@jbrowse/core 5.0.0-beta.1 → 5.0.0-beta.11

package/esm/assemblyManager/assemblyManager.d.ts

@@ -1,12 +1,12 @@
 import type PluginManager from '../PluginManager.ts';
+import type { AnyConfigurationModel } from '../configuration/index.ts';
 import type RpcManager from '../rpc/RpcManager.ts';
 import type { StatusCallback } from '../util/progress.ts';
-import type { StopToken } from '../util/stopToken.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?: StatusCallback;
 }
@@ -26,7 +26,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         error: unknown;
         loadingP: Promise<void> | undefined;
         adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("./refNameMaps.ts").RefNameAliases>>;
-        volatileRegions: import("./assembly.ts").BasicRegion[] | undefined;
+        regions: import("./assembly.ts").BasicRegion[] | undefined;
         refNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
         canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
         cytobands: import("../util/simpleFeature.ts").Feature[] | undefined;
@@ -64,7 +64,6 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         afterAttach(): void;
     } & {
         readonly initialized: boolean;
-        readonly regions: import("./assembly.ts").BasicRegion[] | undefined;
         readonly allRefNames: string[] | undefined;
         readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
         readonly rpcManager: RpcManager;
@@ -82,6 +81,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
@@ -112,141 +112,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
     /**
      * #getter
      */
-    readonly assemblyNameMap: Record<string, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
-        configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
-    }> & {
-        error: unknown;
-        loadingP: Promise<void> | undefined;
-        adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("./refNameMaps.ts").RefNameAliases>>;
-        volatileRegions: 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[];
-            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 regions: import("./assembly.ts").BasicRegion[] | undefined;
-        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;
-    } & {
-        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>>;
-        volatileRegions: 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[];
-            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 regions: import("./assembly.ts").BasicRegion[] | undefined;
-        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;
-    } & {
-        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")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
+    readonly assemblyNameMap: Record<string, Assembly>;
 } & {
     /**
      * #method
@@ -271,7 +137,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         error: unknown;
         loadingP: Promise<void> | undefined;
         adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("./refNameMaps.ts").RefNameAliases>>;
-        volatileRegions: import("./assembly.ts").BasicRegion[] | undefined;
+        regions: import("./assembly.ts").BasicRegion[] | undefined;
         refNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
         canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
         cytobands: import("../util/simpleFeature.ts").Feature[] | undefined;
@@ -309,7 +175,6 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         afterAttach(): void;
     } & {
         readonly initialized: boolean;
-        readonly regions: import("./assembly.ts").BasicRegion[] | undefined;
         readonly allRefNames: string[] | undefined;
         readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
         readonly rpcManager: RpcManager;
@@ -327,6 +192,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
@@ -338,7 +204,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         error: unknown;
         loadingP: Promise<void> | undefined;
         adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("./refNameMaps.ts").RefNameAliases>>;
-        volatileRegions: import("./assembly.ts").BasicRegion[] | undefined;
+        regions: import("./assembly.ts").BasicRegion[] | undefined;
         refNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
         canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
         cytobands: import("../util/simpleFeature.ts").Feature[] | undefined;
@@ -376,7 +242,6 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         afterAttach(): void;
     } & {
         readonly initialized: boolean;
-        readonly regions: import("./assembly.ts").BasicRegion[] | undefined;
         readonly allRefNames: string[] | undefined;
         readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
         readonly rpcManager: RpcManager;
@@ -394,6 +259,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
@@ -425,7 +291,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         error: unknown;
         loadingP: Promise<void> | undefined;
         adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("./refNameMaps.ts").RefNameAliases>>;
-        volatileRegions: import("./assembly.ts").BasicRegion[] | undefined;
+        regions: import("./assembly.ts").BasicRegion[] | undefined;
         refNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
         canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
         cytobands: import("../util/simpleFeature.ts").Feature[] | undefined;
@@ -463,7 +329,6 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         afterAttach(): void;
     } & {
         readonly initialized: boolean;
-        readonly regions: import("./assembly.ts").BasicRegion[] | undefined;
         readonly allRefNames: string[] | undefined;
         readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
         readonly rpcManager: RpcManager;
@@ -481,6 +346,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
@@ -492,7 +358,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         error: unknown;
         loadingP: Promise<void> | undefined;
         adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("./refNameMaps.ts").RefNameAliases>>;
-        volatileRegions: import("./assembly.ts").BasicRegion[] | undefined;
+        regions: import("./assembly.ts").BasicRegion[] | undefined;
         refNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
         canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
         cytobands: import("../util/simpleFeature.ts").Feature[] | undefined;
@@ -530,7 +396,6 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         afterAttach(): void;
     } & {
         readonly initialized: boolean;
-        readonly regions: import("./assembly.ts").BasicRegion[] | undefined;
         readonly allRefNames: string[] | undefined;
         readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
         readonly rpcManager: RpcManager;
@@ -548,6 +413,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
@@ -556,32 +422,24 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
     /**
      * #getter
-     * read via readConfObject, matching how the afterAttach autorun names the
-     * assemblies it creates: get() treats a name found here as "a config
-     * exists, its model is just not built yet", so the two must agree
+     * 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`. What {@link has} knows before the models exist.
