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

package/esm/RootModel/BaseRootModel.d.ts

@@ -48,7 +48,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             error: unknown;
             loadingP: Promise<void> | undefined;
             adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            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;
@@ -86,7 +86,6 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             afterAttach(): void;
         } & {
             readonly initialized: boolean;
-            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             readonly allRefNames: string[] | undefined;
             readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
             readonly rpcManager: RpcManager;
@@ -104,6 +103,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             getCanonicalRefName2(refName: string): string;
             isValidRefName(refName: string): boolean;
         } & {
+            getRefNamePosition(refName: string): number | undefined;
             getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
@@ -119,141 +119,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             } | undefined;
         };
     } & {
-        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("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
-            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
-            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-            loadedGeneticCodes: Record<string, number> | undefined;
-            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
-            statusMessage: string | undefined;
-            statusProgress: number | undefined;
-            statusSource: string | undefined;
-            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
-        } & {
-            getConf(arg: string): any;
-        } & {
-            readonly name: string;
-            readonly aliases: string[];
-            readonly displayName: string;
-            readonly refNameColors: string[];
-        } & {
-            readonly allAliases: string[];
-            hasName(name: string): boolean;
-        } & {
-            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
-            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
-        } & {
-            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
-                regions: import("@jbrowse/core/util").Region[];
-                cytobands: import("@jbrowse/core/util").Feature[];
-                geneticCodes: Record<string, number>;
-            }): void;
-            setError(e: unknown): void;
-            setLoadingP(p?: Promise<void>): void;
-            loadPre(): Promise<void>;
-        } & {
-            load(): Promise<void>;
-        } & {
-            afterAttach(): void;
-        } & {
-            readonly initialized: boolean;
-            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            readonly allRefNames: string[] | undefined;
-            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
-            readonly rpcManager: 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("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
-            getGeneticCodeId(refName: string): number;
-            getSeqAdapterRefName(canonicalRefName: string): string;
-        } & {
-            getCanonicalRefName2(refName: string): string;
-            isValidRefName(refName: string): boolean;
-        } & {
-            getAliasesForRefName(refName: string): string[];
-            getRefNameMapForAdapter(adapterConf: {
-                [x: string]: unknown;
-            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
-            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
-        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
-            configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<IAnyType>>;
-        }, {
-            error: unknown;
-            loadingP: Promise<void> | undefined;
-            adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
-            canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
-            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-            loadedGeneticCodes: Record<string, number> | undefined;
-            lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
-            statusMessage: string | undefined;
-            statusProgress: number | undefined;
-            statusSource: string | undefined;
-            refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
-        } & {
-            getConf(arg: string): any;
-        } & {
-            readonly name: string;
-            readonly aliases: string[];
-            readonly displayName: string;
-            readonly refNameColors: string[];
-        } & {
-            readonly allAliases: string[];
-            hasName(name: string): boolean;
-        } & {
-            setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
-            setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
-        } & {
-            setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
-                regions: import("@jbrowse/core/util").Region[];
-                cytobands: import("@jbrowse/core/util").Feature[];
-                geneticCodes: Record<string, number>;
-            }): void;
-            setError(e: unknown): void;
-            setLoadingP(p?: Promise<void>): void;
-            loadPre(): Promise<void>;
-        } & {
-            load(): Promise<void>;
-        } & {
-            afterAttach(): void;
-        } & {
-            readonly initialized: boolean;
-            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            readonly allRefNames: string[] | undefined;
-            readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
-            readonly rpcManager: 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("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
-            getGeneticCodeId(refName: string): number;
-            getSeqAdapterRefName(canonicalRefName: string): string;
-        } & {
-            getCanonicalRefName2(refName: string): string;
-            isValidRefName(refName: string): boolean;
-        } & {
-            getAliasesForRefName(refName: string): string[];
-            getRefNameMapForAdapter(adapterConf: {
-                [x: string]: unknown;
-            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
-            getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
-        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
+        readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
     } & {
         getCanonicalAssemblyName(asmName: string): string | undefined;
         getDisplayName(asmName: string): string;
@@ -263,7 +129,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             error: unknown;
             loadingP: Promise<void> | undefined;
             adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            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;
@@ -301,7 +167,6 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             afterAttach(): void;
         } & {
             readonly initialized: boolean;
-            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             readonly allRefNames: string[] | undefined;
             readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
             readonly rpcManager: RpcManager;
@@ -319,6 +184,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             getCanonicalRefName2(refName: string): string;
             isValidRefName(refName: string): boolean;
         } & {
+            getRefNamePosition(refName: string): number | undefined;
             getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
@@ -330,7 +196,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             error: unknown;
             loadingP: Promise<void> | undefined;
             adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            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;
