@jbrowse/product-core 2.18.0 → 3.0.0

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 (27) hide show
  1. package/dist/Session/BaseSession.d.ts +2 -34
  2. package/dist/Session/Connections.d.ts +2 -22
  3. package/dist/Session/MultipleViews.d.ts +2 -1705
  4. package/dist/Session/SessionTracks.d.ts +4 -1727
  5. package/dist/Session/Tracks.d.ts +3 -1716
  6. package/dist/ui/AboutDialog.d.ts +1 -2
  7. package/dist/ui/AboutDialog.js +2 -3
  8. package/dist/ui/AboutDialogContents.d.ts +1 -2
  9. package/dist/ui/AboutDialogContents.js +14 -45
  10. package/dist/ui/FileInfoPanel.d.ts +1 -2
  11. package/dist/ui/FileInfoPanel.js +3 -25
  12. package/dist/ui/RefNameInfoDialog.d.ts +1 -2
  13. package/dist/ui/RefNameInfoDialog.js +15 -40
  14. package/esm/Session/BaseSession.d.ts +2 -34
  15. package/esm/Session/Connections.d.ts +2 -22
  16. package/esm/Session/MultipleViews.d.ts +2 -1705
  17. package/esm/Session/SessionTracks.d.ts +4 -1727
  18. package/esm/Session/Tracks.d.ts +3 -1716
  19. package/esm/ui/AboutDialog.d.ts +1 -2
  20. package/esm/ui/AboutDialog.js +2 -3
  21. package/esm/ui/AboutDialogContents.d.ts +1 -2
  22. package/esm/ui/AboutDialogContents.js +14 -22
  23. package/esm/ui/FileInfoPanel.d.ts +1 -2
  24. package/esm/ui/FileInfoPanel.js +3 -2
  25. package/esm/ui/RefNameInfoDialog.d.ts +1 -2
  26. package/esm/ui/RefNameInfoDialog.js +15 -17
  27. package/package.json +3 -3
package/dist/Session/MultipleViews.d.ts CHANGED
@@ -19,1677 +19,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  selection: unknown;
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  hovered: unknown;
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  } & {
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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;
127
- } & {
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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;
150
- setLoadingP(p?: Promise<void>): void;
151
- load(): Promise<void>;
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- loadPre(): Promise<void>;
153
- } & {
154
- 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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- } & {
183
- getConf(arg: string): any;
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- } & {
185
- readonly initialized: boolean;
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- readonly name: string;
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- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
188
- readonly aliases: string[];
189
- readonly displayName: string | undefined;
190
- hasName(name: string): boolean;
191
- readonly allAliases: string[];
192
- readonly allRefNames: string[] | undefined;
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- readonly lowerCaseRefNames: string[] | undefined;
194
- readonly allRefNamesWithLowerCase: string[] | undefined;
195
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
196
- readonly refNameColors: string[];
197
- } & {
198
- readonly refNames: string[] | undefined;
199
- } & {
200
- getCanonicalRefName(refName: string): string | undefined;
201
- getRefNameColor(refName: string): string | undefined;
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- isValidRefName(refName: string): boolean;
203
- } & {
204
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
205
- regions: import("@jbrowse/core/util").Region[];
206
- refNameAliases: {
207
- [x: string]: string;
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- };
209
- lowerCaseRefNameAliases: {
210
- [x: string]: string;
211
- };
212
- cytobands: import("@jbrowse/core/util").Feature[];
213
- }): void;
214
- setError(e: unknown): void;
215
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
216
- setRefNameAliases(aliases: {
217
- [x: string]: string;
218
- }, lowerCaseAliases: {
219
- [x: string]: string;
220
- }): void;
221
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
222
- setLoadingP(p?: Promise<void>): void;
223
- load(): Promise<void>;
224
- loadPre(): Promise<void>;
225
- } & {
226
- getAdapterMapEntry(adapterConf: {
227
- [x: string]: unknown;
228
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
229
- getRefNameMapForAdapter(adapterConf: {
230
- [x: string]: unknown;
231
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
232
- [x: string]: string;
233
- }>;
234
- getReverseRefNameMapForAdapter(adapterConf: {
235
- [x: string]: unknown;
236
