@jbrowse/product-core 3.2.0 → 3.3.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (7) hide show
  1. package/dist/Session/MultipleViews.d.ts +1671 -1
  2. package/dist/Session/SessionTracks.d.ts +1671 -1
  3. package/dist/Session/Tracks.d.ts +1671 -1
  4. package/esm/Session/MultipleViews.d.ts +1671 -1
  5. package/esm/Session/SessionTracks.d.ts +1671 -1
  6. package/esm/Session/Tracks.d.ts +1671 -1
  7. package/package.json +5 -5
package/esm/Session/SessionTracks.d.ts CHANGED
@@ -11,7 +11,1677 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
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  selection: unknown;
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  hovered: unknown;
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  } & {
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- readonly root: import("mobx-state-tree").TypeOrStateTreeNodeToStateTreeNode<ROOT_MODEL_TYPE>;
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+ readonly root: {
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+ jbrowse: any;
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+ session: any;
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+ sessionPath: string;
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+ assemblyManager: {
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+ assemblies: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
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+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
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+ }, {
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+ error: unknown;
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+ loadingP: Promise<void> | undefined;
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+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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+ refNameAliases: {
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+ [x: string]: string;
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+ } | undefined;
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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+ } | undefined;
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+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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+ } & {
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+ getConf(arg: string): any;
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+ } & {
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+ readonly initialized: boolean;
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+ readonly name: string;
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+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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+ readonly aliases: string[];
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+ readonly displayName: string | undefined;
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+ hasName(name: string): boolean;
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+ readonly allAliases: string[];
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+ readonly allRefNames: string[] | undefined;
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+ readonly lowerCaseRefNames: string[] | undefined;
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+ readonly allRefNamesWithLowerCase: string[] | undefined;
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+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
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+ readonly refNameColors: string[];
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+ } & {
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+ readonly refNames: string[] | undefined;
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+ } & {
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+ getCanonicalRefName(refName: string): string | undefined;
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+ getRefNameColor(refName: string): string | undefined;
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+ isValidRefName(refName: string): boolean;
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+ } & {
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+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
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+ regions: import("@jbrowse/core/util").Region[];
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+ refNameAliases: {
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+ [x: string]: string;
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+ };
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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+ };
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+ cytobands: import("@jbrowse/core/util").Feature[];
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+ }): void;
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+ setError(e: unknown): void;
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+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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+ setRefNameAliases(aliases: {
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+ [x: string]: string;
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+ }, lowerCaseAliases: {
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+ [x: string]: string;
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+ }): void;
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+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
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+ setLoadingP(p?: Promise<void>): void;
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+ load(): Promise<void>;
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+ loadPre(): Promise<void>;
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+ } & {
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+ getAdapterMapEntry(adapterConf: {
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+ [x: string]: unknown;
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+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
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+ getRefNameMapForAdapter(adapterConf: {
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+ [x: string]: unknown;
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+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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+ [x: string]: string;
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+ }>;
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+ getReverseRefNameMapForAdapter(adapterConf: {
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+ [x: string]: unknown;
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+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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+ [x: string]: string;
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+ }>;
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+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
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+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
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+ }, {
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+ error: unknown;
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+ loadingP: Promise<void> | undefined;
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+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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+ refNameAliases: {
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+ [x: string]: string;
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+ } | undefined;
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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+ } | undefined;
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+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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+ } & {
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+ getConf(arg: string): any;
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+ } & {
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+ readonly initialized: boolean;
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+ readonly name: string;
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+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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+ readonly aliases: string[];
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+ readonly displayName: string | undefined;
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+ hasName(name: string): boolean;
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+ readonly allAliases: string[];
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+ readonly allRefNames: string[] | undefined;
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+ readonly lowerCaseRefNames: string[] | undefined;
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+ readonly allRefNamesWithLowerCase: string[] | undefined;
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+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
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+ readonly refNameColors: string[];
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+ } & {
