@jbrowse/product-core 3.2.0 → 3.3.0

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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/Tracks.d.ts CHANGED
@@ -9,7 +9,1677 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
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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;
211
+ 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;
235
+ 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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+ } & {
243
+ getConf(arg: string): any;
244
+ } & {
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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;
254
+ readonly allRefNamesWithLowerCase: string[] | undefined;
255
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
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+ readonly refNameColors: string[];
257
+ } & {
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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;
263
+ } & {
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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: {
277
+ [x: string]: string;
278
+ }, 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>;
284
+ loadPre(): Promise<void>;
285
+ } & {
286
+ getAdapterMapEntry(adapterConf: {
287
+ [x: string]: unknown;
288
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
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+ getRefNameMapForAdapter(adapterConf: {
290
+ [x: string]: unknown;
291
+ }, 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>>>;
300
+ } & {
301
+ get(asmName: string): ({
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+ configuration: any;
303
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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+ error: unknown;
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+ loadingP: Promise<void> | undefined;
306
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
307
+ refNameAliases: {
308
+ [x: string]: string;
309
+ } | undefined;
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
312
+ } | undefined;
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+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
314
+ } & {
315
+ getConf(arg: string): any;
316
+ } & {
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+ readonly initialized: boolean;
318
+ readonly name: string;
319
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
320
+ readonly aliases: string[];
321
+ readonly displayName: string | undefined;
322
+ hasName(name: string): boolean;
323
+ readonly allAliases: string[];
324
+ readonly allRefNames: string[] | undefined;
325
+ readonly lowerCaseRefNames: string[] | undefined;
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+ readonly allRefNamesWithLowerCase: string[] | undefined;
327
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
328
+ readonly refNameColors: string[];
329
+ } & {
330
+ readonly refNames: string[] | undefined;
331
+ } & {
332
+ getCanonicalRefName(refName: string): string | undefined;
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+ getRefNameColor(refName: string): string | undefined;
334
+ isValidRefName(refName: string): boolean;
335
+ } & {
336
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
337
+ regions: import("@jbrowse/core/util").Region[];
338
+ refNameAliases: {
339
+ [x: string]: string;
340
+ };
341
+ lowerCaseRefNameAliases: {
342
+ [x: string]: string;
343
+ };
344
+ cytobands: import("@jbrowse/core/util").Feature[];
345
+ }): void;
346
+ setError(e: unknown): void;
347
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
348
+ setRefNameAliases(aliases: {
349
+ [x: string]: string;
350
+ }, lowerCaseAliases: {
351
+ [x: string]: string;
352
+ }): void;
353
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
354
+ setLoadingP(p?: Promise<void>): void;
355
+ load(): Promise<void>;
356
+ loadPre(): Promise<void>;
357
+ } & {
358
+ getAdapterMapEntry(adapterConf: {
359
+ [x: string]: unknown;
360
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
361
+ getRefNameMapForAdapter(adapterConf: {
362
+ [x: string]: unknown;
363
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
364
+ [x: string]: string;
365
+ }>;
366
+ getReverseRefNameMapForAdapter(adapterConf: {
367
+ [x: string]: unknown;
368
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
369
+ [x: string]: string;
370
+ }>;
371
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
372
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
373
+ }, {
374
+ error: unknown;
375
+ loadingP: Promise<void> | undefined;
376
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
377
+ refNameAliases: {
378
+ [x: string]: string;
379
+ } | undefined;
380
+ lowerCaseRefNameAliases: {
381
+ [x: string]: string;
382
+ } | undefined;
383
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
384
+ } & {
385
+ getConf(arg: string): any;
386
+ } & {
387
+ readonly initialized: boolean;
388
+ readonly name: string;
389
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
390
+ readonly aliases: string[];
391
+ readonly displayName: string | undefined;
392
+ hasName(name: string): boolean;
393
+ readonly allAliases: string[];
394
+ readonly allRefNames: string[] | undefined;
395
+ readonly lowerCaseRefNames: string[] | undefined;
396
+ readonly allRefNamesWithLowerCase: string[] | undefined;
397
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
398
+ readonly refNameColors: string[];
399
+ } & {
400
+ readonly refNames: string[] | undefined;
401
+ } & {
402
+ getCanonicalRefName(refName: string): string | undefined;
403
+ getRefNameColor(refName: string): string | undefined;
404
+ isValidRefName(refName: string): boolean;
405
+ } & {
406
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
407
+ regions: import("@jbrowse/core/util").Region[];
408
+ refNameAliases: {
409
+ [x: string]: string;
410
+ };
411
+ lowerCaseRefNameAliases: {
412
+ [x: string]: string;
413
+ };
414
+ cytobands: import("@jbrowse/core/util").Feature[];
415
+ }): void;
416
+ setError(e: unknown): void;
417
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
418
+ setRefNameAliases(aliases: {
419
+ [x: string]: string;
420
+ }, lowerCaseAliases: {
421
+ [x: string]: string;
422
+ }): void;
423
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
424
+ setLoadingP(p?: Promise<void>): void;
425
+ load(): Promise<void>;
426
+ loadPre(): Promise<void>;
427
+ } & {
428
+ getAdapterMapEntry(adapterConf: {
429
+ [x: string]: unknown;
430