-     *
-     * Separate from assemblyNamesList rather than widening it: `get` treats a
-     * name found in that list as "a config exists, its model is just not built
-     * yet", which has to stay the canonical name the autorun will create the
-     * assembly under. A Set because `has` is called per name by per-render
-     * scans over every track in the session.
+     * `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 configuredAssemblyNames: Set<string>;
+    readonly confByName: Map<string, AnyConfigurationModel>;
     /**
      * #getter
      * combined jbrowse.assemblies, session.sessionAssemblies, and
      * session.temporaryAssemblies
      */
-    readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
-        setSubschema(slotName: string, data: Record<string, unknown>): any;
-        setSlot(slotName: string, value: unknown): void;
-    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("../configuration/types.ts").AnyConfigurationSchemaType>)[];
+    readonly assemblyList: AnyConfigurationModel[];
     readonly rpcManager: RpcManager;
 } & {
     /**
@@ -619,7 +477,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         error: unknown;
         loadingP: Promise<void> | undefined;
         adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("./refNameMaps.ts").RefNameAliases>>;
-        volatileRegions: import("./assembly.ts").BasicRegion[] | undefined;
+        regions: import("./assembly.ts").BasicRegion[] | undefined;
         refNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
         canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
         cytobands: import("../util/simpleFeature.ts").Feature[] | undefined;
@@ -657,7 +515,6 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         afterAttach(): void;
     } & {
         readonly initialized: boolean;
-        readonly regions: import("./assembly.ts").BasicRegion[] | undefined;
         readonly allRefNames: string[] | undefined;
         readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
         readonly rpcManager: RpcManager;
@@ -675,6 +532,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
@@ -686,7 +544,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         error: unknown;
         loadingP: Promise<void> | undefined;
         adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("./refNameMaps.ts").RefNameAliases>>;
-        volatileRegions: import("./assembly.ts").BasicRegion[] | undefined;
+        regions: import("./assembly.ts").BasicRegion[] | undefined;
         refNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
         canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
         cytobands: import("../util/simpleFeature.ts").Feature[] | undefined;
@@ -724,7 +582,6 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         afterAttach(): void;
     } & {
         readonly initialized: boolean;
-        readonly regions: import("./assembly.ts").BasicRegion[] | undefined;
         readonly allRefNames: string[] | undefined;
         readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
         readonly rpcManager: RpcManager;
@@ -742,6 +599,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
@@ -753,18 +611,15 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
      * {@link waitForAssembly}, but a name that cannot be resolved is an error
      * rather than an `undefined` for the caller to interpret.
      *
-     * For callers whose result is silently *wrong* without the assembly, not
-     * merely absent: a refName map is the obvious one, since an empty map
-     * means an adapter gets queried with un-renamed refNames, finds nothing,
-     * and the track draws blank with nothing to say why. Failing here instead
-     * puts the name in front of the user, who is the only one who can add the
+     * 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.
      *
-     * Worth using only because the wait is causal now. It used to give up
-     * after a fixed ten seconds, where "not resolved" could equally mean "not
-     * resolved yet" and throwing would have been a race; today it returns
-     * only once every handler and connection that could supply the name has
-     * finished, so there is a real answer to report.