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+ readonly refNames: string[] | undefined;
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+ } & {
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+ getCanonicalRefName(refName: string): string | undefined;
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+ getRefNameColor(refName: string): string | undefined;
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+ isValidRefName(refName: string): boolean;
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+ } & {
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+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
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+ regions: import("@jbrowse/core/util").Region[];
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+ refNameAliases: {
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+ [x: string]: string;
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+ };
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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+ };
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+ cytobands: import("@jbrowse/core/util").Feature[];
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+ }): void;
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+ setError(e: unknown): void;
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+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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+ setRefNameAliases(aliases: {
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+ [x: string]: string;
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+ }, lowerCaseAliases: {
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+ [x: string]: string;
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+ }): void;
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+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
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+ setLoadingP(p?: Promise<void>): void;
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+ load(): Promise<void>;
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+ loadPre(): Promise<void>;
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+ } & {
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+ getAdapterMapEntry(adapterConf: {
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+ [x: string]: unknown;
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+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
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+ getRefNameMapForAdapter(adapterConf: {
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+ [x: string]: unknown;
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+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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+ [x: string]: string;
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+ }>;
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+ getReverseRefNameMapForAdapter(adapterConf: {
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+ [x: string]: unknown;
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+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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+ [x: string]: string;
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+ }>;
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+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
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+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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+ readonly assemblyNameMap: Record<string, {
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+ configuration: any;
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+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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+ error: unknown;
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+ loadingP: Promise<void> | undefined;
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+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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+ refNameAliases: {
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+ [x: string]: string;
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+ } | undefined;
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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+ } | undefined;
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+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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+ } & {
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+ getConf(arg: string): any;
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+ } & {
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+ readonly initialized: boolean;
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+ readonly name: string;
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+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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+ readonly aliases: string[];
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+ readonly displayName: string | undefined;
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+ hasName(name: string): boolean;
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+ readonly allAliases: string[];
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+ readonly allRefNames: string[] | undefined;
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+ readonly lowerCaseRefNames: string[] | undefined;
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+ readonly allRefNamesWithLowerCase: string[] | undefined;
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+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
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+ readonly refNameColors: string[];
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+ } & {
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+ readonly refNames: string[] | undefined;
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+ } & {
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+ getCanonicalRefName(refName: string): string | undefined;
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+ getRefNameColor(refName: string): string | undefined;
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+ isValidRefName(refName: string): boolean;
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+ } & {
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+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
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+ regions: import("@jbrowse/core/util").Region[];
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+ refNameAliases: {
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+ [x: string]: string;
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+ };
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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+ };
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+ cytobands: import("@jbrowse/core/util").Feature[];
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+ }): void;
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+ setError(e: unknown): void;
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+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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+ setRefNameAliases(aliases: {
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+ [x: string]: string;
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+ }, lowerCaseAliases: {
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+ [x: string]: string;
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+ }): void;
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+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
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+ setLoadingP(p?: Promise<void>): void;
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+ load(): Promise<void>;
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+ loadPre(): Promise<void>;
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+ } & {
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+ getAdapterMapEntry(adapterConf: {
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+ [x: string]: unknown;
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+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
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+ getRefNameMapForAdapter(adapterConf: {
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+ [x: string]: unknown;
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+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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+ [x: string]: string;
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+ }>;
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+ getReverseRefNameMapForAdapter(adapterConf: {
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+ [x: string]: unknown;
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+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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+ [x: string]: string;
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+ }>;
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+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
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+ }, {
