@jbrowse/product-core 5.0.0-beta.1 → 5.0.0-beta.10

package/esm/Session/Preferences.d.ts

@@ -11,7 +11,9 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     focusedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType>>, [undefined]>;
     highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    highlightLabelsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     heldForMissingPlugins: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined, import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined, import("../pruneUnbuildableNodes.ts").HeldNode[] | undefined>, [undefined]>;
 }, never>, never>, {
     selection: unknown;
@@ -30,7 +32,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 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;
@@ -68,7 +70,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -86,6 +87,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -101,141 +103,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 } | undefined;
             };
         } & {
-            readonly assemblyNameMap: Record<string, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
-                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
-            }> & {
-                error: unknown;
-                loadingP: Promise<void> | undefined;
-                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
-                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
-                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-                loadedGeneticCodes: Record<string, number> | undefined;
-                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
-                statusMessage: string | undefined;
-                statusProgress: number | undefined;
-                statusSource: string | undefined;
-                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
-            } & {
-                getConf(arg: string): any;
-            } & {
-                readonly name: string;
-                readonly aliases: string[];
-                readonly displayName: string;
-                readonly refNameColors: string[];
-            } & {
-                readonly allAliases: string[];
-                hasName(name: string): boolean;
-            } & {
-                setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
-                setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
-            } & {
-                setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
-                    regions: import("@jbrowse/core/util").Region[];
-                    cytobands: import("@jbrowse/core/util").Feature[];
-                    geneticCodes: Record<string, number>;
-                }): void;
-                setError(e: unknown): void;
-                setLoadingP(p?: Promise<void>): void;
-                loadPre(): Promise<void>;
-            } & {
-                load(): Promise<void>;
-            } & {
-                afterAttach(): void;
-            } & {
-                readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                readonly allRefNames: string[] | undefined;
-                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
-                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-            } & {
-                readonly refNames: string[] | undefined;
-            } & {
-                readonly refNameToIndex: Map<string, number> | undefined;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getRefNameColor(refName: string): string | undefined;
-                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
-                getGeneticCodeId(refName: string): number;
-                getSeqAdapterRefName(canonicalRefName: string): string;
-            } & {
-                getCanonicalRefName2(refName: string): string;
-                isValidRefName(refName: string): boolean;
-            } & {
-                getAliasesForRefName(refName: string): string[];
-                getRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
-                getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
-            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
-                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
-            }, {
-                error: unknown;
-                loadingP: Promise<void> | undefined;
-                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
-                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
-                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-                loadedGeneticCodes: Record<string, number> | undefined;
-                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
-                statusMessage: string | undefined;
-                statusProgress: number | undefined;
-                statusSource: string | undefined;
-                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
-            } & {
-                getConf(arg: string): any;
-            } & {
-                readonly name: string;
-                readonly aliases: string[];
-                readonly displayName: string;
-                readonly refNameColors: string[];
-            } & {
-                readonly allAliases: string[];
-                hasName(name: string): boolean;
-            } & {
-                setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
-                setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
-            } & {
-                setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
-                    regions: import("@jbrowse/core/util").Region[];
-                    cytobands: import("@jbrowse/core/util").Feature[];
-                    geneticCodes: Record<string, number>;
-                }): void;
-                setError(e: unknown): void;
-                setLoadingP(p?: Promise<void>): void;
-                loadPre(): Promise<void>;
-            } & {
-                load(): Promise<void>;
-            } & {
-                afterAttach(): void;
-            } & {
-                readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                readonly allRefNames: string[] | undefined;
-                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
-                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-            } & {
-                readonly refNames: string[] | undefined;
-            } & {
-                readonly refNameToIndex: Map<string, number> | undefined;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getRefNameColor(refName: string): string | undefined;
-                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
-                getGeneticCodeId(refName: string): number;
-                getSeqAdapterRefName(canonicalRefName: string): string;
-            } & {
-                getCanonicalRefName2(refName: string): string;
-                isValidRefName(refName: string): boolean;
-            } & {
-                getAliasesForRefName(refName: string): string[];
-                getRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
-                getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
-            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
+            readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
         } & {
             getCanonicalAssemblyName(asmName: string): string | undefined;
             getDisplayName(asmName: string): string;