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
431
+ getRefNameMapForAdapter(adapterConf: {
432
+ [x: string]: unknown;
433
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
434
+ [x: string]: string;
435
+ }>;
436
+ getReverseRefNameMapForAdapter(adapterConf: {
437
+ [x: string]: unknown;
438
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
439
+ [x: string]: string;
440
+ }>;
441
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
442
+ readonly assemblyNamesList: any[];
443
+ readonly assemblyList: AnyConfigurationModel[];
444
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
445
+ } & {
446
+ waitForAssembly(assemblyName: string): Promise<({
447
+ configuration: any;
448
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
449
+ error: unknown;
450
+ loadingP: Promise<void> | undefined;
451
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
452
+ refNameAliases: {
453
+ [x: string]: string;
454
+ } | undefined;
455
+ lowerCaseRefNameAliases: {
456
+ [x: string]: string;
457
+ } | undefined;
458
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
459
+ } & {
460
+ getConf(arg: string): any;
461
+ } & {
462
+ readonly initialized: boolean;
463
+ readonly name: string;
464
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
465
+ readonly aliases: string[];
466
+ readonly displayName: string | undefined;
467
+ hasName(name: string): boolean;
468
+ readonly allAliases: string[];
469
+ readonly allRefNames: string[] | undefined;
470
+ readonly lowerCaseRefNames: string[] | undefined;
471
+ readonly allRefNamesWithLowerCase: string[] | undefined;
472
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
473
+ readonly refNameColors: string[];
474
+ } & {
475
+ readonly refNames: string[] | undefined;
476
+ } & {
477
+ getCanonicalRefName(refName: string): string | undefined;
478
+ getRefNameColor(refName: string): string | undefined;
479
+ isValidRefName(refName: string): boolean;
480
+ } & {
481
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
482
+ regions: import("@jbrowse/core/util").Region[];
483
+ refNameAliases: {
484
+ [x: string]: string;
485
+ };
486
+ lowerCaseRefNameAliases: {
487
+ [x: string]: string;
488
+ };
489
+ cytobands: import("@jbrowse/core/util").Feature[];
490
+ }): void;
491
+ setError(e: unknown): void;
492
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
493
+ setRefNameAliases(aliases: {
494
+ [x: string]: string;
495
+ }, lowerCaseAliases: {
496
+ [x: string]: string;
497
+ }): void;
498
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
499
+ setLoadingP(p?: Promise<void>): void;
500
+ load(): Promise<void>;
501
+ loadPre(): Promise<void>;
502
+ } & {
503
+ getAdapterMapEntry(adapterConf: {
504
+ [x: string]: unknown;
505
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
506
+ getRefNameMapForAdapter(adapterConf: {
507
+ [x: string]: unknown;
508
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
509
+ [x: string]: string;
510
+ }>;
511
+ getReverseRefNameMapForAdapter(adapterConf: {
512
+ [x: string]: unknown;
513
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
514
+ [x: string]: string;
515
+ }>;
516
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
517
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
518
+ }, {
519
+ error: unknown;
520
+ loadingP: Promise<void> | undefined;
521
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
522
+ refNameAliases: {
523
+ [x: string]: string;
524
+ } | undefined;
525
+ lowerCaseRefNameAliases: {
526
+ [x: string]: string;
527
+ } | undefined;
528
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
529
+ } & {
530
+ getConf(arg: string): any;
531
+ } & {
532
+ readonly initialized: boolean;
533
+ readonly name: string;
534
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
535
+ readonly aliases: string[];
536
+ readonly displayName: string | undefined;
537
+ hasName(name: string): boolean;
538
+ readonly allAliases: string[];
539
+ readonly allRefNames: string[] | undefined;
540
+ readonly lowerCaseRefNames: string[] | undefined;
541
+ readonly allRefNamesWithLowerCase: string[] | undefined;
542
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
543
+ readonly refNameColors: string[];
544
+ } & {
545
+ readonly refNames: string[] | undefined;
546
+ } & {
547
+ getCanonicalRefName(refName: string): string | undefined;
548
+ getRefNameColor(refName: string): string | undefined;
549
+ isValidRefName(refName: string): boolean;
550
+ } & {
551
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
552
+ regions: import("@jbrowse/core/util").Region[];
553
+ refNameAliases: {
554
+ [x: string]: string;
555
+ };
556
+ lowerCaseRefNameAliases: {
557
+ [x: string]: string;
558
+ };
559
+ cytobands: import("@jbrowse/core/util").Feature[];
560
+ }): void;
561
+ setError(e: unknown): void;
562
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
563
+ setRefNameAliases(aliases: {
564
+ [x: string]: string;
565
+ }, lowerCaseAliases: {
566
+ [x: string]: string;
567
+ }): void;
568
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
569
+ setLoadingP(p?: Promise<void>): void;
570
+ load(): Promise<void>;
571
+ loadPre(): Promise<void>;
572
+ } & {
573
+ getAdapterMapEntry(adapterConf: {
574
+ [x: string]: unknown;
575
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
576
+ getRefNameMapForAdapter(adapterConf: {
577
+ [x: string]: unknown;
578
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
579
+ [x: string]: string;
580
+ }>;
581
+ getReverseRefNameMapForAdapter(adapterConf: {
582
+ [x: string]: unknown;
583
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
584
+ [x: string]: string;
585
+ }>;
586
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
587
+ getRefNameMapForAdapter(adapterConf: {
588
+ [x: string]: unknown;
589
+ }, assemblyName: string | undefined, opts: {
590
+ stopToken?: string;
591
+ sessionId: string;
592
+ }): Promise<{
593
+ [x: string]: string;
594
+ } | undefined>;
595
+ getReverseRefNameMapForAdapter(adapterConf: {
596
+ [x: string]: unknown;
597
+ }, assemblyName: string | undefined, opts: {
598
+ stopToken?: string;
599
+ sessionId: string;
600
+ }): Promise<{
601
+ [x: string]: string;
602
+ } | undefined>;
603
+ isValidRefName(refName: string, assemblyName: string): boolean;
604
+ } & {
605
+ afterAttach(): void;
606
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
607
+ addAssembly(configuration: any): void;
608
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
609
+ assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
610
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