@@ -368,7 +234,6 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             afterAttach(): void;
         } & {
             readonly initialized: boolean;
-            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             readonly allRefNames: string[] | undefined;
             readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
             readonly rpcManager: RpcManager;
@@ -386,6 +251,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             getCanonicalRefName2(refName: string): string;
             isValidRefName(refName: string): boolean;
         } & {
+            getRefNamePosition(refName: string): number | undefined;
             getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
@@ -399,7 +265,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             error: unknown;
             loadingP: Promise<void> | undefined;
             adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            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;
@@ -437,7 +303,6 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             afterAttach(): void;
         } & {
             readonly initialized: boolean;
-            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             readonly allRefNames: string[] | undefined;
             readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
             readonly rpcManager: RpcManager;
@@ -455,6 +320,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             getCanonicalRefName2(refName: string): string;
             isValidRefName(refName: string): boolean;
         } & {
+            getRefNamePosition(refName: string): number | undefined;
             getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
@@ -466,7 +332,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             error: unknown;
             loadingP: Promise<void> | undefined;
             adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            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;
@@ -504,7 +370,6 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             afterAttach(): void;
         } & {
             readonly initialized: boolean;
-            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             readonly allRefNames: string[] | undefined;
             readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
             readonly rpcManager: RpcManager;
@@ -522,6 +387,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             getCanonicalRefName2(refName: string): string;
             isValidRefName(refName: string): boolean;
         } & {
+            getRefNamePosition(refName: string): number | undefined;
             getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
@@ -529,11 +395,8 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
         readonly assemblyNamesList: string[];
-        readonly configuredAssemblyNames: Set<string>;
-        readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
-            setSubschema(slotName: string, data: Record<string, unknown>): any;
-            setSlot(slotName: string, value: unknown): void;
-        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+        readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
+        readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
         readonly rpcManager: RpcManager;
     } & {
         settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -544,7 +407,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             error: unknown;
             loadingP: Promise<void> | undefined;
             adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            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;
@@ -582,7 +445,6 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             afterAttach(): void;
         } & {
             readonly initialized: boolean;
-            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             readonly allRefNames: string[] | undefined;
             readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
             readonly rpcManager: RpcManager;
@@ -600,6 +462,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             getCanonicalRefName2(refName: string): string;
             isValidRefName(refName: string): boolean;
         } & {
+            getRefNamePosition(refName: string): number | undefined;
             getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
@@ -611,7 +474,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             error: unknown;
             loadingP: Promise<void> | undefined;
             adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            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;
@@ -649,7 +512,6 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             afterAttach(): void;
         } & {
             readonly initialized: boolean;
-            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             readonly allRefNames: string[] | undefined;
             readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
             readonly rpcManager: RpcManager;
@@ -667,6 +529,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             getCanonicalRefName2(refName: string): string;
             isValidRefName(refName: string): boolean;
         } & {
+            getRefNamePosition(refName: string): number | undefined;
             getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
@@ -679,7 +542,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             error: unknown;
             loadingP: Promise<void> | undefined;
             adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            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;
@@ -717,7 +580,6 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             afterAttach(): void;
         } & {
             readonly initialized: boolean;
-            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             readonly allRefNames: string[] | undefined;
             readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
             readonly rpcManager: RpcManager;
@@ -735,6 +597,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             getCanonicalRefName2(refName: string): string;
             isValidRefName(refName: string): boolean;
         } & {
+            getRefNamePosition(refName: string): number | undefined;
             getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
@@ -746,7 +609,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             error: unknown;
             loadingP: Promise<void> | undefined;
             adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+            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;
@@ -784,7 +647,6 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             afterAttach(): void;
         } & {
             readonly initialized: boolean;
-            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
             readonly allRefNames: string[] | undefined;
             readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
             readonly rpcManager: RpcManager;
@@ -802,6 +664,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             getCanonicalRefName2(refName: string): string;
             isValidRefName(refName: string): boolean;
         } & {
+            getRefNamePosition(refName: string): number | undefined;
             getAliasesForRefName(refName: string): string[];
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
@@ -857,6 +720,9 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
     setSession(sessionSnapshot?: SnapshotIn<IAnyType>): void;
     /**
      * #action
+     * Starts a new session from the config's defaultSession. An `id` in it
+     * (a pasted session export carries one) is dropped, since sessions are
+     * autosaved by id and each new one would otherwise overwrite the last.
      */
     setDefaultSession(): void;
     /**