@@ -245,7 +113,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 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;
@@ -283,7 +151,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -301,6 +168,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -312,7 +180,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 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;
@@ -350,7 +218,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -368,6 +235,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -381,7 +249,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 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;
@@ -419,7 +287,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -437,6 +304,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -448,7 +316,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 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;
@@ -486,7 +354,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -504,6 +371,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -511,11 +379,8 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 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: import("@jbrowse/core/rpc/RpcManager").default;
         } & {
             settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -526,7 +391,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 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;
@@ -564,7 +429,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -582,6 +446,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -593,7 +458,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 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;
@@ -631,7 +496,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -649,6 +513,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -661,7 +526,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 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;
@@ -699,7 +564,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -717,6 +581,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -728,7 +593,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 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;
@@ -766,7 +631,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -784,6 +648,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -822,7 +687,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 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;
@@ -860,7 +725,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -878,6 +742,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -893,141 +758,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 } | undefined;
             };
         } & {
-            readonly assemblyNameMap: Record<string, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
-                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
-            }> & {
-                error: unknown;
-                loadingP: Promise<void> | undefined;
-                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
-                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
-                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-                loadedGeneticCodes: Record<string, number> | undefined;
-                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
-                statusMessage: string | undefined;
-                statusProgress: number | undefined;
-                statusSource: string | undefined;
-                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
-            } & {
-                getConf(arg: string): any;
-            } & {
-                readonly name: string;
-                readonly aliases: string[];
-                readonly displayName: string;
-                readonly refNameColors: string[];
-            } & {
-                readonly allAliases: string[];
-                hasName(name: string): boolean;
-            } & {
-                setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
-                setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
-            } & {
-                setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
-                    regions: import("@jbrowse/core/util").Region[];
-                    cytobands: import("@jbrowse/core/util").Feature[];
-                    geneticCodes: Record<string, number>;
-                }): void;
-                setError(e: unknown): void;
-                setLoadingP(p?: Promise<void>): void;
-                loadPre(): Promise<void>;
-            } & {
-                load(): Promise<void>;
-            } & {
-                afterAttach(): void;
-            } & {
-                readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                readonly allRefNames: string[] | undefined;
-                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
-                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-            } & {
-                readonly refNames: string[] | undefined;
-            } & {
-                readonly refNameToIndex: Map<string, number> | undefined;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getRefNameColor(refName: string): string | undefined;
-                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
-                getGeneticCodeId(refName: string): number;
-                getSeqAdapterRefName(canonicalRefName: string): string;
-            } & {
-                getCanonicalRefName2(refName: string): string;
-                isValidRefName(refName: string): boolean;
-            } & {
-                getAliasesForRefName(refName: string): string[];
-                getRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
-                getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
-            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
-                configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
-            }, {
-                error: unknown;
-                loadingP: Promise<void> | undefined;
-                adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
-                canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
-                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-                loadedGeneticCodes: Record<string, number> | undefined;
-                lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
-                statusMessage: string | undefined;
-                statusProgress: number | undefined;
-                statusSource: string | undefined;
-                refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
-            } & {
-                getConf(arg: string): any;
-            } & {
-                readonly name: string;
-                readonly aliases: string[];
-                readonly displayName: string;
-                readonly refNameColors: string[];
-            } & {
-                readonly allAliases: string[];
-                hasName(name: string): boolean;
-            } & {
-                setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
-                setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
-            } & {
-                setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
-                    regions: import("@jbrowse/core/util").Region[];
-                    cytobands: import("@jbrowse/core/util").Feature[];
-                    geneticCodes: Record<string, number>;
-                }): void;
-                setError(e: unknown): void;