611
+ }, {
612
+ error: unknown;
613
+ loadingP: Promise<void> | undefined;
614
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
615
+ refNameAliases: {
616
+ [x: string]: string;
617
+ } | undefined;
618
+ lowerCaseRefNameAliases: {
619
+ [x: string]: string;
620
+ } | undefined;
621
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
622
+ } & {
623
+ getConf(arg: string): any;
624
+ } & {
625
+ readonly initialized: boolean;
626
+ readonly name: string;
627
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
628
+ readonly aliases: string[];
629
+ readonly displayName: string | undefined;
630
+ hasName(name: string): boolean;
631
+ readonly allAliases: string[];
632
+ readonly allRefNames: string[] | undefined;
633
+ readonly lowerCaseRefNames: string[] | undefined;
634
+ readonly allRefNamesWithLowerCase: string[] | undefined;
635
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
636
+ readonly refNameColors: string[];
637
+ } & {
638
+ readonly refNames: string[] | undefined;
639
+ } & {
640
+ getCanonicalRefName(refName: string): string | undefined;
641
+ getRefNameColor(refName: string): string | undefined;
642
+ isValidRefName(refName: string): boolean;
643
+ } & {
644
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
645
+ regions: import("@jbrowse/core/util").Region[];
646
+ refNameAliases: {
647
+ [x: string]: string;
648
+ };
649
+ lowerCaseRefNameAliases: {
650
+ [x: string]: string;
651
+ };
652
+ cytobands: import("@jbrowse/core/util").Feature[];
653
+ }): void;
654
+ setError(e: unknown): void;
655
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
656
+ setRefNameAliases(aliases: {
657
+ [x: string]: string;
658
+ }, lowerCaseAliases: {
659
+ [x: string]: string;
660
+ }): void;
661
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
662
+ setLoadingP(p?: Promise<void>): void;
663
+ load(): Promise<void>;
664
+ loadPre(): Promise<void>;
665
+ } & {
666
+ getAdapterMapEntry(adapterConf: {
667
+ [x: string]: unknown;
668
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
669
+ getRefNameMapForAdapter(adapterConf: {
670
+ [x: string]: unknown;
671
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
672
+ [x: string]: string;
673
+ }>;
674
+ getReverseRefNameMapForAdapter(adapterConf: {
675
+ [x: string]: unknown;
676
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
677
+ [x: string]: string;
678
+ }>;
679
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
680
+ }, {
681
+ readonly assemblyNameMap: Record<string, {
682
+ configuration: any;
683
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
684
+ error: unknown;
685
+ loadingP: Promise<void> | undefined;
686
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
687
+ refNameAliases: {
688
+ [x: string]: string;
689
+ } | undefined;
690
+ lowerCaseRefNameAliases: {
691
+ [x: string]: string;
692
+ } | undefined;
693
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
694
+ } & {
695
+ getConf(arg: string): any;
696
+ } & {
697
+ readonly initialized: boolean;
698
+ readonly name: string;
699
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
700
+ readonly aliases: string[];
701
+ readonly displayName: string | undefined;
702
+ hasName(name: string): boolean;
703
+ readonly allAliases: string[];
704
+ readonly allRefNames: string[] | undefined;
705
+ readonly lowerCaseRefNames: string[] | undefined;
706
+ readonly allRefNamesWithLowerCase: string[] | undefined;
707
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
708
+ readonly refNameColors: string[];
709
+ } & {
710
+ readonly refNames: string[] | undefined;
711
+ } & {
712
+ getCanonicalRefName(refName: string): string | undefined;
713
+ getRefNameColor(refName: string): string | undefined;
714
+ isValidRefName(refName: string): boolean;
715
+ } & {
716
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
717
+ regions: import("@jbrowse/core/util").Region[];
718
+ refNameAliases: {
719
+ [x: string]: string;
720
+ };
721
+ lowerCaseRefNameAliases: {
722
+ [x: string]: string;
723
+ };
724
+ cytobands: import("@jbrowse/core/util").Feature[];
725
+ }): void;
726
+ setError(e: unknown): void;
727
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
728
+ setRefNameAliases(aliases: {
729
+ [x: string]: string;
730
+ }, lowerCaseAliases: {
731
+ [x: string]: string;
732
+ }): void;
733
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
734
+ setLoadingP(p?: Promise<void>): void;
735
+ load(): Promise<void>;
736
+ loadPre(): Promise<void>;
737
+ } & {
738
+ getAdapterMapEntry(adapterConf: {
739
+ [x: string]: unknown;
740
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
741
+ getRefNameMapForAdapter(adapterConf: {
742
+ [x: string]: unknown;
743
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
744
+ [x: string]: string;
745
+ }>;
746
+ getReverseRefNameMapForAdapter(adapterConf: {
747
+ [x: string]: unknown;
748
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
749
+ [x: string]: string;
750
+ }>;
751
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
752
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
753
+ }, {
754
+ error: unknown;
755
+ loadingP: Promise<void> | undefined;
756
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
757
+ refNameAliases: {
758
+ [x: string]: string;
759
+ } | undefined;
760
+ lowerCaseRefNameAliases: {
761
+ [x: string]: string;
762
+ } | undefined;
763
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
764
+ } & {
765
+ getConf(arg: string): any;
766
+ } & {
767
+ readonly initialized: boolean;
768
+ readonly name: string;
769
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
770
+ readonly aliases: string[];
771
+ readonly displayName: string | undefined;
772
+ hasName(name: string): boolean;
773
+ readonly allAliases: string[];
774
+ readonly allRefNames: string[] | undefined;
775
+ readonly lowerCaseRefNames: string[] | undefined;
776
+ readonly allRefNamesWithLowerCase: string[] | undefined;
777
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
778
+ readonly refNameColors: string[];
779
+ } & {
780
+ readonly refNames: string[] | undefined;
781
+ } & {
782
+ getCanonicalRefName(refName: string): string | undefined;
783
+ getRefNameColor(refName: string): string | undefined;
784
+ isValidRefName(refName: string): boolean;
785
+ } & {
786
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
787
+ regions: import("@jbrowse/core/util").Region[];
788
+ refNameAliases: {
789
+ [x: string]: string;
790
+ };
791
+ lowerCaseRefNameAliases: {
792
+ [x: string]: string;
793
+ };
794