+     * `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>>;
@@ -772,7 +627,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         error: unknown;
         loadingP: Promise<void> | undefined;
         adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("./refNameMaps.ts").RefNameAliases>>;
-        volatileRegions: import("./assembly.ts").BasicRegion[] | undefined;
+        regions: import("./assembly.ts").BasicRegion[] | undefined;
         refNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
         canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
         cytobands: import("../util/simpleFeature.ts").Feature[] | undefined;
@@ -810,7 +665,6 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         afterAttach(): void;
     } & {
         readonly initialized: boolean;
-        readonly regions: import("./assembly.ts").BasicRegion[] | undefined;
         readonly allRefNames: string[] | undefined;
         readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
         readonly rpcManager: RpcManager;
@@ -828,6 +682,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
@@ -839,7 +694,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         error: unknown;
         loadingP: Promise<void> | undefined;
         adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("./refNameMaps.ts").RefNameAliases>>;
-        volatileRegions: import("./assembly.ts").BasicRegion[] | undefined;
+        regions: import("./assembly.ts").BasicRegion[] | undefined;
         refNameAliases: import("./refNameMaps.ts").RefNameAliases | undefined;
         canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
         cytobands: import("../util/simpleFeature.ts").Feature[] | undefined;
@@ -877,7 +732,6 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         afterAttach(): void;
     } & {
         readonly initialized: boolean;
-        readonly regions: import("./assembly.ts").BasicRegion[] | undefined;
         readonly allRefNames: string[] | undefined;
         readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
         readonly rpcManager: RpcManager;
@@ -895,6 +749,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;

package/esm/assemblyManager/assemblyManager.js

@@ -2,6 +2,7 @@ import { addDisposer, getParent, types } from '@jbrowse/mobx-state-tree';
 import { autorun, untracked, when } from 'mobx';
 import { readConfObject } from '../configuration/index.js';
 import assemblyFactory from './assembly.js';
+import { indexAssemblyNames } from './indexAssemblyNames.js';
 // How long waitForAssembly gives a handler that did NOT return a promise.
 // Nothing about such a handler is observable — it was told a name and said
 // nothing back — so there is no event to wait on and the only choices are a
@@ -109,13 +110,10 @@ function assemblyManagerFactory(conf, pm) {
          * #getter
          */
         get assemblyNameMap() {
-            const obj = {};
-            for (const assembly of self.assemblies) {
-                for (const name of assembly.allAliases) {
-                    obj[name] = assembly;
-                }
-            }
-            return obj;
+            return Object.fromEntries(indexAssemblyNames(self.assemblies, a => ({
+                name: a.name,
+                aliases: a.aliases,
+            })));
         },
     }))
         .views(self => ({
@@ -186,7 +184,7 @@ function assemblyManagerFactory(conf, pm) {
         // Both lookups are load-bearing, and the config one has to cover aliases
         // as well: assemblyNameMap is keyed by allAliases ([name, ...aliases]) but
         // only exists once the afterAttach autorun has built the models, while
-        // configuredAssemblyNames answers off the configs from the first render.
+        // confByName answers off the configs from the first render.
         // Screening on the canonical names alone left `vvx` unknown for the whole
         // startup window even though the config for `volvox` names it — a wrong
         // "no", which means the caller re-adds an assembly the session already
@@ -201,8 +199,7 @@ function assemblyManagerFactory(conf, pm) {
         // read is never undefined to the compiler, so `!!` on it infers the
         // literal `true` and `!has(name)` would be dead code at every call site.
         has(asmName) {
-            return (!!self.assemblyNameMap[asmName] ||
-                this.configuredAssemblyNames.has(asmName));
+            return !!self.assemblyNameMap[asmName] || this.confByName.has(asmName);
         },
         /**
          * #method
@@ -219,9 +216,8 @@ function assemblyManagerFactory(conf, pm) {
         },
         /**
          * #getter
-         * read via readConfObject, matching how the afterAttach autorun names the
-         * assemblies it creates: get() treats a name found here as "a config
-         * exists, its model is just not built yet", so the two must agree
+         * the canonical name of every configured assembly, read the way the
+         * afterAttach autorun names the models it builds
          */
         get assemblyNamesList() {
             return this.assemblyList.map(asm => readConfObject(asm, 'name'));
@@ -229,19 +225,15 @@ function assemblyManagerFactory(conf, pm) {
         /**
          * #getter
          * Every name the *configs* answer to — each assembly's `name` and its
-         * `aliases`. What {@link has} knows before the models exist.