package/esm/RootModel/BaseRootModel.js

@@ -1,9 +1,9 @@
 import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
 import assemblyManagerFactory from '@jbrowse/core/assemblyManager';
 import RpcManager from '@jbrowse/core/rpc/RpcManager';
+import { scheduleDetachedDestroy } from '@jbrowse/core/util';
 import { cast, detach, getType, isStateTreeNode, types, } from '@jbrowse/mobx-state-tree';
 import { describeUnbuildableNodes, pruneUnbuildableNodes, } from '../pruneUnbuildableNodes.js';
-import { scheduleDetachedDestroy } from '../scheduleDetachedDestroy.js';
 import { migrateSessionSnapshot } from '../sessionMigrations/index.js';
 import { filterSessionInPlace } from '../sessionUtils.js';
 // `session` is a `types.maybe(sessionModelType)` where `sessionModelType` is the
@@ -87,9 +87,10 @@ export function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionM
             const unbuildable = [];
             let migrated = sessionSnapshot;
             if (sessionSnapshot && typeof sessionSnapshot === 'object') {
+                pluginManager.assertSessionTypesLoaded(sessionSnapshot);
                 // before the cast, because a type this build has no plugin for is a
                 // union failure the try below never gets to see
-                const pruned = pruneUnbuildableNodes(migrateSessionSnapshot(sessionSnapshot), pluginManager, sessionModelType);
+                const pruned = pruneUnbuildableNodes(migrateSessionSnapshot(sessionSnapshot, pluginManager), pluginManager, sessionModelType);
                 migrated = pruned.snapshot;
                 unbuildable.push(...pruned.dropped);
             }
@@ -138,12 +139,14 @@ export function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionM
         },
         /**
          * #action
+         * Starts a new session from the config's defaultSession. An `id` in it
+         * (a pasted session export carries one) is dropped, since sessions are
+         * autosaved by id and each new one would otherwise overwrite the last.
          */
         setDefaultSession() {
-            const { defaultSession } = self.jbrowse;
+            const { id: _id, ...defaultSession } = self.jbrowse.defaultSession;
             this.setSession({
                 ...defaultSession,
-                // timestamp the name so repeated "new session" names don't collide
                 name: `${defaultSession.name || 'New session'} ${new Date().toLocaleString()}`,
             });
         },

package/esm/RootModel/HierarchicalConfig.d.ts

@@ -5,63 +5,37 @@
  */
 export declare function HierarchicalConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     readonly sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot configuration.hierarchical.sort.trackNames
-         * start the track selector with tracks sorted alphabetically inside each
-         * category rather than in config order. Only the initial state — the
-         * selector's own "Sort track names" toggle overrides it from then on
-         */
         readonly trackNames: {
-            readonly type: "boolean";
-            readonly defaultValue: false;
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
         };
-        /**
-         * #slot configuration.hierarchical.sort.categories
-         * start the track selector with categories sorted alphabetically rather
-         * than in config order. Only the initial state — the selector's own
-         * "Sort categories" toggle overrides it from then on
-         */
         readonly categories: {
-            readonly type: "boolean";
-            readonly defaultValue: false;
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    /**
-     * #slot configuration.hierarchical.defaultFolderCategories
-     */
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
     readonly defaultFolderCategories: {
-        readonly type: "stringArray";
-        readonly description: "list of category names to display as folders by default";
-        readonly defaultValue: readonly [];
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
     };
     readonly defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot configuration.hierarchical.defaultCollapsed.categoryNames
-         * named top-level categories that start collapsed, e.g.
-         * `['ENCODE', 'RNA-seq']`. Once a user expands or collapses anything, the
-         * selector remembers their state instead
-         */
         readonly categoryNames: {
-            readonly type: "stringArray";
-            readonly defaultValue: readonly [];
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
         };
-        /**
-         * #slot configuration.hierarchical.defaultCollapsed.topLevelCategories
-         * start every top-level category collapsed, so a config with many
-         * categories opens as a short list rather than a wall of tracks
-         */
         readonly topLevelCategories: {
-            readonly type: "boolean";
-            readonly defaultValue: false;
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
         };
-        /**
-         * #slot configuration.hierarchical.defaultCollapsed.subCategories
-         * start every nested category collapsed while leaving the top level
-         * open, for deeply categorized track sets
-         */
         readonly subCategories: {
-            readonly type: "boolean";
-            readonly defaultValue: false;
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;