+ cytobands: import("@jbrowse/core/util").Feature[];
795
+ }): void;
796
+ setError(e: unknown): void;
797
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
798
+ setRefNameAliases(aliases: {
799
+ [x: string]: string;
800
+ }, lowerCaseAliases: {
801
+ [x: string]: string;
802
+ }): void;
803
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
804
+ setLoadingP(p?: Promise<void>): void;
805
+ load(): Promise<void>;
806
+ loadPre(): Promise<void>;
807
+ } & {
808
+ getAdapterMapEntry(adapterConf: {
809
+ [x: string]: unknown;
810
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
811
+ getRefNameMapForAdapter(adapterConf: {
812
+ [x: string]: unknown;
813
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
814
+ [x: string]: string;
815
+ }>;
816
+ getReverseRefNameMapForAdapter(adapterConf: {
817
+ [x: string]: unknown;
818
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
819
+ [x: string]: string;
820
+ }>;
821
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
822
+ } & {
823
+ get(asmName: string): ({
824
+ configuration: any;
825
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
826
+ error: unknown;
827
+ loadingP: Promise<void> | undefined;
828
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
829
+ refNameAliases: {
830
+ [x: string]: string;
831
+ } | undefined;
832
+ lowerCaseRefNameAliases: {
833
+ [x: string]: string;
834
+ } | undefined;
835
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
836
+ } & {
837
+ getConf(arg: string): any;
838
+ } & {
839
+ readonly initialized: boolean;
840
+ readonly name: string;
841
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
842
+ readonly aliases: string[];
843
+ readonly displayName: string | undefined;
844
+ hasName(name: string): boolean;
845
+ readonly allAliases: string[];
846
+ readonly allRefNames: string[] | undefined;
847
+ readonly lowerCaseRefNames: string[] | undefined;
848
+ readonly allRefNamesWithLowerCase: string[] | undefined;
849
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
850
+ readonly refNameColors: string[];
851
+ } & {
852
+ readonly refNames: string[] | undefined;
853
+ } & {
854
+ getCanonicalRefName(refName: string): string | undefined;
855
+ getRefNameColor(refName: string): string | undefined;
856
+ isValidRefName(refName: string): boolean;
857
+ } & {
858
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
859
+ regions: import("@jbrowse/core/util").Region[];
860
+ refNameAliases: {
861
+ [x: string]: string;
862
+ };
863
+ lowerCaseRefNameAliases: {
864
+ [x: string]: string;
865
+ };
866
+ cytobands: import("@jbrowse/core/util").Feature[];
867
+ }): void;
868
+ setError(e: unknown): void;
869
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
870
+ setRefNameAliases(aliases: {
871
+ [x: string]: string;
872
+ }, lowerCaseAliases: {
873
+ [x: string]: string;
874
+ }): void;
875
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
876
+ setLoadingP(p?: Promise<void>): void;
877
+ load(): Promise<void>;
878
+ loadPre(): Promise<void>;
879
+ } & {
880
+ getAdapterMapEntry(adapterConf: {
881
+ [x: string]: unknown;
882
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
883
+ getRefNameMapForAdapter(adapterConf: {
884
+ [x: string]: unknown;
885
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
886
+ [x: string]: string;
887
+ }>;
888
+ getReverseRefNameMapForAdapter(adapterConf: {
889
+ [x: string]: unknown;
890
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
891
+ [x: string]: string;
892
+ }>;
893
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
894
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
895
+ }, {
896
+ error: unknown;
897
+ loadingP: Promise<void> | undefined;
898
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
899
+ refNameAliases: {
900
+ [x: string]: string;
901
+ } | undefined;
902
+ lowerCaseRefNameAliases: {
903
+ [x: string]: string;
904
+ } | undefined;
905
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
906
+ } & {
907
+ getConf(arg: string): any;
908
+ } & {
909
+ readonly initialized: boolean;
910
+ readonly name: string;
911
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
912
+ readonly aliases: string[];
913
+ readonly displayName: string | undefined;
914
+ hasName(name: string): boolean;
915
+ readonly allAliases: string[];
916
+ readonly allRefNames: string[] | undefined;
917
+ readonly lowerCaseRefNames: string[] | undefined;
918
+ readonly allRefNamesWithLowerCase: string[] | undefined;
919
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
920
+ readonly refNameColors: string[];
921
+ } & {
922
+ readonly refNames: string[] | undefined;
923
+ } & {
924
+ getCanonicalRefName(refName: string): string | undefined;
925
+ getRefNameColor(refName: string): string | undefined;
926
+ isValidRefName(refName: string): boolean;
927
+ } & {
928
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
929
+ regions: import("@jbrowse/core/util").Region[];
930
+ refNameAliases: {
931
+ [x: string]: string;
932
+ };
933
+ lowerCaseRefNameAliases: {
934
+ [x: string]: string;
935
+ };
936
+ cytobands: import("@jbrowse/core/util").Feature[];
937
+ }): void;
938
+ setError(e: unknown): void;
939
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
940
+ setRefNameAliases(aliases: {
941
+ [x: string]: string;
942
+ }, lowerCaseAliases: {
943
+ [x: string]: string;
944
+ }): void;
945
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
946
+ setLoadingP(p?: Promise<void>): void;
947
+ load(): Promise<void>;
948
+ loadPre(): Promise<void>;
949
+ } & {
950
+ getAdapterMapEntry(adapterConf: {
951
+ [x: string]: unknown;
952
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
953
+ getRefNameMapForAdapter(adapterConf: {
954
+ [x: string]: unknown;
955
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
956
+ [x: string]: string;
957
+ }>;
958
+ getReverseRefNameMapForAdapter(adapterConf: {
959
+ [x: string]: unknown;
960
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
961
+ [x: string]: string;
962
+ }>;
963
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
964
+ readonly assemblyNamesList: any[];
965
+ readonly assemblyList: AnyConfigurationModel[];
966
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
967
+ } & {
968
+ waitForAssembly(assemblyName: string): Promise<({
969
+ configuration: any;
970
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
971
+ error: unknown;
972
+ loadingP: Promise<void> | undefined;
973
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
974
+ refNameAliases: {
975
+ [x: string]: string;
976