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+ error: unknown;
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+ loadingP: Promise<void> | undefined;
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+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
237
+ refNameAliases: {
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+ [x: string]: string;
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+ } | undefined;
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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+ } | undefined;
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+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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+ } & {
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+ getConf(arg: string): any;
246
+ } & {
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+ readonly initialized: boolean;
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+ readonly name: string;
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+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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+ readonly aliases: string[];
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+ readonly displayName: string | undefined;
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+ hasName(name: string): boolean;
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+ readonly allAliases: string[];
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+ readonly allRefNames: string[] | undefined;
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+ readonly lowerCaseRefNames: string[] | undefined;
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+ readonly allRefNamesWithLowerCase: string[] | undefined;
257
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
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+ readonly refNameColors: string[];
259
+ } & {
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+ readonly refNames: string[] | undefined;
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+ } & {
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+ getCanonicalRefName(refName: string): string | undefined;
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+ getRefNameColor(refName: string): string | undefined;
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+ isValidRefName(refName: string): boolean;
265
+ } & {
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+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
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+ regions: import("@jbrowse/core/util").Region[];
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+ refNameAliases: {
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+ [x: string]: string;
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+ };
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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+ };
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+ cytobands: import("@jbrowse/core/util").Feature[];
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+ }): void;
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+ setError(e: unknown): void;
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+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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+ setRefNameAliases(aliases: {
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+ [x: string]: string;
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+ }, lowerCaseAliases: {
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+ [x: string]: string;
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+ }): void;
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+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
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+ setLoadingP(p?: Promise<void>): void;
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+ load(): Promise<void>;
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+ loadPre(): Promise<void>;
287
+ } & {
288
+ getAdapterMapEntry(adapterConf: {
289
+ [x: string]: unknown;
290
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
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+ getRefNameMapForAdapter(adapterConf: {
292
+ [x: string]: unknown;
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+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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+ [x: string]: string;
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+ }>;
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+ getReverseRefNameMapForAdapter(adapterConf: {
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+ [x: string]: unknown;
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+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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+ [x: string]: string;
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+ }>;
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+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
302
+ } & {
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+ get(asmName: string): ({
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+ configuration: any;
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+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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+ error: unknown;
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+ loadingP: Promise<void> | undefined;
308
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
309
+ refNameAliases: {
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+ [x: string]: string;
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+ } | undefined;
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
314
+ } | undefined;
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+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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+ } & {
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+ getConf(arg: string): any;
318
+ } & {
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+ readonly initialized: boolean;
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+ readonly name: string;
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+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
322
+ readonly aliases: string[];
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+ readonly displayName: string | undefined;
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+ hasName(name: string): boolean;
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+ readonly allAliases: string[];
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+ readonly allRefNames: string[] | undefined;
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+ readonly lowerCaseRefNames: string[] | undefined;
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+ readonly allRefNamesWithLowerCase: string[] | undefined;
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+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
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+ readonly refNameColors: string[];
331
+ } & {
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+ readonly refNames: string[] | undefined;
333
+ } & {
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+ getCanonicalRefName(refName: string): string | undefined;
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+ getRefNameColor(refName: string): string | undefined;
336
+ isValidRefName(refName: string): boolean;
337
+ } & {
338
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
339
+ regions: import("@jbrowse/core/util").Region[];
340
+ refNameAliases: {
341
+ [x: string]: string;
342
+ };
343
+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
345
+ };
346
+ cytobands: import("@jbrowse/core/util").Feature[];
347
+ }): void;
348
+ setError(e: unknown): void;
349
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
350
+ setRefNameAliases(aliases: {
351
+ [x: string]: string;
352
+ }, lowerCaseAliases: {
353
+ [x: string]: string;
354
+ }): void;
355
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
356
+ setLoadingP(p?: Promise<void>): void;
357
+ load(): Promise<void>;
358
+ loadPre(): Promise<void>;
359
+ } & {
360
+ getAdapterMapEntry(adapterConf: {
361
+ [x: string]: unknown;
362
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
363
+ getRefNameMapForAdapter(adapterConf: {
364
+ [x: string]: unknown;
365
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
366
+ [x: string]: string;
367
+ }>;
368
+ getReverseRefNameMapForAdapter(adapterConf: {
369
+ [x: string]: unknown;
370
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
371
+ [x: string]: string;
372
+ }>;
373
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
374
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
375
+ }, {
376
+ error: unknown;
377
+ loadingP: Promise<void> | undefined;
378
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
379
+ refNameAliases: {
380
+ [x: string]: string;
381
+ } | undefined;
382
+ lowerCaseRefNameAliases: {
383
+ [x: string]: string;
384
+ } | undefined;
385
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
386
+ } & {
387
+ getConf(arg: string): any;
388
+ } & {
389
+ readonly initialized: boolean;
390
+ readonly name: string;
391
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
392
+ readonly aliases: string[];
393
+ readonly displayName: string | undefined;
394
