@jbrowse/product-core 2.11.2 → 2.12.1

package/dist/Session/SessionTracks.d.ts

@@ -67,7 +67,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -129,7 +129,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -193,7 +193,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -255,7 +255,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -319,7 +319,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -381,7 +381,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -400,11 +400,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 }>;
             }, 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<({
@@ -452,7 +448,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -514,7 +510,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -535,7 +531,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
             }, assemblyName: string | undefined, opts: {
-                signal?: AbortSignal | undefined;
+                signal?: AbortSignal;
                 sessionId: string;
             }): Promise<{
                 [x: string]: string | undefined;
@@ -543,7 +539,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
             getReverseRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
             }, assemblyName: string | undefined, opts: {
-                signal?: AbortSignal | undefined;
+                signal?: AbortSignal;
                 sessionId: string;
             }): Promise<{
                 [x: string]: string | undefined;
@@ -551,135 +547,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
             isValidRefName(refName: string, assemblyName: string): boolean;
         } & {
             afterAttach(): void;
-            removeAssembly(asm: {
-                configuration: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                error: unknown; /**
-                 * #action
-                 */
-                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>>;
-            }, {
-                error: unknown; /**
-                 * #action
-                 */
-                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<{
@@ -728,7 +596,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -792,7 +660,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -854,7 +722,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -918,7 +786,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -980,7 +848,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -999,11 +867,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 }>;
             }, 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<({
@@ -1051,7 +915,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -1113,7 +977,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -1134,7 +998,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
             }, assemblyName: string | undefined, opts: {
-                signal?: AbortSignal | undefined;
+                signal?: AbortSignal;
                 sessionId: string;
             }): Promise<{
                 [x: string]: string | undefined;
@@ -1142,7 +1006,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
             getReverseRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
             }, assemblyName: string | undefined, opts: {
-                signal?: AbortSignal | undefined;
+                signal?: AbortSignal;
                 sessionId: string;
             }): Promise<{
                 [x: string]: string | undefined;
@@ -1150,135 +1014,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
             isValidRefName(refName: string, assemblyName: string): boolean;
         } & {
             afterAttach(): void;
-            removeAssembly(asm: {
-                configuration: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                error: unknown; /**
-                 * #action
-                 */
-                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>>;
-            }, {
-                error: unknown; /**
-                 * #action
-                 */
-                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]>>;
@@ -1290,7 +1026,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
         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;
@@ -1344,7 +1080,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -1408,7 +1144,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -1470,7 +1206,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -1534,7 +1270,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -1596,7 +1332,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -1615,11 +1351,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                 }>;
             }, 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<({
@@ -1667,7 +1399,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -1729,7 +1461,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
                     [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>;
             } & {
@@ -1750,7 +1482,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
             getRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
             }, assemblyName: string | undefined, opts: {
-                signal?: AbortSignal | undefined;
+                signal?: AbortSignal;
                 sessionId: string;
             }): Promise<{
                 [x: string]: string | undefined;
@@ -1758,7 +1490,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
             getReverseRefNameMapForAdapter(adapterConf: {
                 [x: string]: unknown;
             }, assemblyName: string | undefined, opts: {
-                signal?: AbortSignal | undefined;
+                signal?: AbortSignal;
                 sessionId: string;
             }): Promise<{
                 [x: string]: string | undefined;
@@ -1766,135 +1498,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
             isValidRefName(refName: string, assemblyName: string): boolean;
         } & {
             afterAttach(): void;
-            removeAssembly(asm: {
-                configuration: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                error: unknown; /**
-                 * #action
-                 */
-                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>>;
-            }, {
-                error: unknown; /**
-                 * #action
-                 */
-                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]>;
@@ -1906,7 +1510,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
         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;
@@ -1917,7 +1521,13 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
     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;
@@ -1925,14 +1535,22 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
     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;
             defaultValue: never[];
             description: string;
         };
-        sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+        sequence: import("@jbrowse/core/configuration" /**
+         * #getter
+         */).AnyConfigurationSchemaType;
         refNameColors: {
             type: string;
             defaultValue: never[];
@@ -1957,102 +1575,22 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
 } & {
     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;
-                /** Session mixin MST type for a session that has `sessionTracks` */
-                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;
 } & {
     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>)[];
 } & {
     addTrackConf(trackConf: AnyConfiguration): any;
-    deleteTrackConf(trackConf: {
-        [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>): any;
+    deleteTrackConf(trackConf: AnyConfigurationModel): any;
 } & {
     /**
      * #getter
@@ -2060,7 +1598,13 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
     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>)[];
 } & {
     /**