+ } | undefined;
977
+ lowerCaseRefNameAliases: {
978
+ [x: string]: string;
979
+ } | undefined;
980
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
981
+ } & {
982
+ getConf(arg: string): any;
983
+ } & {
984
+ readonly initialized: boolean;
985
+ readonly name: string;
986
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
987
+ readonly aliases: string[];
988
+ readonly displayName: string | undefined;
989
+ hasName(name: string): boolean;
990
+ readonly allAliases: string[];
991
+ readonly allRefNames: string[] | undefined;
992
+ readonly lowerCaseRefNames: string[] | undefined;
993
+ readonly allRefNamesWithLowerCase: string[] | undefined;
994
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
995
+ readonly refNameColors: string[];
996
+ } & {
997
+ readonly refNames: string[] | undefined;
998
+ } & {
999
+ getCanonicalRefName(refName: string): string | undefined;
1000
+ getRefNameColor(refName: string): string | undefined;
1001
+ isValidRefName(refName: string): boolean;
1002
+ } & {
1003
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1004
+ regions: import("@jbrowse/core/util").Region[];
1005
+ refNameAliases: {
1006
+ [x: string]: string;
1007
+ };
1008
+ lowerCaseRefNameAliases: {
1009
+ [x: string]: string;
1010
+ };
1011
+ cytobands: import("@jbrowse/core/util").Feature[];
1012
+ }): void;
1013
+ setError(e: unknown): void;
1014
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1015
+ setRefNameAliases(aliases: {
1016
+ [x: string]: string;
1017
+ }, lowerCaseAliases: {
1018
+ [x: string]: string;
1019
+ }): void;
1020
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1021
+ setLoadingP(p?: Promise<void>): void;
1022
+ load(): Promise<void>;
1023
+ loadPre(): Promise<void>;
1024
+ } & {
1025
+ getAdapterMapEntry(adapterConf: {
1026
+ [x: string]: unknown;
1027
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1028
+ getRefNameMapForAdapter(adapterConf: {
1029
+ [x: string]: unknown;
1030
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1031
+ [x: string]: string;
1032
+ }>;
1033
+ getReverseRefNameMapForAdapter(adapterConf: {
1034
+ [x: string]: unknown;
1035
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1036
+ [x: string]: string;
1037
+ }>;
1038
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1039
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1040
+ }, {
1041
+ error: unknown;
1042
+ loadingP: Promise<void> | undefined;
1043
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1044
+ refNameAliases: {
1045
+ [x: string]: string;
1046
+ } | undefined;
1047
+ lowerCaseRefNameAliases: {
1048
+ [x: string]: string;
1049
+ } | undefined;
1050
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1051
+ } & {
1052
+ getConf(arg: string): any;
1053
+ } & {
1054
+ readonly initialized: boolean;
1055
+ readonly name: string;
1056
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1057
+ readonly aliases: string[];
1058
+ readonly displayName: string | undefined;
1059
+ hasName(name: string): boolean;
1060
+ readonly allAliases: string[];
1061
+ readonly allRefNames: string[] | undefined;
1062
+ readonly lowerCaseRefNames: string[] | undefined;
1063
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1064
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1065
+ readonly refNameColors: string[];
1066
+ } & {
1067
+ readonly refNames: string[] | undefined;
1068
+ } & {
1069
+ getCanonicalRefName(refName: string): string | undefined;
1070
+ getRefNameColor(refName: string): string | undefined;
1071
+ isValidRefName(refName: string): boolean;
1072
+ } & {
1073
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1074
+ regions: import("@jbrowse/core/util").Region[];
1075
+ refNameAliases: {
1076
+ [x: string]: string;
1077
+ };
1078
+ lowerCaseRefNameAliases: {
1079
+ [x: string]: string;
1080
+ };
1081
+ cytobands: import("@jbrowse/core/util").Feature[];
1082
+ }): void;
1083
+ setError(e: unknown): void;
1084
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1085
+ setRefNameAliases(aliases: {
1086
+ [x: string]: string;
1087
+ }, lowerCaseAliases: {
1088
+ [x: string]: string;
1089
+ }): void;
1090
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1091
+ setLoadingP(p?: Promise<void>): void;
1092
+ load(): Promise<void>;
1093
+ loadPre(): Promise<void>;
1094
+ } & {
1095
+ getAdapterMapEntry(adapterConf: {
1096
+ [x: string]: unknown;
1097
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1098
+ getRefNameMapForAdapter(adapterConf: {
1099
+ [x: string]: unknown;
1100
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1101
+ [x: string]: string;
1102
+ }>;
1103
+ getReverseRefNameMapForAdapter(adapterConf: {
1104
+ [x: string]: unknown;
1105
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1106
+ [x: string]: string;
1107
+ }>;
1108
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1109
+ getRefNameMapForAdapter(adapterConf: {
1110
+ [x: string]: unknown;
1111
+ }, assemblyName: string | undefined, opts: {
1112
+ stopToken?: string;
1113
+ sessionId: string;
1114
+ }): Promise<{
1115
+ [x: string]: string;
1116
+ } | undefined>;
1117
+ getReverseRefNameMapForAdapter(adapterConf: {
1118
+ [x: string]: unknown;
1119
+ }, assemblyName: string | undefined, opts: {
1120
+ stopToken?: string;
1121
+ sessionId: string;
1122
+ }): Promise<{
1123
+ [x: string]: string;
1124
+ } | undefined>;
1125
+ isValidRefName(refName: string, assemblyName: string): boolean;
1126
+ } & {
1127
+ afterAttach(): void;
1128
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1129
+ addAssembly(configuration: any): void;
1130
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
1131
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1132
+ rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1133
+ adminMode: boolean;
1134
+ error: unknown;
1135
+ textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1136
+ pluginManager: PluginManager;
1137
+ } & {
1138
+ setError(error: unknown): void;
1139
+ setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1140
+ setDefaultSession(): void;
1141
+ setSessionPath(path: string): void;
1142
+ renameCurrentSession(newName: string): void;
1143
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1144
+ jbrowse: import("mobx-state-tree").IAnyType;
1145
+ session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
1146
+ sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1147
+ assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1148
+ assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1149
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1150