+ hasName(name: string): boolean;
395
+ readonly allAliases: string[];
396
+ readonly allRefNames: string[] | undefined;
397
+ readonly lowerCaseRefNames: string[] | undefined;
398
+ readonly allRefNamesWithLowerCase: string[] | undefined;
399
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
400
+ readonly refNameColors: string[];
401
+ } & {
402
+ readonly refNames: string[] | undefined;
403
+ } & {
404
+ getCanonicalRefName(refName: string): string | undefined;
405
+ getRefNameColor(refName: string): string | undefined;
406
+ isValidRefName(refName: string): boolean;
407
+ } & {
408
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
409
+ regions: import("@jbrowse/core/util").Region[];
410
+ refNameAliases: {
411
+ [x: string]: string;
412
+ };
413
+ lowerCaseRefNameAliases: {
414
+ [x: string]: string;
415
+ };
416
+ cytobands: import("@jbrowse/core/util").Feature[];
417
+ }): void;
418
+ setError(e: unknown): void;
419
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
420
+ setRefNameAliases(aliases: {
421
+ [x: string]: string;
422
+ }, lowerCaseAliases: {
423
+ [x: string]: string;
424
+ }): void;
425
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
426
+ setLoadingP(p?: Promise<void>): void;
427
+ load(): Promise<void>;
428
+ loadPre(): Promise<void>;
429
+ } & {
430
+ getAdapterMapEntry(adapterConf: {
431
+ [x: string]: unknown;
432
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
433
+ getRefNameMapForAdapter(adapterConf: {
434
+ [x: string]: unknown;
435
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
436
+ [x: string]: string;
437
+ }>;
438
+ getReverseRefNameMapForAdapter(adapterConf: {
439
+ [x: string]: unknown;
440
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
441
+ [x: string]: string;
442
+ }>;
443
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
444
+ readonly assemblyNamesList: any[];
445
+ readonly assemblyList: AnyConfigurationModel[];
446
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
447
+ } & {
448
+ waitForAssembly(assemblyName: string): Promise<({
449
+ configuration: any;
450
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
451
+ error: unknown;
452
+ loadingP: Promise<void> | undefined;
453
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
454
+ refNameAliases: {
455
+ [x: string]: string;
456
+ } | undefined;
457
+ lowerCaseRefNameAliases: {
458
+ [x: string]: string;
459
+ } | undefined;
460
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
461
+ } & {
462
+ getConf(arg: string): any;
463
+ } & {
464
+ readonly initialized: boolean;
465
+ readonly name: string;
466
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
467
+ readonly aliases: string[];
468
+ readonly displayName: string | undefined;
469
+ hasName(name: string): boolean;
470
+ readonly allAliases: string[];
471
+ readonly allRefNames: string[] | undefined;
472
+ readonly lowerCaseRefNames: string[] | undefined;
473
+ readonly allRefNamesWithLowerCase: string[] | undefined;
474
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
475
+ readonly refNameColors: string[];
476
+ } & {
477
+ readonly refNames: string[] | undefined;
478
+ } & {
479
+ getCanonicalRefName(refName: string): string | undefined;
480
+ getRefNameColor(refName: string): string | undefined;
481
+ isValidRefName(refName: string): boolean;
482
+ } & {
483
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
484
+ regions: import("@jbrowse/core/util").Region[];
485
+ refNameAliases: {
486
+ [x: string]: string;
487
+ };
488
+ lowerCaseRefNameAliases: {
489
+ [x: string]: string;
490
+ };
491
+ cytobands: import("@jbrowse/core/util").Feature[];
492
+ }): void;
493
+ setError(e: unknown): void;
494
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
495
+ setRefNameAliases(aliases: {
496
+ [x: string]: string;
497
+ }, lowerCaseAliases: {
498
+ [x: string]: string;
499
+ }): void;
500
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
501
+ setLoadingP(p?: Promise<void>): void;
502
+ load(): Promise<void>;
503
+ loadPre(): Promise<void>;
504
+ } & {
505
+ getAdapterMapEntry(adapterConf: {
506
+ [x: string]: unknown;
507
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
508
+ getRefNameMapForAdapter(adapterConf: {
509
+ [x: string]: unknown;
510
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
511
+ [x: string]: string;
512
+ }>;
513
+ getReverseRefNameMapForAdapter(adapterConf: {
514
+ [x: string]: unknown;
515
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
516
+ [x: string]: string;
517
+ }>;
518
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
519
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
520
+ }, {
521
+ error: unknown;
522
+ loadingP: Promise<void> | undefined;
523
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
524
+ refNameAliases: {
525
+ [x: string]: string;
526
+ } | undefined;
527
+ lowerCaseRefNameAliases: {
528
+ [x: string]: string;
529
+ } | undefined;
530
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
531
+ } & {
532
+ getConf(arg: string): any;
533
+ } & {
534
+ readonly initialized: boolean;
535
+ readonly name: string;
536
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
537
+ readonly aliases: string[];
538
+ readonly displayName: string | undefined;
539
+ hasName(name: string): boolean;
540
+ readonly allAliases: string[];
541
+ readonly allRefNames: string[] | undefined;
542
+ readonly lowerCaseRefNames: string[] | undefined;
543
+ readonly allRefNamesWithLowerCase: string[] | undefined;
544
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
545
+ readonly refNameColors: string[];
546
+ } & {
547
+ readonly refNames: string[] | undefined;
548
+ } & {
549
+ getCanonicalRefName(refName: string): string | undefined;
550
+ getRefNameColor(refName: string): string | undefined;
551
+ isValidRefName(refName: string): boolean;
552
+ } & {
553
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
554
+ regions: import("@jbrowse/core/util").Region[];
555
+ refNameAliases: {
556
+ [x: string]: string;
557
+ };
558
+ lowerCaseRefNameAliases: {
559
+ [x: string]: string;
560
+ };
561
+ cytobands: import("@jbrowse/core/util").Feature[];
562
+ }): void;
563
+ setError(e: unknown): void;
564
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
565
+ setRefNameAliases(aliases: {
566
+ [x: string]: string;
567
+ }, lowerCaseAliases: {
568
+ [x: string]: string;
569
+ }): void;
570
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
571
+ setLoadingP(p?: Promise<void>): void;
572
+ load(): Promise<void>;
573
+ loadPre(): Promise<void>;
574
+ } & {
575
+ getAdapterMapEntry(adapterConf: {
576
+ [x: string]: unknown;
577
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
578
+ getRefNameMapForAdapter(adapterConf: {
579
+ [x: string]: unknown;
580
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
581
+ [x: string]: string;
582
+ }>;
583
+ getReverseRefNameMapForAdapter(adapterConf: {
584
+ [x: string]: unknown;
585
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
586
+ [x: string]: string;
587
+ }>;
588
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
589
+ getRefNameMapForAdapter(adapterConf: {
590
+ [x: string]: unknown;
591
+ }, assemblyName: string | undefined, opts: {
592
+ stopToken?: string;
593
+ sessionId: string;
594
+ }): Promise<{
595
+ [x: string]: string;
596
+ } | undefined>;
597
+ getReverseRefNameMapForAdapter(adapterConf: {
598
+ [x: string]: unknown;
599
+ }, assemblyName: string | undefined, opts: {
600
+ stopToken?: string;
601
+ sessionId: string;
602
+ }): Promise<{
603
+ [x: string]: string;
604
+ } | undefined>;
605
+ isValidRefName(refName: string, assemblyName: string): boolean;
606
+ } & {
607
+ afterAttach(): void;
608
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
609
+ addAssembly(configuration: any): void;
610
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
611
+ assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
612
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
613
+ }, {
614
+ error: unknown;
615
+ loadingP: Promise<void> | undefined;
616
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
617
+ refNameAliases: {
618
+ [x: string]: string;
619
+ } | undefined;
620
+ lowerCaseRefNameAliases: {
621
+ [x: string]: string;
622
+ } | undefined;
623
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
624
+ } & {
625
+ getConf(arg: string): any;
626
+ } & {
627
+ readonly initialized: boolean;
628
+ readonly name: string;
629
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
630
+ readonly aliases: string[];
631
+ readonly displayName: string | undefined;
632
+ hasName(name: string): boolean;
633
+ readonly allAliases: string[];
634
+ readonly allRefNames: string[] | undefined;
635
+ readonly lowerCaseRefNames: string[] | undefined;
636
+ readonly allRefNamesWithLowerCase: string[] | undefined;
637
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
638
+ readonly refNameColors: string[];
639
+ } & {
640
+ readonly refNames: string[] | undefined;
641
+ } & {
642
+ getCanonicalRefName(refName: string): string | undefined;
643
+ getRefNameColor(refName: string): string | undefined;
644
+ isValidRefName(refName: string): boolean;
645
+ } & {
646
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
647
+ regions: import("@jbrowse/core/util").Region[];
648
+ refNameAliases: {
649
+ [x: string]: string;
650
+ };
651
+ lowerCaseRefNameAliases: {
652
+ [x: string]: string;
653
+ };
654
+ cytobands: import("@jbrowse/core/util").Feature[];