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
237
- [x: string]: string;
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- }>;
239
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
240
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
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- }, {
242
- error: unknown;
243
- loadingP: Promise<void> | undefined;
244
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
245
- refNameAliases: {
246
- [x: string]: string;
247
- } | undefined;
248
- lowerCaseRefNameAliases: {
249
- [x: string]: string;
250
- } | undefined;
251
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
252
- } & {
253
- getConf(arg: string): any;
254
- } & {
255
- readonly initialized: boolean;
256
- readonly name: string;
257
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
258
- readonly aliases: string[];
259
- readonly displayName: string | undefined;
260
- hasName(name: string): boolean;
261
- readonly allAliases: string[];
262
- readonly allRefNames: string[] | undefined;
263
- readonly lowerCaseRefNames: string[] | undefined;
264
- readonly allRefNamesWithLowerCase: string[] | undefined;
265
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
266
- readonly refNameColors: string[];
267
- } & {
268
- readonly refNames: string[] | undefined;
269
- } & {
270
- getCanonicalRefName(refName: string): string | undefined;
271
- getRefNameColor(refName: string): string | undefined;
272
- isValidRefName(refName: string): boolean;
273
- } & {
274
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
275
- regions: import("@jbrowse/core/util").Region[];
276
- refNameAliases: {
277
- [x: string]: string;
278
- };
279
- lowerCaseRefNameAliases: {
280
- [x: string]: string;
281
- };
282
- cytobands: import("@jbrowse/core/util").Feature[];
283
- }): void;
284
- setError(e: unknown): void;
285
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
286
- setRefNameAliases(aliases: {
287
- [x: string]: string;
288
- }, lowerCaseAliases: {
289
- [x: string]: string;
290
- }): void;
291
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
292
- setLoadingP(p?: Promise<void>): void;
293
- load(): Promise<void>;
294
- loadPre(): Promise<void>;
295
- } & {
296
- getAdapterMapEntry(adapterConf: {
297
- [x: string]: unknown;
298
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
299
- getRefNameMapForAdapter(adapterConf: {
300
- [x: string]: unknown;
301
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
302
- [x: string]: string;
303
- }>;
304
- getReverseRefNameMapForAdapter(adapterConf: {
305
- [x: string]: unknown;
306
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
307
- [x: string]: string;
308
- }>;
309
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
310
- } & {
311
- get(asmName: string): ({
312
- configuration: any;
313
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
314
- error: unknown;
315
- loadingP: Promise<void> | undefined;
316
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
317
- refNameAliases: {
318
- [x: string]: string;
319
- } | undefined;
320
- lowerCaseRefNameAliases: {
321
- [x: string]: string;
322
- } | undefined;
323
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
324
- } & {
325
- getConf(arg: string): any;
326
- } & {
327
- readonly initialized: boolean;
328
- readonly name: string;
329
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
330
- readonly aliases: string[];
331
- readonly displayName: string | undefined;
332
- hasName(name: string): boolean;
333
- readonly allAliases: string[];
334
- readonly allRefNames: string[] | undefined;
335
- readonly lowerCaseRefNames: string[] | undefined;
336
- readonly allRefNamesWithLowerCase: string[] | undefined;
337
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
338
- readonly refNameColors: string[];
339
- } & {
340
- readonly refNames: string[] | undefined;
341
- } & {
342
- getCanonicalRefName(refName: string): string | undefined;
343
- getRefNameColor(refName: string): string | undefined;
344
- isValidRefName(refName: string): boolean;
345
- } & {
346
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
347
- regions: import("@jbrowse/core/util").Region[];
348
- refNameAliases: {
349
- [x: string]: string;
350
- };
351
- lowerCaseRefNameAliases: {
352
- [x: string]: string;
353
- };
354
- cytobands: import("@jbrowse/core/util").Feature[];
355
- }): void;
356
- setError(e: unknown): void;
357
