@jbrowse/product-core 2.6.1

package/dist/RootModel/BaseRootModel.d.ts

@@ -0,0 +1,607 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+import { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager';
+import RpcManager from '@jbrowse/core/rpc/RpcManager';
+import { IAnyType, Instance, SnapshotIn } from 'mobx-state-tree';
+import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
+/**
+ * #stateModel BaseRootModel
+ * #category root
+ * factory function for the Base-level root model shared by all products
+ */
+export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionModelType, assemblyConfigSchema, }: {
+    pluginManager: PluginManager;
+    jbrowseModelType: IAnyType;
+    sessionModelType: IAnyType;
+    assemblyConfigSchema: BaseAssemblyConfigSchema;
+}): import("mobx-state-tree").IModelType<{
+    /**
+     * #property
+     * `jbrowse` is a mapping of the config.json into the in-memory state
+     * tree
+     */
+    jbrowse: IAnyType;
+    /**
+     * #property
+     * `session` encompasses the currently active state of the app, including
+     * views open, tracks open in those views, etc.
+     */
+    session: import("mobx-state-tree").IMaybe<IAnyType>;
+    /**
+     * #property
+     */
+    sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    /**
+     * #property
+     */
+    assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
+        assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+            configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
+        }, {
+            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;
+        } & {
+            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: RpcManager;
+            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: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+            getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+            /** Type guard for checking if something is a JB root model */
+            getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }, {
+        readonly assemblyNameMap: {
+            [key: string]: ({
+                configuration: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                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;
+            } & {
+                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: RpcManager;
+                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: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                    [x: string]: string | undefined;
+                }>;
+                getReverseRefNameMapForAdapter(adapterConf: 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<IAnyType>>;
+            }, {
+                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;
+            } & {
+                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: RpcManager;
+                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: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                    [x: string]: string | undefined;
+                }>;
+                getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                    [x: string]: string | undefined;
+                }>;
+            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
+        };
+    } & {
+        get(asmName: string): ({
+            configuration: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            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;
+        } & {
+            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: RpcManager;
+            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: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+            getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+            getReverseRefNameMapForAdapter(adapterConf: 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<IAnyType>>;
+        }, {
+            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;
+        } & {
+            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: RpcManager;
+            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: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+            getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+            getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+        }, 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 rpcManager: RpcManager;
+    } & {
+        waitForAssembly(assemblyName: string): Promise<({
+            configuration: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            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;
+        } & {
+            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: RpcManager;
+            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: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+            getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+            getReverseRefNameMapForAdapter(adapterConf: 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<IAnyType>>;
+        }, {
+            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;
+        } & {
+            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: RpcManager;
+            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: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+            getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+            getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
+        getRefNameMapForAdapter(adapterConf: unknown, assemblyName: string | undefined, opts: {
+            signal?: AbortSignal | undefined;
+            sessionId: string;
+        }): Promise<{
+            [x: string]: string | undefined;
+        } | undefined>;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, assemblyName: string | undefined, opts: {
+            signal?: AbortSignal | undefined;
+            sessionId: string;
+        }): Promise<{
+            [x: string]: string | undefined;
+        } | undefined>;
+        isValidRefName(refName: string, assemblyName: string): boolean;
+    } & {
+        afterAttach(): void;
+        removeAssembly(asm: {
+            configuration: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            error: unknown; /**
+             * #property
+             * `session` encompasses the currently active state of the app, including
+             * views open, tracks open in those views, etc.
+             */
+            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; /**
+             * #property
+             */
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+        } & {
+            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: RpcManager;
+            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: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+            getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+            getReverseRefNameMapForAdapter(adapterConf: 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<IAnyType>>;
+        }, {
+            error: unknown; /**
+             * #property
+             * `session` encompasses the currently active state of the app, including
+             * views open, tracks open in those views, etc.
+             */
+            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; /**
+             * #property
+             */
+            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+        } & {
+            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: RpcManager;
+            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: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+            getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+            getReverseRefNameMapForAdapter(adapterConf: 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;
+        addAssembly(configuration: any): void;
+        replaceAssembly(idx: number, configuration: any): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+}, {
+    rpcManager: RpcManager;
+    adminMode: boolean;
+    isAssemblyEditing: boolean;
+    error: unknown;
+    textSearchManager: TextSearchManager;
+    pluginManager: PluginManager;
+} & {
+    /**
+     * #action
+     */
+    setError(error: unknown): void;
+    /**
+     * #action
+     */
+    setSession(sessionSnapshot?: SnapshotIn<IAnyType>): void;
+    /**
+     * #action
+     */
+    setDefaultSession(): void;
+    /**
+     * #action
+     */
+    setSessionPath(path: string): void;
+    /**
+     * #action
+     */
+    renameCurrentSession(newName: string): void;
+    /**
+     * #action
+     */
+    setAssemblyEditing(flag: boolean): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export type BaseRootModelType = ReturnType<typeof BaseRootModelFactory>;
+export type BaseRootModel = Instance<BaseRootModelType>;
+/** Type guard for checking if something is a JB root model */
+export declare function isRootModel(thing: unknown): thing is BaseRootModelType;