655
+ }): void;
656
+ setError(e: unknown): void;
657
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
658
+ setRefNameAliases(aliases: {
659
+ [x: string]: string;
660
+ }, lowerCaseAliases: {
661
+ [x: string]: string;
662
+ }): void;
663
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
664
+ setLoadingP(p?: Promise<void>): void;
665
+ load(): Promise<void>;
666
+ loadPre(): Promise<void>;
667
+ } & {
668
+ getAdapterMapEntry(adapterConf: {
669
+ [x: string]: unknown;
670
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
671
+ getRefNameMapForAdapter(adapterConf: {
672
+ [x: string]: unknown;
673
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
674
+ [x: string]: string;
675
+ }>;
676
+ getReverseRefNameMapForAdapter(adapterConf: {
677
+ [x: string]: unknown;
678
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
679
+ [x: string]: string;
680
+ }>;
681
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
682
+ }, {
683
+ readonly assemblyNameMap: Record<string, {
684
+ configuration: any;
685
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
686
+ error: unknown;
687
+ loadingP: Promise<void> | undefined;
688
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
689
+ refNameAliases: {
690
+ [x: string]: string;
691
+ } | undefined;
692
+ lowerCaseRefNameAliases: {
693
+ [x: string]: string;
694
+ } | undefined;
695
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
696
+ } & {
697
+ getConf(arg: string): any;
698
+ } & {
699
+ readonly initialized: boolean;
700
+ readonly name: string;
701
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
702
+ readonly aliases: string[];
703
+ readonly displayName: string | undefined;
704
+ hasName(name: string): boolean;
705
+ readonly allAliases: string[];
706
+ readonly allRefNames: string[] | undefined;
707
+ readonly lowerCaseRefNames: string[] | undefined;
708
+ readonly allRefNamesWithLowerCase: string[] | undefined;
709
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
710
+ readonly refNameColors: string[];
711
+ } & {
712
+ readonly refNames: string[] | undefined;
713
+ } & {
714
+ getCanonicalRefName(refName: string): string | undefined;
715
+ getRefNameColor(refName: string): string | undefined;
716
+ isValidRefName(refName: string): boolean;
717
+ } & {
718
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
719
+ regions: import("@jbrowse/core/util").Region[];
720
+ refNameAliases: {
721
+ [x: string]: string;
722
+ };
723
+ lowerCaseRefNameAliases: {
724
+ [x: string]: string;
725
+ };
726
+ cytobands: import("@jbrowse/core/util").Feature[];
727
+ }): void;
728
+ setError(e: unknown): void;
729
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
730
+ setRefNameAliases(aliases: {
731
+ [x: string]: string;
732
+ }, lowerCaseAliases: {
733
+ [x: string]: string;
734
+ }): void;
735
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
736
+ setLoadingP(p?: Promise<void>): void;
737
+ load(): Promise<void>;
738
+ loadPre(): Promise<void>;
739
+ } & {
740
+ getAdapterMapEntry(adapterConf: {
741
+ [x: string]: unknown;
742
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
743
+ getRefNameMapForAdapter(adapterConf: {
744
+ [x: string]: unknown;
745
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
746
+ [x: string]: string;
747
+ }>;
748
+ getReverseRefNameMapForAdapter(adapterConf: {
749
+ [x: string]: unknown;
750
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
751
+ [x: string]: string;
752
+ }>;
753
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
754
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
755
+ }, {
756
+ error: unknown;
757
+ loadingP: Promise<void> | undefined;
758
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
759
+ refNameAliases: {
760
+ [x: string]: string;
761
+ } | undefined;
762
+ lowerCaseRefNameAliases: {
763
+ [x: string]: string;
764
+ } | undefined;
765
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
766
+ } & {
767
+ getConf(arg: string): any;
768
+ } & {
769
+ readonly initialized: boolean;
770
+ readonly name: string;
771
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
772
+ readonly aliases: string[];
773
+ readonly displayName: string | undefined;
774
+ hasName(name: string): boolean;
775
+ readonly allAliases: string[];
776
+ readonly allRefNames: string[] | undefined;
777
+ readonly lowerCaseRefNames: string[] | undefined;
778
+ readonly allRefNamesWithLowerCase: string[] | undefined;
779
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
780
+ readonly refNameColors: string[];
781
+ } & {
782
+ readonly refNames: string[] | undefined;
783
+ } & {
784
+ getCanonicalRefName(refName: string): string | undefined;
785
+ getRefNameColor(refName: string): string | undefined;
786
+ isValidRefName(refName: string): boolean;
787
+ } & {
788
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
789
+ regions: import("@jbrowse/core/util").Region[];
790
+ refNameAliases: {
791
+ [x: string]: string;
792
+ };
793
+ lowerCaseRefNameAliases: {
794
+ [x: string]: string;
795
+ };
796
+ cytobands: import("@jbrowse/core/util").Feature[];
797
+ }): void;
798
+ setError(e: unknown): void;
799
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
800
+ setRefNameAliases(aliases: {
801
+ [x: string]: string;
802
+ }, lowerCaseAliases: {
803
+ [x: string]: string;
804
+ }): void;
805
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
806
+ setLoadingP(p?: Promise<void>): void;
807
+ load(): Promise<void>;
808
+ loadPre(): Promise<void>;
809
+ } & {
810
+ getAdapterMapEntry(adapterConf: {
811
+ [x: string]: unknown;
812
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
813
+ getRefNameMapForAdapter(adapterConf: {
814
+ [x: string]: unknown;
815
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
816
+ [x: string]: string;
817
+ }>;
818
+ getReverseRefNameMapForAdapter(adapterConf: {
819
+ [x: string]: unknown;
820
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
821
+ [x: string]: string;
822
+ }>;
823
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
824
+ } & {
825
+ get(asmName: string): ({
826
+ configuration: any;
827
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
828
+ error: unknown;
829
+ loadingP: Promise<void> | undefined;
830
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
831
+ refNameAliases: {
832
+ [x: string]: string;
833
+ } | undefined;
834
+ lowerCaseRefNameAliases: {
835
+ [x: string]: string;
836
+ } | undefined;
837
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
838
+ } & {
839
+ getConf(arg: string): any;
840
+ } & {
841
+ readonly initialized: boolean;
842
+ readonly name: string;
843
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
844
+ readonly aliases: string[];
845
+ readonly displayName: string | undefined;
846
+ hasName(name: string): boolean;
847
+ readonly allAliases: string[];
848
+ readonly allRefNames: string[] | undefined;
849
+ readonly lowerCaseRefNames: string[] | undefined;
850
+ readonly allRefNamesWithLowerCase: string[] | undefined;
851
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
852
+ readonly refNameColors: string[];
853
+ } & {
854
+ readonly refNames: string[] | undefined;
855
+ } & {
856
+ getCanonicalRefName(refName: string): string | undefined;
857
+ getRefNameColor(refName: string): string | undefined;
858
+ isValidRefName(refName: string): boolean;
859
+ } & {
860
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
861
+ regions: import("@jbrowse/core/util").Region[];
862
+ refNameAliases: {
863
+ [x: string]: string;
864
+ };
865
+ lowerCaseRefNameAliases: {
866
+ [x: string]: string;
867
+ };
868
+ cytobands: import("@jbrowse/core/util").Feature[];
869
+ }): void;
870
+ setError(e: unknown): void;
871
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
872
+ setRefNameAliases(aliases: {
873
+ [x: string]: string;
874
+ }, lowerCaseAliases: {
875
+ [x: string]: string;
876
+ }): void;
877
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
878
+ setLoadingP(p?: Promise<void>): void;
879
+ load(): Promise<void>;
880
+ loadPre(): Promise<void>;
881
+ } & {
882
+ getAdapterMapEntry(adapterConf: {
883
+ [x: string]: unknown;
884
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
885
+ getRefNameMapForAdapter(adapterConf: {
886
+ [x: string]: unknown;
887
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
888
+ [x: string]: string;
889
+ }>;
890
+ getReverseRefNameMapForAdapter(adapterConf: {
891
+ [x: string]: unknown;
892
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
893
+ [x: string]: string;
894
+ }>;
895
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
896
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
897
+ }, {
898
+ error: unknown;
899
+ loadingP: Promise<void> | undefined;
900
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
901
+ refNameAliases: {
902
+ [x: string]: string;
903
+ } | undefined;
904
+ lowerCaseRefNameAliases: {
905
+ [x: string]: string;
906
+ } | undefined;
907
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
908
+ } & {
909
+ getConf(arg: string): any;
910
+ } & {
911
+ readonly initialized: boolean;
912
+ readonly name: string;
913
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
914
+ readonly aliases: string[];
915
+ readonly displayName: string | undefined;
916
+ hasName(name: string): boolean;
917
+ readonly allAliases: string[];
918
+ readonly allRefNames: string[] | undefined;
919
+ readonly lowerCaseRefNames: string[] | undefined;
920