+ }, {
1151
+ error: unknown;
1152
+ loadingP: Promise<void> | undefined;
1153
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1154
+ refNameAliases: {
1155
+ [x: string]: string;
1156
+ } | undefined;
1157
+ lowerCaseRefNameAliases: {
1158
+ [x: string]: string;
1159
+ } | undefined;
1160
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1161
+ } & {
1162
+ getConf(arg: string): any;
1163
+ } & {
1164
+ readonly initialized: boolean;
1165
+ readonly name: string;
1166
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1167
+ readonly aliases: string[];
1168
+ readonly displayName: string | undefined;
1169
+ hasName(name: string): boolean;
1170
+ readonly allAliases: string[];
1171
+ readonly allRefNames: string[] | undefined;
1172
+ readonly lowerCaseRefNames: string[] | undefined;
1173
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1174
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1175
+ readonly refNameColors: string[];
1176
+ } & {
1177
+ readonly refNames: string[] | undefined;
1178
+ } & {
1179
+ getCanonicalRefName(refName: string): string | undefined;
1180
+ getRefNameColor(refName: string): string | undefined;
1181
+ isValidRefName(refName: string): boolean;
1182
+ } & {
1183
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1184
+ regions: import("@jbrowse/core/util").Region[];
1185
+ refNameAliases: {
1186
+ [x: string]: string;
1187
+ };
1188
+ lowerCaseRefNameAliases: {
1189
+ [x: string]: string;
1190
+ };
1191
+ cytobands: import("@jbrowse/core/util").Feature[];
1192
+ }): void;
1193
+ setError(e: unknown): void;
1194
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1195
+ setRefNameAliases(aliases: {
1196
+ [x: string]: string;
1197
+ }, lowerCaseAliases: {
1198
+ [x: string]: string;
1199
+ }): void;
1200
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1201
+ setLoadingP(p?: Promise<void>): void;
1202
+ load(): Promise<void>;
1203
+ loadPre(): Promise<void>;
1204
+ } & {
1205
+ getAdapterMapEntry(adapterConf: {
1206
+ [x: string]: unknown;
1207
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1208
+ getRefNameMapForAdapter(adapterConf: {
1209
+ [x: string]: unknown;
1210
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1211
+ [x: string]: string;
1212
+ }>;
1213
+ getReverseRefNameMapForAdapter(adapterConf: {
1214
+ [x: string]: unknown;
1215
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1216
+ [x: string]: string;
1217
+ }>;
1218
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1219
+ }, {
1220
+ readonly assemblyNameMap: Record<string, {
1221
+ configuration: any;
1222
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1223
+ error: unknown;
1224
+ loadingP: Promise<void> | undefined;
1225
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1226
+ refNameAliases: {
1227
+ [x: string]: string;
1228
+ } | undefined;
1229
+ lowerCaseRefNameAliases: {
1230
+ [x: string]: string;
1231
+ } | undefined;
1232
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1233
+ } & {
1234
+ getConf(arg: string): any;
1235
+ } & {
1236
+ readonly initialized: boolean;
1237
+ readonly name: string;
1238
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1239
+ readonly aliases: string[];
1240
+ readonly displayName: string | undefined;
1241
+ hasName(name: string): boolean;
1242
+ readonly allAliases: string[];
1243
+ readonly allRefNames: string[] | undefined;
1244
+ readonly lowerCaseRefNames: string[] | undefined;
1245
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1246
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1247
+ readonly refNameColors: string[];
1248
+ } & {
1249
+ readonly refNames: string[] | undefined;
1250
+ } & {
1251
+ getCanonicalRefName(refName: string): string | undefined;
1252
+ getRefNameColor(refName: string): string | undefined;
1253
+ isValidRefName(refName: string): boolean;
1254
+ } & {
1255
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1256
+ regions: import("@jbrowse/core/util").Region[];
1257
+ refNameAliases: {
1258
+ [x: string]: string;
1259
+ };
1260
+ lowerCaseRefNameAliases: {
1261
+ [x: string]: string;
1262
+ };
1263
+ cytobands: import("@jbrowse/core/util").Feature[];
1264
+ }): void;
1265
+ setError(e: unknown): void;
1266
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1267
+ setRefNameAliases(aliases: {
1268
+ [x: string]: string;
1269
+ }, lowerCaseAliases: {
1270
+ [x: string]: string;
1271
+ }): void;
1272
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1273
+ setLoadingP(p?: Promise<void>): void;
1274
+ load(): Promise<void>;
1275
+ loadPre(): Promise<void>;
1276
+ } & {
1277
+ getAdapterMapEntry(adapterConf: {
1278
+ [x: string]: unknown;
1279
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1280
+ getRefNameMapForAdapter(adapterConf: {
1281
+ [x: string]: unknown;
1282
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1283
+ [x: string]: string;
1284
+ }>;
1285
+ getReverseRefNameMapForAdapter(adapterConf: {
1286
+ [x: string]: unknown;
1287
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1288
+ [x: string]: string;
1289
+ }>;
1290
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1291
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1292
+ }, {
1293
+ error: unknown;
1294
+ loadingP: Promise<void> | undefined;
1295
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1296
+ refNameAliases: {
1297
+ [x: string]: string;
1298
+ } | undefined;
1299
+ lowerCaseRefNameAliases: {
1300
+ [x: string]: string;
1301
+ } | undefined;
1302
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1303
+ } & {
1304
+ getConf(arg: string): any;
1305
+ } & {
1306
+ readonly initialized: boolean;
1307
+ readonly name: string;
1308
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1309
+ readonly aliases: string[];
1310
+ readonly displayName: string | undefined;
1311
+ hasName(name: string): boolean;
1312
+ readonly allAliases: string[];
1313
+ readonly allRefNames: string[] | undefined;
1314
+ readonly lowerCaseRefNames: string[] | undefined;
1315
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1316
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1317
+ readonly refNameColors: string[];
1318
+ } & {
1319
+ readonly refNames: string[] | undefined;
1320
+ } & {
1321
+ getCanonicalRefName(refName: string): string | undefined;
1322
+ getRefNameColor(refName: string): string | undefined;
1323
+ isValidRefName(refName: string): boolean;
1324
+ } & {
1325
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1326
+ regions: import("@jbrowse/core/util").Region[];
1327