package/esm/RootModel/PreferencesConfig.d.ts

@@ -7,47 +7,31 @@
  * override map layered over config defaults, at app scope.
  */
 export declare function PreferencesConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot configuration.preferences.animationMode
-     * controls feature-layout animations: 'enabled' always animates (the
-     * default), 'system' respects the OS prefers-reduced-motion setting,
-     * 'disabled' never animates
-     */
     readonly animationMode: {
-        readonly model: import("@jbrowse/mobx-state-tree").ISimpleType<"disabled" | "enabled" | "system">;
-        readonly type: "stringEnum";
-        readonly defaultValue: "enabled";
+        type: "stringEnum";
+    } & {
+        model: import("@jbrowse/mobx-state-tree").ISimpleType<"disabled" | "enabled" | "system">;
+    } & {
+        defaultValue: string;
     };
-    /**
-     * #slot configuration.preferences.scrollZoom
-     * when true, scrolling the mouse wheel over a track zooms in and out
-     * without holding Ctrl. Applies globally to all wheel-zoom views.
-     */
     readonly scrollZoom: {
-        readonly type: "boolean";
-        readonly defaultValue: false;
+        type: "boolean";
+    } & {
+        defaultValue: boolean;
     };
-    /**
-     * #slot configuration.preferences.numberGrouping
-     * when true (the default), numbers are displayed with thousand separators
-     * — `chr1:1,234,567`. Turn it off to render them bare, which is what you
-     * want if you copy coordinates out of JBrowse into tools that won't accept
-     * the commas. Applies to every displayed number, and takes effect on
-     * reload.
-     */
     readonly numberGrouping: {
-        readonly type: "boolean";
-        readonly defaultValue: true;
+        type: "boolean";
+    } & {
+        defaultValue: boolean;
     };
-    /**
-     * #slot configuration.preferences.useWorkspaces
-     * when true, views open in the tabbed/tiled workspace layout rather than
-     * stacked vertically. Only the default: a session that names
-     * `useWorkspaces` itself (a shared snapshot, or a session spec carrying a
-     * `layout`) still wins, and a user's own toggle overrides it.
-     */
     readonly useWorkspaces: {
-        readonly type: "boolean";
-        readonly defaultValue: false;
+        type: "boolean";
+    } & {
+        defaultValue: boolean;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    readonly developerMode: {
+        type: "boolean";
+    } & {
+        defaultValue: boolean;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;

package/esm/RootModel/PreferencesConfig.js

@@ -37,9 +37,8 @@ export function PreferencesConfigSchemaFactory() {
         /**
          * #slot configuration.preferences.numberGrouping
          * when true (the default), numbers are displayed with thousand separators
-         * — `chr1:1,234,567`. Turn it off to render them bare, which is what you
-         * want if you copy coordinates out of JBrowse into tools that won't accept
-         * the commas. Applies to every displayed number, and takes effect on
+         * (`chr1:1,234,567`). Turn it off to display them without separators, for
+         * copying coordinates into tools that won't accept the commas. Applies to every displayed number, and takes effect on
          * reload.
          */
         numberGrouping: {
@@ -57,5 +56,20 @@ export function PreferencesConfigSchemaFactory() {
             type: 'boolean',
             defaultValue: false,
         },
+        /**
+         * #slot configuration.preferences.developerMode
+         * when true, the ordering-contract checks a display or plugin can break
+         * report themselves in the app rather than only in a development build.
+         * Off by default and deliberately not in the Preferences dialog: the
+         * messages are about code, and a reader who cannot change the code cannot
+         * act on one. Turn it on for a site that is running a plugin under
+         * development; a plugin author needs nothing here, since a plugin served
+         * from localhost arms the same channel on its own, as does
+         * `localStorage.jbrowseDeveloperMode`. Takes effect on reload.
+         */
+        developerMode: {
+            type: 'boolean',
+            defaultValue: false,
+        },
     });
 }