+ readonly allRefNamesWithLowerCase: string[] | undefined;
921
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
922
+ readonly refNameColors: string[];
923
+ } & {
924
+ readonly refNames: string[] | undefined;
925
+ } & {
926
+ getCanonicalRefName(refName: string): string | undefined;
927
+ getRefNameColor(refName: string): string | undefined;
928
+ isValidRefName(refName: string): boolean;
929
+ } & {
930
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
931
+ regions: import("@jbrowse/core/util").Region[];
932
+ refNameAliases: {
933
+ [x: string]: string;
934
+ };
935
+ lowerCaseRefNameAliases: {
936
+ [x: string]: string;
937
+ };
938
+ cytobands: import("@jbrowse/core/util").Feature[];
939
+ }): void;
940
+ setError(e: unknown): void;
941
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
942
+ setRefNameAliases(aliases: {
943
+ [x: string]: string;
944
+ }, lowerCaseAliases: {
945
+ [x: string]: string;
946
+ }): void;
947
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
948
+ setLoadingP(p?: Promise<void>): void;
949
+ load(): Promise<void>;
950
+ loadPre(): Promise<void>;
951
+ } & {
952
+ getAdapterMapEntry(adapterConf: {
953
+ [x: string]: unknown;
954
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
955
+ getRefNameMapForAdapter(adapterConf: {
956
+ [x: string]: unknown;
957
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
958
+ [x: string]: string;
959
+ }>;
960
+ getReverseRefNameMapForAdapter(adapterConf: {
961
+ [x: string]: unknown;
962
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
963
+ [x: string]: string;
964
+ }>;
965
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
966
+ readonly assemblyNamesList: any[];
967
+ readonly assemblyList: AnyConfigurationModel[];
968
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
969
+ } & {
970
+ waitForAssembly(assemblyName: string): Promise<({
971
+ configuration: any;
972
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
973
+ error: unknown;
974
+ loadingP: Promise<void> | undefined;
975
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
976
+ refNameAliases: {
977
+ [x: string]: string;
978
+ } | undefined;
979
+ lowerCaseRefNameAliases: {
980
+ [x: string]: string;
981
+ } | undefined;
982
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
983
+ } & {
984
+ getConf(arg: string): any;
985
+ } & {
986
+ readonly initialized: boolean;
987
+ readonly name: string;
988
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
989
+ readonly aliases: string[];
990
+ readonly displayName: string | undefined;
991
+ hasName(name: string): boolean;
992
+ readonly allAliases: string[];
993
+ readonly allRefNames: string[] | undefined;
994
+ readonly lowerCaseRefNames: string[] | undefined;
995
+ readonly allRefNamesWithLowerCase: string[] | undefined;
996
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
997
+ readonly refNameColors: string[];
998
+ } & {
999
+ readonly refNames: string[] | undefined;
1000
+ } & {
1001
+ getCanonicalRefName(refName: string): string | undefined;
1002
+ getRefNameColor(refName: string): string | undefined;
1003
+ isValidRefName(refName: string): boolean;
1004
+ } & {
1005
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1006
+ regions: import("@jbrowse/core/util").Region[];
1007
+ refNameAliases: {
1008
+ [x: string]: string;
1009
+ };
1010
+ lowerCaseRefNameAliases: {
1011
+ [x: string]: string;
1012
+ };
1013
+ cytobands: import("@jbrowse/core/util").Feature[];
1014
+ }): void;
1015
+ setError(e: unknown): void;
1016
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1017
+ setRefNameAliases(aliases: {
1018
+ [x: string]: string;
1019
+ }, lowerCaseAliases: {
1020
+ [x: string]: string;
1021
+ }): void;
1022
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1023
+ setLoadingP(p?: Promise<void>): void;
1024
+ load(): Promise<void>;
1025
+ loadPre(): Promise<void>;
1026
+ } & {
1027
+ getAdapterMapEntry(adapterConf: {
1028
+ [x: string]: unknown;
1029
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1030
+ getRefNameMapForAdapter(adapterConf: {
1031
+ [x: string]: unknown;
1032
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1033
+ [x: string]: string;
1034
+ }>;
1035
+ getReverseRefNameMapForAdapter(adapterConf: {
1036
+ [x: string]: unknown;
1037
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1038
+ [x: string]: string;
1039
+ }>;
1040
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1041
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1042
+ }, {
1043
+ error: unknown;
1044
+ loadingP: Promise<void> | undefined;
1045
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1046
+ refNameAliases: {
1047
+ [x: string]: string;
1048
+ } | undefined;
1049
+ lowerCaseRefNameAliases: {
1050
+ [x: string]: string;
1051
+ } | undefined;
1052
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1053
+ } & {
1054
+ getConf(arg: string): any;
1055
+ } & {
1056
+ readonly initialized: boolean;
1057
+ readonly name: string;
1058
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1059
+ readonly aliases: string[];
1060
+ readonly displayName: string | undefined;
1061
+ hasName(name: string): boolean;
1062
+ readonly allAliases: string[];
1063
+ readonly allRefNames: string[] | undefined;
1064
+ readonly lowerCaseRefNames: string[] | undefined;
1065
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1066
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1067
+ readonly refNameColors: string[];
1068
+ } & {
1069
+ readonly refNames: string[] | undefined;
1070
+ } & {
1071
+ getCanonicalRefName(refName: string): string | undefined;
1072
+ getRefNameColor(refName: string): string | undefined;
1073
+ isValidRefName(refName: string): boolean;
1074
+ } & {
1075
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1076
+ regions: import("@jbrowse/core/util").Region[];
1077
+ refNameAliases: {
1078
+ [x: string]: string;
1079
+ };
1080
+ lowerCaseRefNameAliases: {
1081
+ [x: string]: string;
1082
+ };
1083
+ cytobands: import("@jbrowse/core/util").Feature[];
1084
+ }): void;
1085
+ setError(e: unknown): void;
1086
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1087
+ setRefNameAliases(aliases: {
1088
+ [x: string]: string;
1089
+ }, lowerCaseAliases: {
1090
+ [x: string]: string;
1091
+ }): void;
1092
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1093
+ setLoadingP(p?: Promise<void>): void;
1094
+ load(): Promise<void>;
1095
+ loadPre(): Promise<void>;
1096
+ } & {
1097
+ getAdapterMapEntry(adapterConf: {
1098
+ [x: string]: unknown;
1099
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1100
+ getRefNameMapForAdapter(adapterConf: {
1101
+ [x: string]: unknown;
1102
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1103
+ [x: string]: string;
1104
+ }>;
1105
+ getReverseRefNameMapForAdapter(adapterConf: {
1106
+ [x: string]: unknown;
1107
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1108
+ [x: string]: string;
1109
+ }>;
1110
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1111
+ getRefNameMapForAdapter(adapterConf: {
1112
+ [x: string]: unknown;
1113
+ }, assemblyName: string | undefined, opts: {
1114
+ stopToken?: string;
1115
+ sessionId: string;
1116
+ }): Promise<{
1117
+ [x: string]: string;
1118
+ } | undefined>;
1119
+ getReverseRefNameMapForAdapter(adapterConf: {
1120
+ [x: string]: unknown;
1121
+ }, assemblyName: string | undefined, opts: {
1122
+ stopToken?: string;
1123
+ sessionId: string;
1124
+ }): Promise<{
1125
+ [x: string]: string;
1126
+ } | undefined>;
1127
+ isValidRefName(refName: string, assemblyName: string): boolean;
1128
+ } & {
1129
+ afterAttach(): void;
1130
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1131
+ addAssembly(configuration: any): void;
1132
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
1133
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1134
+ rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1135
+ adminMode: boolean;
1136
+ error: unknown;
1137
+ textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1138
+ pluginManager: PluginManager;
1139
+ } & {
1140
+ setError(error: unknown): void;
1141
+ setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1142
+ setDefaultSession(): void;
1143
+ setSessionPath(path: string): void;
1144
+ renameCurrentSession(newName: string): void;
1145
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1146
+ jbrowse: import("mobx-state-tree").IAnyType;
1147
+ session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
1148
+ sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1149
+ assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1150
+ assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1151
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1152
+ }, {
1153
+ error: unknown;
1154
+ loadingP: Promise<void> | undefined;
1155
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1156
+ refNameAliases: {
1157
+ [x: string]: string;
1158
+ } | undefined;
1159
+ lowerCaseRefNameAliases: {
1160
+ [x: string]: string;
1161
+ } | undefined;
1162
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1163
+ } & {
1164
+ getConf(arg: string): any;
1165
+ } & {
1166
+ readonly initialized: boolean;
1167
+ readonly name: string;
1168
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1169
+ readonly aliases: string[];
1170
+ readonly displayName: string | undefined;
1171
+ hasName(name: string): boolean;
1172
+ readonly allAliases: string[];
1173
+ readonly allRefNames: string[] | undefined;
