@jbrowse/product-core 2.11.2 → 2.12.1

package/dist/Session/Tracks.d.ts

@@ -29,9 +29,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: {
                     [x: string]: string | undefined;
-                } | undefined; /**
-                 * #action
-                 */
+                } | undefined;
                 lowerCaseRefNameAliases: {
                     [x: string]: string | undefined;
                 } | undefined;
@@ -67,7 +65,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -93,9 +91,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: {
                     [x: string]: string | undefined;
-                } | undefined; /**
-                 * #action
-                 */
+                } | undefined;
                 lowerCaseRefNameAliases: {
                     [x: string]: string | undefined;
                 } | undefined;
@@ -131,7 +127,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -195,7 +191,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -257,7 +253,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -321,7 +317,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -383,7 +379,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -402,11 +398,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 }>;
             }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
             readonly assemblyNamesList: any[];
-            readonly assemblyList: ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: unknown): any;
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+            readonly assemblyList: AnyConfigurationModel[];
             readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         } & {
             waitForAssembly(assemblyName: string): Promise<({
@@ -454,7 +446,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -516,7 +508,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -537,7 +529,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
             }, assemblyName: string | undefined, opts: {
-                signal?: AbortSignal | undefined;
+                signal?: AbortSignal;
                 sessionId: string;
             }): Promise<{
                 [x: string]: string | undefined;
@@ -545,7 +537,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
             getReverseRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
             }, assemblyName: string | undefined, opts: {
-                signal?: AbortSignal | undefined;
+                signal?: AbortSignal;
                 sessionId: string;
             }): Promise<{
                 [x: string]: string | undefined;
@@ -553,137 +545,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
             isValidRefName(refName: string, assemblyName: string): boolean;
         } & {
             afterAttach(): void;
-            removeAssembly(asm: {
-                configuration: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                /**
-                 * #action
-                 */
-                error: unknown;
-                loaded: boolean;
-                loadingP: Promise<void> | undefined;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                lowerCaseRefNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-            } & {
-                getConf(arg: string): any;
-            } & {
-                readonly initialized: boolean;
-                readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                readonly aliases: string[];
-                readonly displayName: string | undefined;
-                hasName(name: string): boolean;
-                readonly allAliases: string[];
-                readonly allRefNames: string[] | undefined;
-                readonly lowerCaseRefNames: string[] | undefined;
-                readonly allRefNamesWithLowerCase: string[] | undefined;
-                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-                readonly refNameColors: string[];
-            } & {
-                readonly refNames: string[] | undefined;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getRefNameColor(refName: string): string | undefined;
-                isValidRefName(refName: string): boolean;
-            } & {
-                setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
-                setError(e: unknown): void;
-                setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-                setRefNameAliases(aliases: {
-                    [x: string]: string | undefined;
-                }, lcAliases: {
-                    [x: string]: string | undefined;
-                }): void;
-                setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
-                load(): Promise<void>;
-                loadPre(): Promise<void>;
-            } & {
-                getAdapterMapEntry(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                getRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-                getReverseRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-            } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-            }, {
-                /**
-                 * #action
-                 */
-                error: unknown;
-                loaded: boolean;
-                loadingP: Promise<void> | undefined;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                lowerCaseRefNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-            } & {
-                getConf(arg: string): any;
-            } & {
-                readonly initialized: boolean;
-                readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                readonly aliases: string[];
-                readonly displayName: string | undefined;
-                hasName(name: string): boolean;
-                readonly allAliases: string[];
-                readonly allRefNames: string[] | undefined;
-                readonly lowerCaseRefNames: string[] | undefined;
-                readonly allRefNamesWithLowerCase: string[] | undefined;
-                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-                readonly refNameColors: string[];
-            } & {
-                readonly refNames: string[] | undefined;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getRefNameColor(refName: string): string | undefined;
-                isValidRefName(refName: string): boolean;
-            } & {
-                setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
-                setError(e: unknown): void;
-                setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-                setRefNameAliases(aliases: {
-                    [x: string]: string | undefined;
-                }, lcAliases: {