+ refNameAliases: {
1328
+ [x: string]: string;
1329
+ };
1330
+ lowerCaseRefNameAliases: {
1331
+ [x: string]: string;
1332
+ };
1333
+ cytobands: import("@jbrowse/core/util").Feature[];
1334
+ }): void;
1335
+ setError(e: unknown): void;
1336
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1337
+ setRefNameAliases(aliases: {
1338
+ [x: string]: string;
1339
+ }, lowerCaseAliases: {
1340
+ [x: string]: string;
1341
+ }): void;
1342
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1343
+ setLoadingP(p?: Promise<void>): void;
1344
+ load(): Promise<void>;
1345
+ loadPre(): Promise<void>;
1346
+ } & {
1347
+ getAdapterMapEntry(adapterConf: {
1348
+ [x: string]: unknown;
1349
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1350
+ getRefNameMapForAdapter(adapterConf: {
1351
+ [x: string]: unknown;
1352
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1353
+ [x: string]: string;
1354
+ }>;
1355
+ getReverseRefNameMapForAdapter(adapterConf: {
1356
+ [x: string]: unknown;
1357
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1358
+ [x: string]: string;
1359
+ }>;
1360
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
1361
+ } & {
1362
+ get(asmName: string): ({
1363
+ configuration: any;
1364
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1365
+ error: unknown;
1366
+ loadingP: Promise<void> | undefined;
1367
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1368
+ refNameAliases: {
1369
+ [x: string]: string;
1370
+ } | undefined;
1371
+ lowerCaseRefNameAliases: {
1372
+ [x: string]: string;
1373
+ } | undefined;
1374
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1375
+ } & {
1376
+ getConf(arg: string): any;
1377
+ } & {
1378
+ readonly initialized: boolean;
1379
+ readonly name: string;
1380
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1381
+ readonly aliases: string[];
1382
+ readonly displayName: string | undefined;
1383
+ hasName(name: string): boolean;
1384
+ readonly allAliases: string[];
1385
+ readonly allRefNames: string[] | undefined;
1386
+ readonly lowerCaseRefNames: string[] | undefined;
1387
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1388
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1389
+ readonly refNameColors: string[];
1390
+ } & {
1391
+ readonly refNames: string[] | undefined;
1392
+ } & {
1393
+ getCanonicalRefName(refName: string): string | undefined;
1394
+ getRefNameColor(refName: string): string | undefined;
1395
+ isValidRefName(refName: string): boolean;
1396
+ } & {
1397
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1398
+ regions: import("@jbrowse/core/util").Region[];
1399
+ refNameAliases: {
1400
+ [x: string]: string;
1401
+ };
1402
+ lowerCaseRefNameAliases: {
1403
+ [x: string]: string;
1404
+ };
1405
+ cytobands: import("@jbrowse/core/util").Feature[];
1406
+ }): void;
1407
+ setError(e: unknown): void;
1408
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1409
+ setRefNameAliases(aliases: {
1410
+ [x: string]: string;
1411
+ }, lowerCaseAliases: {
1412
+ [x: string]: string;
1413
+ }): void;
1414
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1415
+ setLoadingP(p?: Promise<void>): void;
1416
+ load(): Promise<void>;
1417
+ loadPre(): Promise<void>;
1418
+ } & {
1419
+ getAdapterMapEntry(adapterConf: {
1420
+ [x: string]: unknown;
1421
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1422
+ getRefNameMapForAdapter(adapterConf: {
1423
+ [x: string]: unknown;
1424
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1425
+ [x: string]: string;
1426
+ }>;
1427
+ getReverseRefNameMapForAdapter(adapterConf: {
1428
+ [x: string]: unknown;
1429
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1430
+ [x: string]: string;
1431
+ }>;
1432
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1433
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1434
+ }, {
1435
+ error: unknown;
1436
+ loadingP: Promise<void> | undefined;
1437
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1438
+ refNameAliases: {
1439
+ [x: string]: string;
1440
+ } | undefined;
1441
+ lowerCaseRefNameAliases: {
1442
+ [x: string]: string;
1443
+ } | undefined;
1444
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1445
+ } & {
1446
+ getConf(arg: string): any;
1447
+ } & {
1448
+ readonly initialized: boolean;
1449
+ readonly name: string;
1450
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1451
+ readonly aliases: string[];
1452
+ readonly displayName: string | undefined;
1453
+ hasName(name: string): boolean;
1454
+ readonly allAliases: string[];
1455
+ readonly allRefNames: string[] | undefined;
1456
+ readonly lowerCaseRefNames: string[] | undefined;
1457
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1458
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1459
+ readonly refNameColors: string[];
1460
+ } & {
1461
+ readonly refNames: string[] | undefined;
1462
+ } & {
1463
+ getCanonicalRefName(refName: string): string | undefined;
1464
+ getRefNameColor(refName: string): string | undefined;
1465
+ isValidRefName(refName: string): boolean;
1466
+ } & {
1467
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1468
+ regions: import("@jbrowse/core/util").Region[];
1469
+ refNameAliases: {
1470
+ [x: string]: string;
1471
+ };
1472
+ lowerCaseRefNameAliases: {
1473
+ [x: string]: string;
1474
+ };
1475
+ cytobands: import("@jbrowse/core/util").Feature[];
1476
+ }): void;
1477
+ setError(e: unknown): void;
1478
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1479
+ setRefNameAliases(aliases: {
1480
+ [x: string]: string;
1481
+ }, lowerCaseAliases: {
1482
+ [x: string]: string;
1483
+ }): void;
1484
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1485
+ setLoadingP(p?: Promise<void>): void;
1486
+ load(): Promise<void>;
1487
+ loadPre(): Promise<void>;
1488
+ } & {
1489
+ getAdapterMapEntry(adapterConf: {
1490
+ [x: string]: unknown;
1491
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1492
+ getRefNameMapForAdapter(adapterConf: {
1493
+ [x: string]: unknown;
1494
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1495
+ [x: string]: string;
1496
+ }>;
1497
+ getReverseRefNameMapForAdapter(adapterConf: {
1498
+ [x: string]: unknown;
1499
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1500
+ [x: string]: string;
1501
+ }>;
1502
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1503
+ readonly assemblyNamesList: any[];
1504
+ readonly assemblyList: AnyConfigurationModel[];
1505
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1506
+ } & {
1507
+ waitForAssembly(assemblyName: string): Promise<({