1174
+ readonly lowerCaseRefNames: string[] | undefined;
1175
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1176
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1177
+ readonly refNameColors: string[];
1178
+ } & {
1179
+ readonly refNames: string[] | undefined;
1180
+ } & {
1181
+ getCanonicalRefName(refName: string): string | undefined;
1182
+ getRefNameColor(refName: string): string | undefined;
1183
+ isValidRefName(refName: string): boolean;
1184
+ } & {
1185
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1186
+ regions: import("@jbrowse/core/util").Region[];
1187
+ refNameAliases: {
1188
+ [x: string]: string;
1189
+ };
1190
+ lowerCaseRefNameAliases: {
1191
+ [x: string]: string;
1192
+ };
1193
+ cytobands: import("@jbrowse/core/util").Feature[];
1194
+ }): void;
1195
+ setError(e: unknown): void;
1196
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1197
+ setRefNameAliases(aliases: {
1198
+ [x: string]: string;
1199
+ }, lowerCaseAliases: {
1200
+ [x: string]: string;
1201
+ }): void;
1202
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1203
+ setLoadingP(p?: Promise<void>): void;
1204
+ load(): Promise<void>;
1205
+ loadPre(): Promise<void>;
1206
+ } & {
1207
+ getAdapterMapEntry(adapterConf: {
1208
+ [x: string]: unknown;
1209
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1210
+ getRefNameMapForAdapter(adapterConf: {
1211
+ [x: string]: unknown;
1212
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1213
+ [x: string]: string;
1214
+ }>;
1215
+ getReverseRefNameMapForAdapter(adapterConf: {
1216
+ [x: string]: unknown;
1217
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1218
+ [x: string]: string;
1219
+ }>;
1220
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1221
+ }, {
1222
+ readonly assemblyNameMap: Record<string, {
1223
+ configuration: any;
1224
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1225
+ error: unknown;
1226
+ loadingP: Promise<void> | undefined;
1227
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1228
+ refNameAliases: {
1229
+ [x: string]: string;
1230
+ } | undefined;
1231
+ lowerCaseRefNameAliases: {
1232
+ [x: string]: string;
1233
+ } | undefined;
1234
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1235
+ } & {
1236
+ getConf(arg: string): any;
1237
+ } & {
1238
+ readonly initialized: boolean;
1239
+ readonly name: string;
1240
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1241
+ readonly aliases: string[];
1242
+ readonly displayName: string | undefined;
1243
+ hasName(name: string): boolean;
1244
+ readonly allAliases: string[];
1245
+ readonly allRefNames: string[] | undefined;
1246
+ readonly lowerCaseRefNames: string[] | undefined;
1247
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1248
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1249
+ readonly refNameColors: string[];
1250
+ } & {
1251
+ readonly refNames: string[] | undefined;
1252
+ } & {
1253
+ getCanonicalRefName(refName: string): string | undefined;
1254
+ getRefNameColor(refName: string): string | undefined;
1255
+ isValidRefName(refName: string): boolean;
1256
+ } & {
1257
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1258
+ regions: import("@jbrowse/core/util").Region[];
1259
+ refNameAliases: {
1260
+ [x: string]: string;
1261
+ };
1262
+ lowerCaseRefNameAliases: {
1263
+ [x: string]: string;
1264
+ };
1265
+ cytobands: import("@jbrowse/core/util").Feature[];
1266
+ }): void;
1267
+ setError(e: unknown): void;
1268
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1269
+ setRefNameAliases(aliases: {
1270
+ [x: string]: string;
1271
+ }, lowerCaseAliases: {
1272
+ [x: string]: string;
1273
+ }): void;
1274
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1275
+ setLoadingP(p?: Promise<void>): void;
1276
+ load(): Promise<void>;
1277
+ loadPre(): Promise<void>;
1278
+ } & {
1279
+ getAdapterMapEntry(adapterConf: {
1280
+ [x: string]: unknown;
1281
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1282
+ getRefNameMapForAdapter(adapterConf: {
1283
+ [x: string]: unknown;
1284
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1285
+ [x: string]: string;
1286
+ }>;
1287
+ getReverseRefNameMapForAdapter(adapterConf: {
1288
+ [x: string]: unknown;
1289
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1290
+ [x: string]: string;
1291
+ }>;
1292
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1293
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1294
+ }, {
1295
+ error: unknown;
1296
+ loadingP: Promise<void> | undefined;
1297
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1298
+ refNameAliases: {
1299
+ [x: string]: string;
1300
+ } | undefined;
1301
+ lowerCaseRefNameAliases: {
1302
+ [x: string]: string;
1303
+ } | undefined;
1304
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1305
+ } & {
1306
+ getConf(arg: string): any;
1307
+ } & {
1308
+ readonly initialized: boolean;
1309
+ readonly name: string;
1310
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1311
+ readonly aliases: string[];
1312
+ readonly displayName: string | undefined;
1313
+ hasName(name: string): boolean;
1314
+ readonly allAliases: string[];
1315
+ readonly allRefNames: string[] | undefined;
1316
+ readonly lowerCaseRefNames: string[] | undefined;
1317
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1318
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1319
+ readonly refNameColors: string[];
1320
+ } & {
1321
+ readonly refNames: string[] | undefined;
1322
+ } & {
1323
+ getCanonicalRefName(refName: string): string | undefined;
1324
+ getRefNameColor(refName: string): string | undefined;
1325
+ isValidRefName(refName: string): boolean;
1326
+ } & {
1327
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1328
+ regions: import("@jbrowse/core/util").Region[];
1329
+ refNameAliases: {
1330
+ [x: string]: string;
1331
+ };
1332
+ lowerCaseRefNameAliases: {
1333
+ [x: string]: string;
1334
+ };
1335
+ cytobands: import("@jbrowse/core/util").Feature[];
1336
+ }): void;
1337
+ setError(e: unknown): void;
1338
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1339
+ setRefNameAliases(aliases: {
1340
+ [x: string]: string;
1341
+ }, lowerCaseAliases: {
1342
+ [x: string]: string;
1343
+ }): void;
1344
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1345
+ setLoadingP(p?: Promise<void>): void;
1346
+ load(): Promise<void>;
1347
+ loadPre(): Promise<void>;
1348
+ } & {
1349
+ getAdapterMapEntry(adapterConf: {
1350
+ [x: string]: unknown;
1351
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1352
+ getRefNameMapForAdapter(adapterConf: {
1353
+ [x: string]: unknown;
1354
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1355
+ [x: string]: string;
1356
+ }>;
1357
+ getReverseRefNameMapForAdapter(adapterConf: {
1358
+ [x: string]: unknown;
1359
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1360
+ [x: string]: string;
1361
+ }>;
1362
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
1363
+ } & {
1364
+ get(asmName: string): ({
1365
+ configuration: any;
1366
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1367
+ error: unknown;
1368
+ loadingP: Promise<void> | undefined;
1369
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1370
+ refNameAliases: {
1371
+ [x: string]: string;
1372
+ } | undefined;
1373
+ lowerCaseRefNameAliases: {
1374
+ [x: string]: string;
1375
+ } | undefined;
1376
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1377
+ } & {
1378
+ getConf(arg: string): any;
1379
+ } & {
1380
+ readonly initialized: boolean;
1381
+ readonly name: string;
1382
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1383
+ readonly aliases: string[];
1384
+ readonly displayName: string | undefined;
1385
+ hasName(name: string): boolean;
1386
+ readonly allAliases: string[];
1387
+ readonly allRefNames: string[] | undefined;
1388
+ readonly lowerCaseRefNames: string[] | undefined;
1389
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1390
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1391
+ readonly refNameColors: string[];
1392
+ } & {
1393
+ readonly refNames: string[] | undefined;
1394
+ } & {
1395
+ getCanonicalRefName(refName: string): string | undefined;
1396
+ getRefNameColor(refName: string): string | undefined;
1397
+ isValidRefName(refName: string): boolean;
1398
+ } & {
1399
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1400
+ regions: import("@jbrowse/core/util").Region[];
1401
+ refNameAliases: {
1402
+ [x: string]: string;
1403
+ };
1404
+ lowerCaseRefNameAliases: {
1405
+ [x: string]: string;
1406
+ };
1407
+ cytobands: import("@jbrowse/core/util").Feature[];
1408
+ }): void;
1409
+ setError(e: unknown): void;
1410
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1411
+ setRefNameAliases(aliases: {
1412
+ [x: string]: string;
1413
+ }, lowerCaseAliases: {
1414
+ [x: string]: string;
1415
+ }): void;
1416
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1417
+ setLoadingP(p?: Promise<void>): void;
1418
+ load(): Promise<void>;
1419
+ loadPre(): Promise<void>;
1420
+ } & {
1421
+ getAdapterMapEntry(adapterConf: {
1422
+ [x: string]: unknown;
1423
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1424
+ getRefNameMapForAdapter(adapterConf: {
1425
+ [x: string]: unknown;
1426
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1427
+ [x: string]: string;
1428
+ }>;
1429
+ getReverseRefNameMapForAdapter(adapterConf: {
1430
+ [x: string]: unknown;
1431
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1432