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
358
- setRefNameAliases(aliases: {
359
- [x: string]: string;
360
- }, lowerCaseAliases: {
361
- [x: string]: string;
362
- }): void;
363
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
364
- setLoadingP(p?: Promise<void>): void;
365
- load(): Promise<void>;
366
- loadPre(): Promise<void>;
367
- } & {
368
- getAdapterMapEntry(adapterConf: {
369
- [x: string]: unknown;
370
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
371
- getRefNameMapForAdapter(adapterConf: {
372
- [x: string]: unknown;
373
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
374
- [x: string]: string;
375
- }>;
376
- getReverseRefNameMapForAdapter(adapterConf: {
377
- [x: string]: unknown;
378
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
379
- [x: string]: string;
380
- }>;
381
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
382
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
383
- }, {
384
- error: unknown;
385
- loadingP: Promise<void> | undefined;
386
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
387
- refNameAliases: {
388
- [x: string]: string;
389
- } | undefined;
390
- lowerCaseRefNameAliases: {
391
- [x: string]: string;
392
- } | undefined;
393
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
394
- } & {
395
- getConf(arg: string): any;
396
- } & {
397
- readonly initialized: boolean;
398
- readonly name: string;
399
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
400
- readonly aliases: string[];
401
- readonly displayName: string | undefined;
402
- hasName(name: string): boolean;
403
- readonly allAliases: string[];
404
- readonly allRefNames: string[] | undefined;
405
- readonly lowerCaseRefNames: string[] | undefined;
406
- readonly allRefNamesWithLowerCase: string[] | undefined;
407
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
408
- readonly refNameColors: string[];
409
- } & {
410
- readonly refNames: string[] | undefined;
411
- } & {
412
- getCanonicalRefName(refName: string): string | undefined;
413
- getRefNameColor(refName: string): string | undefined;
414
- isValidRefName(refName: string): boolean;
415
- } & {
416
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
417
- regions: import("@jbrowse/core/util").Region[];
418
- refNameAliases: {
419
- [x: string]: string;
420
- };
421
- lowerCaseRefNameAliases: {
422
- [x: string]: string;
423
- };
424
- cytobands: import("@jbrowse/core/util").Feature[];
425
- }): void;
426
- setError(e: unknown): void;
427
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
428
- setRefNameAliases(aliases: {
429
- [x: string]: string;
430
- }, lowerCaseAliases: {
431
- [x: string]: string;
432
- }): void;
433
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
434
- setLoadingP(p?: Promise<void>): void;
435
- load(): Promise<void>;
436
- loadPre(): Promise<void>;
437
- } & {
438
- getAdapterMapEntry(adapterConf: {
439
- [x: string]: unknown;
440
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
441
- getRefNameMapForAdapter(adapterConf: {
442
- [x: string]: unknown;
443
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
444
- [x: string]: string;
445
- }>;
446
- getReverseRefNameMapForAdapter(adapterConf: {
447
- [x: string]: unknown;
448
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
449
- [x: string]: string;
450
- }>;
451
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
452
- readonly assemblyNamesList: any[];
453
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
454
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
455
- } & {
456
- waitForAssembly(assemblyName: string): Promise<({
457
- configuration: any;
458
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
459
- error: unknown;
460
- loadingP: Promise<void> | undefined;
461
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
462
- refNameAliases: {
463
- [x: string]: string;
464
- } | undefined;
465
- lowerCaseRefNameAliases: {
466
- [x: string]: string;
467
- } | undefined;
468
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
469
- } & {
470
- getConf(arg: string): any;
471
- } & {
472
- readonly initialized: boolean;
473
- readonly name: string;
474
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
475
- readonly aliases: string[];
476
- readonly displayName: string | undefined;
477
- hasName(name: string): boolean;
478
- readonly allAliases: string[];
479
- readonly allRefNames: string[] | undefined;
480
