        }, options: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<import("./assembly.ts").RefNameMap>;
+        load(): Promise<void>;
+    } & {
+        afterAttach(): void;
+    } & {
+        readonly initialized: boolean;
+        readonly allRefNames: string[] | undefined;
+        readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
+        readonly rpcManager: RpcManager;
+    } & {
+        readonly refNames: string[] | undefined;
+    } & {
+        readonly refNameToIndex: Map<string, number> | undefined;
+    } & {
+        getCanonicalRefName(refName: string): string | undefined;
+        getRefNameColor(refName: string): string | undefined;
+        getRegionForRefName(refName: string): import("./assembly.ts").BasicRegion | undefined;
+        getGeneticCodeId(refName: string): number;
+        getSeqAdapterRefName(canonicalRefName: string): string;
+    } & {
+        getCanonicalRefName2(refName: string): string;
+        isValidRefName(refName: string): boolean;
+    } & {
+        getRefNamePosition(refName: string): number | undefined;
+        getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        afterCreate(): void;
-    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
-    getRefNameMapForAdapter(adapterConf: AdapterConf, assemblyName: string | undefined, opts: AssemblyBaseOpts): Promise<{
-        [x: string]: string;
-    } | undefined>;
-    getReverseRefNameMapForAdapter(adapterConf: AdapterConf, assemblyName: string | undefined, opts: AssemblyBaseOpts): Promise<{
-        [x: string]: string;
-    } | undefined>;
+        }, options: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<import("./refNameMaps.ts").RefNameAliases>;
+        getRefNameMismatch(adapterCacheKey: string): import("./refNameMismatch.ts").RefNameMismatch | undefined;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
+    /**
+     * #method
+     * The refName map for an adapter under `assemblyName`. Throws if the
+     * assembly cannot be resolved — see {@link requireAssembly}. No
+     * `assemblyName` at all is not a failure, just nothing to rename.
+     */
+    getRefNameMapForAdapter(adapterConf: AdapterConf, assemblyName: string | undefined, opts: AssemblyBaseOpts): Promise<import("./refNameMaps.ts").RefNameAliases>;
+    /**
+     * #method
+     */
     isValidRefName(refName: string, assemblyName: string): boolean;
 } & {
     afterAttach(): void;
+    /**
+     * #action
+     * private: you would generally want to add to manipulate
+     * jbrowse.assemblies, session.sessionAssemblies, or
+     * session.temporaryAssemblies instead of using this directly
+     */
     removeAssembly(asm: Assembly): void;
+    /**
+     * #action
+     * private: you would generally want to add to manipulate
+     * jbrowse.assemblies, session.sessionAssemblies, or
+     * session.temporaryAssemblies instead of using this directly
+     *
+     * this can take an active instance of an assembly, in which case it is
+     * referred to, or it can take an identifier e.g. assembly name, which is
+     * used as a reference. snapshots cannot be used
+     */
     addAssembly(configuration: any): void;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export default assemblyManagerFactory;