+ [x: string]: string;
1433
+ }>;
1434
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1435
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1436
+ }, {
1437
+ error: unknown;
1438
+ loadingP: Promise<void> | undefined;
1439
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1440
+ refNameAliases: {
1441
+ [x: string]: string;
1442
+ } | undefined;
1443
+ lowerCaseRefNameAliases: {
1444
+ [x: string]: string;
1445
+ } | undefined;
1446
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1447
+ } & {
1448
+ getConf(arg: string): any;
1449
+ } & {
1450
+ readonly initialized: boolean;
1451
+ readonly name: string;
1452
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1453
+ readonly aliases: string[];
1454
+ readonly displayName: string | undefined;
1455
+ hasName(name: string): boolean;
1456
+ readonly allAliases: string[];
1457
+ readonly allRefNames: string[] | undefined;
1458
+ readonly lowerCaseRefNames: string[] | undefined;
1459
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1460
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1461
+ readonly refNameColors: string[];
1462
+ } & {
1463
+ readonly refNames: string[] | undefined;
1464
+ } & {
1465
+ getCanonicalRefName(refName: string): string | undefined;
1466
+ getRefNameColor(refName: string): string | undefined;
1467
+ isValidRefName(refName: string): boolean;
1468
+ } & {
1469
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1470
+ regions: import("@jbrowse/core/util").Region[];
1471
+ refNameAliases: {
1472
+ [x: string]: string;
1473
+ };
1474
+ lowerCaseRefNameAliases: {
1475
+ [x: string]: string;
1476
+ };
1477
+ cytobands: import("@jbrowse/core/util").Feature[];
1478
+ }): void;
1479
+ setError(e: unknown): void;
1480
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1481
+ setRefNameAliases(aliases: {
1482
+ [x: string]: string;
1483
+ }, lowerCaseAliases: {
1484
+ [x: string]: string;
1485
+ }): void;
1486
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1487
+ setLoadingP(p?: Promise<void>): void;
1488
+ load(): Promise<void>;
1489
+ loadPre(): Promise<void>;
1490
+ } & {
1491
+ getAdapterMapEntry(adapterConf: {
1492
+ [x: string]: unknown;
1493
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1494
+ getRefNameMapForAdapter(adapterConf: {
1495
+ [x: string]: unknown;
1496
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1497
+ [x: string]: string;
1498
+ }>;
1499
+ getReverseRefNameMapForAdapter(adapterConf: {
1500
+ [x: string]: unknown;
1501
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1502
+ [x: string]: string;
1503
+ }>;
1504
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1505
+ readonly assemblyNamesList: any[];
1506
+ readonly assemblyList: AnyConfigurationModel[];
1507
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1508
+ } & {
1509
+ waitForAssembly(assemblyName: string): Promise<({
1510
+ configuration: any;
1511
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1512
+ error: unknown;
1513
+ loadingP: Promise<void> | undefined;
1514
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1515
+ refNameAliases: {
1516
+ [x: string]: string;
1517
+ } | undefined;
1518
+ lowerCaseRefNameAliases: {
1519
+ [x: string]: string;
1520
+ } | undefined;
1521
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1522
+ } & {
1523
+ getConf(arg: string): any;
1524
+ } & {
1525
+ readonly initialized: boolean;
1526
+ readonly name: string;
1527
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1528
+ readonly aliases: string[];
1529
+ readonly displayName: string | undefined;
1530
+ hasName(name: string): boolean;
1531
+ readonly allAliases: string[];
1532
+ readonly allRefNames: string[] | undefined;
1533
+ readonly lowerCaseRefNames: string[] | undefined;
1534
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1535
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1536
+ readonly refNameColors: string[];
1537
+ } & {
1538
+ readonly refNames: string[] | undefined;
1539
+ } & {
1540
+ getCanonicalRefName(refName: string): string | undefined;
1541
+ getRefNameColor(refName: string): string | undefined;
1542
+ isValidRefName(refName: string): boolean;
1543
+ } & {
1544
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1545
+ regions: import("@jbrowse/core/util").Region[];
1546
+ refNameAliases: {
1547
+ [x: string]: string;
1548
+ };
1549
+ lowerCaseRefNameAliases: {
1550
+ [x: string]: string;
1551
+ };
1552
+ cytobands: import("@jbrowse/core/util").Feature[];
1553
+ }): void;
1554
+ setError(e: unknown): void;
1555
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1556
+ setRefNameAliases(aliases: {
1557
+ [x: string]: string;
1558
+ }, lowerCaseAliases: {
1559
+ [x: string]: string;
1560
+ }): void;
1561
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1562
+ setLoadingP(p?: Promise<void>): void;
1563
+ load(): Promise<void>;
1564
+ loadPre(): Promise<void>;
1565
+ } & {
1566
+ getAdapterMapEntry(adapterConf: {
1567
+ [x: string]: unknown;
1568
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1569
+ getRefNameMapForAdapter(adapterConf: {
1570
+ [x: string]: unknown;
1571
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1572
+ [x: string]: string;
1573
+ }>;
1574
+ getReverseRefNameMapForAdapter(adapterConf: {
1575
+ [x: string]: unknown;
1576
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1577
+ [x: string]: string;
1578
+ }>;
1579
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1580
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1581
+ }, {
1582
+ error: unknown;
1583
+ loadingP: Promise<void> | undefined;
1584
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1585
+ refNameAliases: {
1586
+ [x: string]: string;
1587
+ } | undefined;
1588
+ lowerCaseRefNameAliases: {
1589
+ [x: string]: string;
1590
+ } | undefined;
1591
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1592
+ } & {
1593
+ getConf(arg: string): any;
1594
+ } & {
1595
+ readonly initialized: boolean;
1596
+ readonly name: string;
1597
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1598
+ readonly aliases: string[];
1599
+ readonly displayName: string | undefined;
1600
+ hasName(name: string): boolean;
1601
+ readonly allAliases: string[];
1602
+ readonly allRefNames: string[] | undefined;
1603
+ readonly lowerCaseRefNames: string[] | undefined;
1604
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1605
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1606
+ readonly refNameColors: string[];
1607
+ } & {
1608
+ readonly refNames: string[] | undefined;
1609
+ } & {
1610
+ getCanonicalRefName(refName: string): string | undefined;
1611
+ getRefNameColor(refName: string): string | undefined;
1612
+ isValidRefName(refName: string): boolean;
1613
+ } & {
1614
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1615
+ regions: import("@jbrowse/core/util").Region[];
1616
+ refNameAliases: {
1617
+ [x: string]: string;
1618
+ };
1619
+ lowerCaseRefNameAliases: {
1620
+ [x: string]: string;
1621
+ };
1622
+ cytobands: import("@jbrowse/core/util").Feature[];
1623
+ }): void;
1624
+ setError(e: unknown): void;
1625
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1626
+ setRefNameAliases(aliases: {
1627
+ [x: string]: string;
1628
+ }, lowerCaseAliases: {
1629
+ [x: string]: string;
1630
+ }): void;
1631
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1632
+ setLoadingP(p?: Promise<void>): void;
1633
+ load(): Promise<void>;
1634
+ loadPre(): Promise<void>;
1635
+ } & {
1636
+ getAdapterMapEntry(adapterConf: {
1637
+ [x: string]: unknown;
1638
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1639
+ getRefNameMapForAdapter(adapterConf: {
1640
+ [x: string]: unknown;
1641
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1642
+ [x: string]: string;
1643
+ }>;
1644
+ getReverseRefNameMapForAdapter(adapterConf: {
1645
+ [x: string]: unknown;
1646
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1647
+ [x: string]: string;
1648
+ }>;
1649
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1650
+ getRefNameMapForAdapter(adapterConf: {
1651
+ [x: string]: unknown;
1652
+ }, assemblyName: string | undefined, opts: {
1653
+ stopToken?: string;
1654
+ sessionId: string;
1655
+ }): Promise<{
1656
+ [x: string]: string;
1657
+ } | undefined>;
1658
+ getReverseRefNameMapForAdapter(adapterConf: {
1659
+ [x: string]: unknown;
1660
+ }, assemblyName: string | undefined, opts: {
1661
+ stopToken?: string;
1662
+ sessionId: string;
1663
+ }): Promise<{
1664
+ [x: string]: string;
1665
+ } | undefined>;
1666
+ isValidRefName(refName: string, assemblyName: string): boolean;
1667
+ } & {
1668
+ afterAttach(): void;
1669
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1670
+ addAssembly(configuration: any): void;
1671
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
1672
+ }, {
1673
+ rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1674
+ adminMode: boolean;
1675
+ error: unknown;
1676
+ textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1677
+ pluginManager: PluginManager;
1678
+ } & {
1679
+ setError(error: unknown): void;
1680
+ setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1681
+ setDefaultSession(): void;
1682
+ setSessionPath(path: string): void;
1683
+ renameCurrentSession(newName: string): void;
1684
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
15
1685
  } & {
16
1686
  readonly jbrowse: any;
17
1687
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;