- readonly lowerCaseRefNames: string[] | undefined;
481
- readonly allRefNamesWithLowerCase: string[] | undefined;
482
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
483
- readonly refNameColors: string[];
484
- } & {
485
- readonly refNames: string[] | undefined;
486
- } & {
487
- getCanonicalRefName(refName: string): string | undefined;
488
- getRefNameColor(refName: string): string | undefined;
489
- isValidRefName(refName: string): boolean;
490
- } & {
491
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
492
- regions: import("@jbrowse/core/util").Region[];
493
- refNameAliases: {
494
- [x: string]: string;
495
- };
496
- lowerCaseRefNameAliases: {
497
- [x: string]: string;
498
- };
499
- cytobands: import("@jbrowse/core/util").Feature[];
500
- }): void;
501
- setError(e: unknown): void;
502
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
503
- setRefNameAliases(aliases: {
504
- [x: string]: string;
505
- }, lowerCaseAliases: {
506
- [x: string]: string;
507
- }): void;
508
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
509
- setLoadingP(p?: Promise<void>): void;
510
- load(): Promise<void>;
511
- loadPre(): Promise<void>;
512
- } & {
513
- getAdapterMapEntry(adapterConf: {
514
- [x: string]: unknown;
515
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
516
- getRefNameMapForAdapter(adapterConf: {
517
- [x: string]: unknown;
518
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
519
- [x: string]: string;
520
- }>;
521
- getReverseRefNameMapForAdapter(adapterConf: {
522
- [x: string]: unknown;
523
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
524
- [x: string]: string;
525
- }>;
526
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
527
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
528
- }, {
529
- error: unknown;
530
- loadingP: Promise<void> | undefined;
531
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
532
- refNameAliases: {
533
- [x: string]: string;
534
- } | undefined;
535
- lowerCaseRefNameAliases: {
536
- [x: string]: string;
537
- } | undefined;
538
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
539
- } & {
540
- getConf(arg: string): any;
541
- } & {
542
- readonly initialized: boolean;
543
- readonly name: string;
544
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
545
- readonly aliases: string[];
546
- readonly displayName: string | undefined;
547
- hasName(name: string): boolean;
548
- readonly allAliases: string[];
549
- readonly allRefNames: string[] | undefined;
550
- readonly lowerCaseRefNames: string[] | undefined;
551
- readonly allRefNamesWithLowerCase: string[] | undefined;
552
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
553
- readonly refNameColors: string[];
554
- } & {
555
- readonly refNames: string[] | undefined;
556
- } & {
557
- getCanonicalRefName(refName: string): string | undefined;
558
- getRefNameColor(refName: string): string | undefined;
559
- isValidRefName(refName: string): boolean;
560
- } & {
561
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
562
- regions: import("@jbrowse/core/util").Region[];
563
- refNameAliases: {
564
- [x: string]: string;
565
- };
566
- lowerCaseRefNameAliases: {
567
- [x: string]: string;
568
- };
569
- cytobands: import("@jbrowse/core/util").Feature[];
570
- }): void;
571
- setError(e: unknown): void;
572
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
573
- setRefNameAliases(aliases: {
574
- [x: string]: string;
575
- }, lowerCaseAliases: {
576
- [x: string]: string;
577
- }): void;
578
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
579
- setLoadingP(p?: Promise<void>): void;
580
- load(): Promise<void>;
581
- loadPre(): Promise<void>;
582
- } & {
583
- getAdapterMapEntry(adapterConf: {
584
- [x: string]: unknown;
585
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
586
- getRefNameMapForAdapter(adapterConf: {
587
- [x: string]: unknown;
588
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
589
- [x: string]: string;
590
- }>;
591
- getReverseRefNameMapForAdapter(adapterConf: {
592
- [x: string]: unknown;
593
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
594
- [x: string]: string;
595
- }>;
596
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
597
- getRefNameMapForAdapter(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
- getReverseRefNameMapForAdapter(adapterConf: {
606
- [x: string]: unknown;
607
- }, assemblyName: string | undefined, opts: {
608
- stopToken?: string;
609