1508
+ configuration: any;
1509
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1510
+ error: unknown;
1511
+ loadingP: Promise<void> | undefined;
1512
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1513
+ refNameAliases: {
1514
+ [x: string]: string;
1515
+ } | undefined;
1516
+ lowerCaseRefNameAliases: {
1517
+ [x: string]: string;
1518
+ } | undefined;
1519
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1520
+ } & {
1521
+ getConf(arg: string): any;
1522
+ } & {
1523
+ readonly initialized: boolean;
1524
+ readonly name: string;
1525
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1526
+ readonly aliases: string[];
1527
+ readonly displayName: string | undefined;
1528
+ hasName(name: string): boolean;
1529
+ readonly allAliases: string[];
1530
+ readonly allRefNames: string[] | undefined;
1531
+ readonly lowerCaseRefNames: string[] | undefined;
1532
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1533
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1534
+ readonly refNameColors: string[];
1535
+ } & {
1536
+ readonly refNames: string[] | undefined;
1537
+ } & {
1538
+ getCanonicalRefName(refName: string): string | undefined;
1539
+ getRefNameColor(refName: string): string | undefined;
1540
+ isValidRefName(refName: string): boolean;
1541
+ } & {
1542
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1543
+ regions: import("@jbrowse/core/util").Region[];
1544
+ refNameAliases: {
1545
+ [x: string]: string;
1546
+ };
1547
+ lowerCaseRefNameAliases: {
1548
+ [x: string]: string;
1549
+ };
1550
+ cytobands: import("@jbrowse/core/util").Feature[];
1551
+ }): void;
1552
+ setError(e: unknown): void;
1553
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1554
+ setRefNameAliases(aliases: {
1555
+ [x: string]: string;
1556
+ }, lowerCaseAliases: {
1557
+ [x: string]: string;
1558
+ }): void;
1559
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1560
+ setLoadingP(p?: Promise<void>): void;
1561
+ load(): Promise<void>;
1562
+ loadPre(): Promise<void>;
1563
+ } & {
1564
+ getAdapterMapEntry(adapterConf: {
1565
+ [x: string]: unknown;
1566
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1567
+ getRefNameMapForAdapter(adapterConf: {
1568
+ [x: string]: unknown;
1569
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1570
+ [x: string]: string;
1571
+ }>;
1572
+ getReverseRefNameMapForAdapter(adapterConf: {
1573
+ [x: string]: unknown;
1574
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1575
+ [x: string]: string;
1576
+ }>;
1577
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1578
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1579
+ }, {
1580
+ error: unknown;
1581
+ loadingP: Promise<void> | undefined;
1582
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1583
+ refNameAliases: {
1584
+ [x: string]: string;
1585
+ } | undefined;
1586
+ lowerCaseRefNameAliases: {
1587
+ [x: string]: string;
1588
+ } | undefined;
1589
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1590
+ } & {
1591
+ getConf(arg: string): any;
1592
+ } & {
1593
+ readonly initialized: boolean;
1594
+ readonly name: string;
1595
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1596
+ readonly aliases: string[];
1597
+ readonly displayName: string | undefined;
1598
+ hasName(name: string): boolean;
1599
+ readonly allAliases: string[];
1600
+ readonly allRefNames: string[] | undefined;
1601
+ readonly lowerCaseRefNames: string[] | undefined;
1602
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1603
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1604
+ readonly refNameColors: string[];
1605
+ } & {
1606
+ readonly refNames: string[] | undefined;
1607
+ } & {
1608
+ getCanonicalRefName(refName: string): string | undefined;
1609
+ getRefNameColor(refName: string): string | undefined;
1610
+ isValidRefName(refName: string): boolean;
1611
+ } & {
1612
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1613
+ regions: import("@jbrowse/core/util").Region[];
1614
+ refNameAliases: {
1615
+ [x: string]: string;
1616
+ };
1617
+ lowerCaseRefNameAliases: {
1618
+ [x: string]: string;
1619
+ };
1620
+ cytobands: import("@jbrowse/core/util").Feature[];
1621
+ }): void;
1622
+ setError(e: unknown): void;
1623
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1624
+ setRefNameAliases(aliases: {
1625
+ [x: string]: string;
1626
+ }, lowerCaseAliases: {
1627
+ [x: string]: string;
1628
+ }): void;
1629
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1630
+ setLoadingP(p?: Promise<void>): void;
1631
+ load(): Promise<void>;
1632
+ loadPre(): Promise<void>;
1633
+ } & {
1634
+ getAdapterMapEntry(adapterConf: {
1635
+ [x: string]: unknown;
1636
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1637
+ getRefNameMapForAdapter(adapterConf: {
1638
+ [x: string]: unknown;
1639
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1640
+ [x: string]: string;
1641
+ }>;
1642
+ getReverseRefNameMapForAdapter(adapterConf: {
1643
+ [x: string]: unknown;
1644
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1645
+ [x: string]: string;
1646
+ }>;
1647
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1648
+ getRefNameMapForAdapter(adapterConf: {
1649
+ [x: string]: unknown;
1650
+ }, assemblyName: string | undefined, opts: {
1651
+ stopToken?: string;
1652
+ sessionId: string;
1653
+ }): Promise<{
1654
+ [x: string]: string;
1655
+ } | undefined>;
1656
+ getReverseRefNameMapForAdapter(adapterConf: {
1657
+ [x: string]: unknown;
1658
+ }, assemblyName: string | undefined, opts: {
1659
+ stopToken?: string;
1660
+ sessionId: string;
1661
+ }): Promise<{
1662
+ [x: string]: string;
1663
+ } | undefined>;
1664
+ isValidRefName(refName: string, assemblyName: string): boolean;
1665
+ } & {
1666
+ afterAttach(): void;
1667
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1668
+ addAssembly(configuration: any): void;
1669
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
1670
+ }, {
1671
+ rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1672
+ adminMode: boolean;
1673
+ error: unknown;
1674
+ textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1675
+ pluginManager: PluginManager;
1676
+ } & {
1677
+ setError(error: unknown): void;
1678
+ setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1679
+ setDefaultSession(): void;
1680
+ setSessionPath(path: string): void;
1681
+ renameCurrentSession(newName: string): void;
1682
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
13
1683
  } & {
14
1684
  readonly jbrowse: any;
15
1685
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;