-                    [x: string]: string | undefined;
-                }): void;
-                setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
-                load(): Promise<void>;
-                loadPre(): Promise<void>;
-            } & {
-                getAdapterMapEntry(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                getRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-                getReverseRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): void;
+            removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
             addAssembly(configuration: any): void;
             replaceAssembly(idx: number, configuration: any): void;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
@@ -696,9 +558,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: {
                     [x: string]: string | undefined;
-                } | undefined; /**
-                 * #action
-                 */
+                } | undefined;
                 lowerCaseRefNameAliases: {
                     [x: string]: string | undefined;
                 } | undefined;
@@ -734,7 +594,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -798,7 +658,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -860,7 +720,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -924,7 +784,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -986,7 +846,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -1005,11 +865,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 }>;
             }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
             readonly assemblyNamesList: any[];
-            readonly assemblyList: ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: unknown): any;
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+            readonly assemblyList: AnyConfigurationModel[];
             readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         } & {
             waitForAssembly(assemblyName: string): Promise<({
@@ -1057,7 +913,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -1119,7 +975,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -1140,7 +996,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
             }, assemblyName: string | undefined, opts: {
-                signal?: AbortSignal | undefined;
+                signal?: AbortSignal;
                 sessionId: string;
             }): Promise<{
                 [x: string]: string | undefined;
@@ -1148,7 +1004,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
             getReverseRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
             }, assemblyName: string | undefined, opts: {
-                signal?: AbortSignal | undefined;
+                signal?: AbortSignal;
                 sessionId: string;
             }): Promise<{
                 [x: string]: string | undefined;
@@ -1156,137 +1012,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
             isValidRefName(refName: string, assemblyName: string): boolean;
         } & {
             afterAttach(): void;
-            removeAssembly(asm: {
-                configuration: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                /**
-                 * #action
-                 */
-                error: unknown;
-                loaded: boolean;
-                loadingP: Promise<void> | undefined;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                lowerCaseRefNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-            } & {
-                getConf(arg: string): any;
-            } & {
-                readonly initialized: boolean;
-                readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                readonly aliases: string[];
-                readonly displayName: string | undefined;
-                hasName(name: string): boolean;
-                readonly allAliases: string[];
-                readonly allRefNames: string[] | undefined;
-                readonly lowerCaseRefNames: string[] | undefined;
-                readonly allRefNamesWithLowerCase: string[] | undefined;
-                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-                readonly refNameColors: string[];
-            } & {
-                readonly refNames: string[] | undefined;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getRefNameColor(refName: string): string | undefined;
-                isValidRefName(refName: string): boolean;
-            } & {
-                setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
-                setError(e: unknown): void;
-                setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-                setRefNameAliases(aliases: {
-                    [x: string]: string | undefined;
-                }, lcAliases: {
-                    [x: string]: string | undefined;
-                }): void;
-                setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
-                load(): Promise<void>;
-                loadPre(): Promise<void>;
-            } & {
-                getAdapterMapEntry(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                getRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-                getReverseRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-            } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-            }, {
-                /**
-                 * #action
-                 */
-                error: unknown;
-                loaded: boolean;
-                loadingP: Promise<void> | undefined;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                lowerCaseRefNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-            } & {
-                getConf(arg: string): any;
-            } & {
-                readonly initialized: boolean;
-                readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                readonly aliases: string[];
-                readonly displayName: string | undefined;
-                hasName(name: string): boolean;
-                readonly allAliases: string[];
-                readonly allRefNames: string[] | undefined;
-                readonly lowerCaseRefNames: string[] | undefined;
-                readonly allRefNamesWithLowerCase: string[] | undefined;
-                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-                readonly refNameColors: string[];
-            } & {
-                readonly refNames: string[] | undefined;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getRefNameColor(refName: string): string | undefined;
-                isValidRefName(refName: string): boolean;
-            } & {
-                setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
-                setError(e: unknown): void;