- sessionId: string;
610
- }): Promise<{
611
- [x: string]: string;
612
- } | undefined>;
613
- isValidRefName(refName: string, assemblyName: string): boolean;
614
- } & {
615
- afterAttach(): void;
616
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
617
- addAssembly(configuration: any): void;
618
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
619
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
620
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
621
- }, {
622
- error: unknown;
623
- loadingP: Promise<void> | undefined;
624
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
625
- refNameAliases: {
626
- [x: string]: string;
627
- } | undefined;
628
- lowerCaseRefNameAliases: {
629
- [x: string]: string;
630
- } | undefined;
631
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
632
- } & {
633
- getConf(arg: string): any;
634
- } & {
635
- readonly initialized: boolean;
636
- readonly name: string;
637
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
638
- readonly aliases: string[];
639
- readonly displayName: string | undefined;
640
- hasName(name: string): boolean;
641
- readonly allAliases: string[];
642
- readonly allRefNames: string[] | undefined;
643
- readonly lowerCaseRefNames: string[] | undefined;
644
- readonly allRefNamesWithLowerCase: string[] | undefined;
645
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
646
- readonly refNameColors: string[];
647
- } & {
648
- readonly refNames: string[] | undefined;
649
- } & {
650
- getCanonicalRefName(refName: string): string | undefined;
651
- getRefNameColor(refName: string): string | undefined;
652
- isValidRefName(refName: string): boolean;
653
- } & {
654
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
655
- regions: import("@jbrowse/core/util").Region[];
656
- refNameAliases: {
657
- [x: string]: string;
658
- };
659
- lowerCaseRefNameAliases: {
660
- [x: string]: string;
661
- };
662
- cytobands: import("@jbrowse/core/util").Feature[];
663
- }): void;
664
- setError(e: unknown): void;
665
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
666
- setRefNameAliases(aliases: {
667
- [x: string]: string;
668
- }, lowerCaseAliases: {
669
- [x: string]: string;
670
- }): void;
671
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
672
- setLoadingP(p?: Promise<void>): void;
673
- load(): Promise<void>;
674
- loadPre(): Promise<void>;
675
- } & {
676
- getAdapterMapEntry(adapterConf: {
677
- [x: string]: unknown;
678
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
679
- getRefNameMapForAdapter(adapterConf: {
680
- [x: string]: unknown;
681
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
682
- [x: string]: string;
683
- }>;
684
- getReverseRefNameMapForAdapter(adapterConf: {
685
- [x: string]: unknown;
686
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
687
- [x: string]: string;
688
- }>;
689
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
690
- }, {
691
- readonly assemblyNameMap: Record<string, {
692
- configuration: any;
693
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
694
- error: unknown;
695
- loadingP: Promise<void> | undefined;
696
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
697
- refNameAliases: {
698
- [x: string]: string;
699
- } | undefined;
700
- lowerCaseRefNameAliases: {
701
- [x: string]: string;
702
- } | undefined;
703
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
704
- } & {
705
- getConf(arg: string): any;
706
- } & {
707
- readonly initialized: boolean;
708
- readonly name: string;
709
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
710
- readonly aliases: string[];
711
- readonly displayName: string | undefined;
712
- hasName(name: string): boolean;
713
- readonly allAliases: string[];
714
- readonly allRefNames: string[] | undefined;
715
- readonly lowerCaseRefNames: string[] | undefined;
716
- readonly allRefNamesWithLowerCase: string[] | undefined;
717
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
718
- readonly refNameColors: string[];
719
- } & {
720
- readonly refNames: string[] | undefined;
721
- } & {
722
- getCanonicalRefName(refName: string): string | undefined;
723
- getRefNameColor(refName: string): string | undefined;
724
- isValidRefName(refName: string): boolean;
725
- } & {
726
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
727
- regions: import("@jbrowse/core/util").Region[];
728
- refNameAliases: {
729
- [x: string]: string;
730
- };
731
