@jbrowse/plugin-linear-genome-view 2.7.2 → 2.9.0

package/dist/index.d.ts

@@ -979,7 +979,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
-                toggleTrack(trackId: string): void;
+                toggleTrack(trackId: string): boolean;
                 setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
                 toggleCenterLine(): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
@@ -1029,6 +1029,122 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 moveTo(start?: import("./LinearGenomeView").BpOffset | undefined, end?: import("./LinearGenomeView").BpOffset | undefined): void;
                 navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
+                navToSearchString({ input, assembly, }: {
+                    input: string;
+                    assembly: {
+                        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;
+                    } & {
+                        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: 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<import("mobx-state-tree").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;
+                    } & {
+                        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: 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>>;
+                }): Promise<void>;
                 navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
                 navTo(query: import("./LinearGenomeView").NavLocation): void;
                 navToMultiple(locations: import("./LinearGenomeView").NavLocation[]): void;
@@ -1170,7 +1286,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
-                toggleTrack(trackId: string): void;
+                toggleTrack(trackId: string): boolean;
                 setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
                 toggleCenterLine(): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
@@ -1220,6 +1336,122 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 moveTo(start?: import("./LinearGenomeView").BpOffset | undefined, end?: import("./LinearGenomeView").BpOffset | undefined): void;
                 navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
+                navToSearchString({ input, assembly, }: {
+                    input: string;
+                    assembly: {
+                        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;
+                    } & {
+                        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: 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<import("mobx-state-tree").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;
+                    } & {
+                        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: 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>>;
+                }): Promise<void>;
                 navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
                 navTo(query: import("./LinearGenomeView").NavLocation): void;
                 navToMultiple(locations: import("./LinearGenomeView").NavLocation[]): void;
@@ -1371,7 +1603,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
-                toggleTrack(trackId: string): void;
+                toggleTrack(trackId: string): boolean;
                 setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
                 toggleCenterLine(): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
@@ -1421,6 +1653,122 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 moveTo(start?: import("./LinearGenomeView").BpOffset | undefined, end?: import("./LinearGenomeView").BpOffset | undefined): void;
                 navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
+                navToSearchString({ input, assembly, }: {
+                    input: string;
+                    assembly: {
+                        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;
+                    } & {
+                        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: 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<import("mobx-state-tree").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;
+                    } & {
+                        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: 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>>;
+                }): Promise<void>;
                 navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
                 navTo(query: import("./LinearGenomeView").NavLocation): void;
                 navToMultiple(locations: import("./LinearGenomeView").NavLocation[]): void;
@@ -1562,7 +1910,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
-                toggleTrack(trackId: string): void;
+                toggleTrack(trackId: string): boolean;
                 setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
                 toggleCenterLine(): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
@@ -1612,6 +1960,122 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 moveTo(start?: import("./LinearGenomeView").BpOffset | undefined, end?: import("./LinearGenomeView").BpOffset | undefined): void;
                 navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
+                navToSearchString({ input, assembly, }: {
+                    input: string;
+                    assembly: {
+                        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;
+                    } & {
+                        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: 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<import("mobx-state-tree").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;
+                    } & {
+                        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: 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>>;
+                }): Promise<void>;
                 navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
                 navTo(query: import("./LinearGenomeView").NavLocation): void;
                 navToMultiple(locations: import("./LinearGenomeView").NavLocation[]): void;
@@ -1763,7 +2227,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
-                toggleTrack(trackId: string): void;
+                toggleTrack(trackId: string): boolean;
                 setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
                 toggleCenterLine(): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
@@ -1813,6 +2277,122 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 moveTo(start?: import("./LinearGenomeView").BpOffset | undefined, end?: import("./LinearGenomeView").BpOffset | undefined): void;
                 navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
+                navToSearchString({ input, assembly, }: {
+                    input: string;
+                    assembly: {
+                        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;
+                    } & {
+                        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: 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<import("mobx-state-tree").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;
+                    } & {
+                        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: 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>>;
+                }): Promise<void>;
                 navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
                 navTo(query: import("./LinearGenomeView").NavLocation): void;
                 navToMultiple(locations: import("./LinearGenomeView").NavLocation[]): void;
@@ -1954,7 +2534,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 moveTrack(movingId: string, targetId: string): void;
                 closeView(): void;
-                toggleTrack(trackId: string): void;
+                toggleTrack(trackId: string): boolean;
                 setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
                 toggleCenterLine(): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
@@ -2004,6 +2584,122 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 moveTo(start?: import("./LinearGenomeView").BpOffset | undefined, end?: import("./LinearGenomeView").BpOffset | undefined): void;
                 navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
+                navToSearchString({ input, assembly, }: {
+                    input: string;
+                    assembly: {
+                        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;
+                    } & {
+                        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: 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<import("mobx-state-tree").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;
+                    } & {
+                        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: 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>>;
+                }): Promise<void>;
                 navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
                 navTo(query: import("./LinearGenomeView").NavLocation): void;
                 navToMultiple(locations: import("./LinearGenomeView").NavLocation[]): void;