-                setLoadingP(p?: Promise<void>): void;
-                loadPre(): Promise<void>;
-            } & {
-                load(): Promise<void>;
-            } & {
-                afterAttach(): void;
-            } & {
-                readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                readonly allRefNames: string[] | undefined;
-                readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
-                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-            } & {
-                readonly refNames: string[] | undefined;
-            } & {
-                readonly refNameToIndex: Map<string, number> | undefined;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getRefNameColor(refName: string): string | undefined;
-                getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
-                getGeneticCodeId(refName: string): number;
-                getSeqAdapterRefName(canonicalRefName: string): string;
-            } & {
-                getCanonicalRefName2(refName: string): string;
-                isValidRefName(refName: string): boolean;
-            } & {
-                getAliasesForRefName(refName: string): string[];
-                getRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
-                getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
-            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
+            readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
         } & {
             getCanonicalAssemblyName(asmName: string): string | undefined;
             getDisplayName(asmName: string): string;
@@ -1037,7 +768,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 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;
@@ -1075,7 +806,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1093,6 +823,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -1104,7 +835,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 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;
@@ -1142,7 +873,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1160,6 +890,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -1173,7 +904,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 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;
@@ -1211,7 +942,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1229,6 +959,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -1240,7 +971,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 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;
@@ -1278,7 +1009,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1296,6 +1026,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -1303,11 +1034,8 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 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: import("@jbrowse/core/rpc/RpcManager").default;
         } & {
             settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -1318,7 +1046,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 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;
@@ -1356,7 +1084,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1374,6 +1101,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -1385,7 +1113,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 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;
@@ -1423,7 +1151,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1441,6 +1168,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -1453,7 +1181,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 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;
@@ -1491,7 +1219,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1509,6 +1236,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -1520,7 +1248,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 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;
@@ -1558,7 +1286,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 afterAttach(): void;
             } & {
                 readonly initialized: boolean;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly allRefNames: string[] | undefined;
                 readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
                 readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1576,6 +1303,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
                 getCanonicalRefName2(refName: string): string;
                 isValidRefName(refName: string): boolean;
             } & {
+                getRefNamePosition(refName: string): number | undefined;
                 getAliasesForRefName(refName: string): string[];
                 getRefNameMapForAdapter(adapterConf: {
                     [x: string]: unknown;
@@ -1607,10 +1335,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
 } & {
     readonly jbrowse: any;
     readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-    readonly configuration: 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 configuration: import("@jbrowse/core/configuration").ConfigNodeProps<any> & import("@jbrowse/core/configuration").ConfigNodeActions & import("@jbrowse/core/configuration").ConfigNodeBrand<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
     readonly adminMode: boolean;
     readonly textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
 } & {
@@ -1620,12 +1345,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
 } & {
     getPreferenceDefault(key: string): unknown;
     getPreference(key: string): unknown;
-    getDisplayTypeDefault(displayType: string, slot: string): unknown;
-    getDisplayTypeDefaults(): {
-        displayType: string;
-        slot: string;
-        value: unknown;
-    }[];
     getPreferenceChanges(): import("@jbrowse/core/util").TrackConfigChange[];
 } & {
     readonly animationMode: import("@jbrowse/core/util").AnimationMode;
@@ -1637,17 +1356,20 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
     clearSelection(): void;
     setHovered(thing: unknown): void;
     setHighlightsVisible(arg: boolean): void;
-    revealHighlights(): void;
+    setHighlightLabelsVisible(arg: boolean): void;
+    addHighlight(highlight: import("@jbrowse/core/util/highlights").HighlightType): void;
+    removeHighlight(highlight: import("@jbrowse/core/util/highlights").HighlightType): void;
+    updateHighlight(old: import("@jbrowse/core/util/highlights").HighlightType, updates: Partial<import("@jbrowse/core/util/highlights").HighlightType>): void;
+    setHighlights(highlights: import("@jbrowse/core/util/highlights").HighlightType[]): void;
     setPreferenceOverride(key: string, value: unknown): void;
     clearPreferenceOverrides(): void;
     clearPreferenceOverride(key: string): void;
-    resetPreferenceChange(path: string[]): void;
     setScrollZoom(flag: boolean): void;
-    setDisplayTypeDefault(displayType: string, slot: string, value: unknown): void;
     setName(str: string): void;
     setFocusedViewId(viewId: string | undefined): void;
     removeActiveDialog(): void;
     queueDialog(doneCallback: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
+    removeDialog(entry: [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
 } & {
     snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
     errorDialog: import("@jbrowse/core/ui/SnackbarModel").ErrorDialogState | undefined;
@@ -1662,4 +1384,6 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
     removeSnackbarMessage(message: string): void;
 } & {
     afterAttach(): void;
+} & {
+    afterAttach(): void;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;