-                setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-                setRefNameAliases(aliases: {
-                    [x: string]: string | undefined;
-                }, lcAliases: {
-                    [x: string]: string | undefined;
-                }): void;
-                setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
-                load(): Promise<void>;
-                loadPre(): Promise<void>;
-            } & {
-                getAdapterMapEntry(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                getRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-                getReverseRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): void;
+            removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
             addAssembly(configuration: any): void;
             replaceAssembly(idx: number, configuration: any): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
@@ -1298,7 +1024,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
         pluginManager: PluginManager;
     } & {
         setError(error: unknown): void;
-        setSession(sessionSnapshot?: any): void;
+        setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
         setDefaultSession(): void;
         setSessionPath(path: string): void;
         renameCurrentSession(newName: string): void;
@@ -1316,9 +1042,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 refNameAliases: {
                     [x: string]: string | undefined;
-                } | undefined; /**
-                 * #action
-                 */
+                } | undefined;
                 lowerCaseRefNameAliases: {
                     [x: string]: string | undefined;
                 } | undefined;
@@ -1354,7 +1078,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -1418,7 +1142,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -1480,7 +1204,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -1544,7 +1268,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -1606,7 +1330,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -1625,11 +1349,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                 }>;
             }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
             readonly assemblyNamesList: any[];
-            readonly assemblyList: ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: unknown): any;
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+            readonly assemblyList: AnyConfigurationModel[];
             readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         } & {
             waitForAssembly(assemblyName: string): Promise<({
@@ -1677,7 +1397,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -1739,7 +1459,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
                     [x: string]: string | undefined;
                 }): void;
                 setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
+                setLoadingP(p?: Promise<void>): void;
                 load(): Promise<void>;
                 loadPre(): Promise<void>;
             } & {
@@ -1760,7 +1480,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
             }, assemblyName: string | undefined, opts: {
-                signal?: AbortSignal | undefined;
+                signal?: AbortSignal;
                 sessionId: string;
             }): Promise<{
                 [x: string]: string | undefined;
@@ -1768,7 +1488,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
             getReverseRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
             }, assemblyName: string | undefined, opts: {
-                signal?: AbortSignal | undefined;
+                signal?: AbortSignal;
                 sessionId: string;
             }): Promise<{
                 [x: string]: string | undefined;
@@ -1776,137 +1496,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
             isValidRefName(refName: string, assemblyName: string): boolean;
         } & {
             afterAttach(): void;
-            removeAssembly(asm: {
-                configuration: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                /**
-                 * #action
-                 */
-                error: unknown;
-                loaded: boolean;
-                loadingP: Promise<void> | undefined;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                lowerCaseRefNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-            } & {
-                getConf(arg: string): any;
-            } & {
-                readonly initialized: boolean;
-                readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                readonly aliases: string[];
-                readonly displayName: string | undefined;
-                hasName(name: string): boolean;
-                readonly allAliases: string[];
-                readonly allRefNames: string[] | undefined;
-                readonly lowerCaseRefNames: string[] | undefined;
-                readonly allRefNamesWithLowerCase: string[] | undefined;
-                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-                readonly refNameColors: string[];
-            } & {
-                readonly refNames: string[] | undefined;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getRefNameColor(refName: string): string | undefined;
-                isValidRefName(refName: string): boolean;
-            } & {
-                setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
-                setError(e: unknown): void;
-                setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-                setRefNameAliases(aliases: {
-                    [x: string]: string | undefined;
-                }, lcAliases: {
-                    [x: string]: string | undefined;
-                }): void;
-                setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
-                load(): Promise<void>;
-                loadPre(): Promise<void>;
-            } & {
-                getAdapterMapEntry(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                getRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-                getReverseRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-            } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-            }, {
-                /**
-                 * #action
-                 */
-                error: unknown;
-                loaded: boolean;
-                loadingP: Promise<void> | undefined;
-                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                refNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                lowerCaseRefNameAliases: {
-                    [x: string]: string | undefined;