-         *
-         * Separate from assemblyNamesList rather than widening it: `get` treats a
-         * name found in that list as "a config exists, its model is just not built
-         * yet", which has to stay the canonical name the autorun will create the
-         * assembly under. A Set because `has` is called per name by per-render
-         * scans over every track in the session.
+         * `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`.
          */
-        get configuredAssemblyNames() {
-            return new Set(this.assemblyList.flatMap(asm => [
-                readConfObject(asm, 'name'),
-                ...(readConfObject(asm, 'aliases') ?? []),
-            ]));
+        get confByName() {
+            return indexAssemblyNames(this.assemblyList, asm => ({
+                name: readConfObject(asm, 'name'),
+                aliases: readConfObject(asm, 'aliases') ?? [],
+            }));
         },
         /**
          * #getter
@@ -298,9 +290,10 @@ function assemblyManagerFactory(conf, pm) {
             // Nothing left that could still produce it. Both clauses are things
             // that end on their own, so this needs no bound of its own.
             const settled = () => 
-            // a config carrying the name is already in the tree and the
-            // afterAttach autorun is about to build its model
-            !self.assemblyNamesList.includes(assemblyName) &&
+            // a config answering to the name, as its name or an alias, is
+            // already in the tree and the afterAttach autorun is about to build
+            // its model
+            !self.confByName.has(assemblyName) &&
                 // a connection mid-fetch could be carrying it. Every loading
                 // connection counts, not just one naming this assembly: a connection
                 // config need not declare what it will turn out to provide, and
@@ -343,18 +336,15 @@ function assemblyManagerFactory(conf, pm) {
          * {@link waitForAssembly}, but a name that cannot be resolved is an error
          * rather than an `undefined` for the caller to interpret.
          *
-         * For callers whose result is silently *wrong* without the assembly, not
-         * merely absent: a refName map is the obvious one, since an empty map
-         * means an adapter gets queried with un-renamed refNames, finds nothing,
-         * and the track draws blank with nothing to say why. Failing here instead
-         * puts the name in front of the user, who is the only one who can add the
+         * 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.
          *
-         * Worth using only because the wait is causal now. It used to give up
-         * after a fixed ten seconds, where "not resolved" could equally mean "not
-         * resolved yet" and throwing would have been a race; today it returns
-         * only once every handler and connection that could supply the name has
-         * finished, so there is a real answer to report.
+         * `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.
          */
         async requireAssembly(assemblyName) {
             const assembly = await this.waitForAssembly(assemblyName);
@@ -389,23 +379,29 @@ function assemblyManagerFactory(conf, pm) {
     }))
         .actions(self => ({
         afterAttach() {
+            const reconcile = (assemblyConfs) => {
+                // filter() returns a new plain array, so removing from
+                // self.assemblies in the loop below does not skip elements
+                // (removeAssembly splices the live observable array)
+                const orphaned = self.assemblies.filter(a => !a.configuration);
+                for (const asm of orphaned) {
+                    this.removeAssembly(asm);
+                }
+                const built = new Set(self.assemblies.map(a => a.name));
+                for (const conf of assemblyConfs) {
+                    if (!built.has(readConfObject(conf, 'name'))) {
+                        this.addAssembly(conf);
+                    }
+                }
+            };
+            // also here, because an enclosing action defers the autorun's first
+            // run, and a load waiting on the model would wait for that
+            reconcile(self.assemblyList);
             addDisposer(self, autorun(() => {
                 const assemblyConfs = self.assemblyList;
                 // eslint-disable-next-line no-restricted-syntax -- self-write: removes from the assemblies it reads
                 untracked(() => {
-                    // filter() returns a new plain array, so removing from
-                    // self.assemblies in the loop below does not skip elements
-                    // (removeAssembly splices the live observable array)
-                    const orphaned = self.assemblies.filter(a => !a.configuration);
-                    for (const asm of orphaned) {
-                        this.removeAssembly(asm);
-                    }
-                    for (const conf of assemblyConfs) {
-                        const name = readConfObject(conf, 'name');
-                        if (!self.assemblies.some(a => a.name === name)) {
-                            this.addAssembly(conf);
-                        }
-                    }
+                    reconcile(assemblyConfs);
                 });
             }, { name: 'assemblyManagerAfterAttach' }));
         },