-                } | undefined;
-                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-            } & {
-                getConf(arg: string): any;
-            } & {
-                readonly initialized: boolean;
-                readonly name: string;
-                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-                readonly aliases: string[];
-                readonly displayName: string | undefined;
-                hasName(name: string): boolean;
-                readonly allAliases: string[];
-                readonly allRefNames: string[] | undefined;
-                readonly lowerCaseRefNames: string[] | undefined;
-                readonly allRefNamesWithLowerCase: string[] | undefined;
-                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-                readonly refNameColors: string[];
-            } & {
-                readonly refNames: string[] | undefined;
-            } & {
-                getCanonicalRefName(refName: string): string | undefined;
-                getRefNameColor(refName: string): string | undefined;
-                isValidRefName(refName: string): boolean;
-            } & {
-                setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
-                setError(e: unknown): void;
-                setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-                setRefNameAliases(aliases: {
-                    [x: string]: string | undefined;
-                }, lcAliases: {
-                    [x: string]: string | undefined;
-                }): void;
-                setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-                setLoadingP(p?: Promise<void> | undefined): void;
-                load(): Promise<void>;
-                loadPre(): Promise<void>;
-            } & {
-                getAdapterMapEntry(adapterConf: {
-                    [x: string]: unknown;
-                }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-                getRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-                getReverseRefNameMapForAdapter(adapterConf: {
-                    [x: string]: unknown;
-                }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                    [x: string]: string | undefined;
-                }>;
-            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): void;
+            removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
             addAssembly(configuration: any): void;
             replaceAssembly(idx: number, configuration: any): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
@@ -1918,7 +1508,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
         pluginManager: PluginManager;
     } & {
         setError(error: unknown): void;
-        setSession(sessionSnapshot?: any): void;
+        setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
         setDefaultSession(): void;
         setSessionPath(path: string): void;
         renameCurrentSession(newName: string): void;
@@ -1929,7 +1519,13 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
     readonly configuration: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
     readonly adminMode: boolean;
     readonly textSearchManager: import("@jbrowse/core/util").TextSearchManager;
@@ -1937,7 +1533,13 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
     readonly assemblies: ({
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         aliases: {
             type: string;
@@ -1969,88 +1571,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
 } & {
     getReferring(object: IAnyStateTreeNode): import("./ReferenceManagement").ReferringNode[];
 } & {
-    removeReferring(referring: import("./ReferenceManagement").ReferringNode[], track: {
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        name: {
-            description: string;
-            type: string;
-            defaultValue: string;
-        };
-        assemblyNames: {
-            description: string;
-            type: string;
-            defaultValue: string[];
-        };
-        description: {
-            description: string;
-            type: string;
-            defaultValue: string;
-        };
-        category: {
-            description: string;
-            type: string;
-            defaultValue: never[];
-        };
-        metadata: {
-            type: string;
-            description: string;
-            defaultValue: {};
-        };
-        adapter: import("mobx-state-tree").IAnyModelType;
-        textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            indexingAttributes: {
-                type: string;
-                description: string;
-                defaultValue: string[];
-            };
-            indexingFeatureTypesToExclude: {
-                type: string;
-                description: string;
-                defaultValue: string[];
-            };
-            textSearchAdapter: import("mobx-state-tree").IAnyModelType;
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-        displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-        formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            feature: {
-                type: string;
-                description: string;
-                defaultValue: {};
-                contextVariable: string[];
-            };
-            subfeatures: {
-                type: string;
-                description: string;
-                defaultValue: {};
-                contextVariable: string[];
-            };
-            depth: {
-                type: string;
-                defaultValue: number;
-                description: string;
-            };
-            maxDepth: {
-                type: string;
-                defaultValue: number;
-                description: string;
-            };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-        formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            config: {
-                type: string;
-                description: string;
-                defaultValue: {};
-                contextVariable: string[];
-            };
-            hideUris: {
-                type: string;
-                defaultValue: boolean;
-            };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>>, callbacks: Function[], dereferenceTypeCount: Record<string, number>): void;
+    removeReferring(referring: import("./ReferenceManagement").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: Function[], dereferenceTypeCount: Record<string, number>): void;
 } & {
     /**
      * #getter
@@ -2058,7 +1579,13 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
     readonly tracks: ({
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
 } & {
     /**