- lowerCaseRefNameAliases: {
732
- [x: string]: string;
733
- };
734
- cytobands: import("@jbrowse/core/util").Feature[];
735
- }): void;
736
- setError(e: unknown): void;
737
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
738
- setRefNameAliases(aliases: {
739
- [x: string]: string;
740
- }, lowerCaseAliases: {
741
- [x: string]: string;
742
- }): void;
743
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
744
- setLoadingP(p?: Promise<void>): void;
745
- load(): Promise<void>;
746
- loadPre(): Promise<void>;
747
- } & {
748
- getAdapterMapEntry(adapterConf: {
749
- [x: string]: unknown;
750
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
751
- getRefNameMapForAdapter(adapterConf: {
752
- [x: string]: unknown;
753
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
754
- [x: string]: string;
755
- }>;
756
- getReverseRefNameMapForAdapter(adapterConf: {
757
- [x: string]: unknown;
758
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
759
- [x: string]: string;
760
- }>;
761
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
762
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
763
- }, {
764
- error: unknown;
765
- loadingP: Promise<void> | undefined;
766
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
767
- refNameAliases: {
768
- [x: string]: string;
769
- } | undefined;
770
- lowerCaseRefNameAliases: {
771
- [x: string]: string;
772
- } | undefined;
773
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
774
- } & {
775
- getConf(arg: string): any;
776
- } & {
777
- readonly initialized: boolean;
778
- readonly name: string;
779
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
780
- readonly aliases: string[];
781
- readonly displayName: string | undefined;
782
- hasName(name: string): boolean;
783
- readonly allAliases: string[];
784
- readonly allRefNames: string[] | undefined;
785
- readonly lowerCaseRefNames: string[] | undefined;
786
- readonly allRefNamesWithLowerCase: string[] | undefined;
787
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
788
- readonly refNameColors: string[];
789
- } & {
790
- readonly refNames: string[] | undefined;
791
- } & {
792
- getCanonicalRefName(refName: string): string | undefined;
793
- getRefNameColor(refName: string): string | undefined;
794
- isValidRefName(refName: string): boolean;
795
- } & {
796
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
797
- regions: import("@jbrowse/core/util").Region[];
798
- refNameAliases: {
799
- [x: string]: string;
800
- };
801
- lowerCaseRefNameAliases: {
802
- [x: string]: string;
803
- };
804
- cytobands: import("@jbrowse/core/util").Feature[];
805
- }): void;
806
- setError(e: unknown): void;
807
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
808
- setRefNameAliases(aliases: {
809
- [x: string]: string;
810
- }, lowerCaseAliases: {
811
- [x: string]: string;
812
- }): void;
813
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
814
- setLoadingP(p?: Promise<void>): void;
815
- load(): Promise<void>;
816
- loadPre(): Promise<void>;
817
- } & {
818
- getAdapterMapEntry(adapterConf: {
819
- [x: string]: unknown;
820
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
821
- getRefNameMapForAdapter(adapterConf: {
822
- [x: string]: unknown;
823
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
824
- [x: string]: string;
825
- }>;
826
- getReverseRefNameMapForAdapter(adapterConf: {
827
- [x: string]: unknown;
828
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
829
- [x: string]: string;
830
- }>;
831
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
832
- } & {
833
- get(asmName: string): ({
834
- configuration: any;
835
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
836
- error: unknown;
837
- loadingP: Promise<void> | undefined;
838
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
839
- refNameAliases: {
840
- [x: string]: string;
841
- } | undefined;
842
- lowerCaseRefNameAliases: {
843
- [x: string]: string;
844
- } | undefined;
845
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
846
- } & {
847
- getConf(arg: string): any;
848
- } & {
849
- readonly initialized: boolean;
850
- readonly name: string;
851
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
852
- readonly aliases: string[];
853
- readonly displayName: string | undefined;
854
- hasName(name: string): boolean;
855
- readonly allAliases: string[];
856
- readonly allRefNames: string[] | undefined;
857
- readonly lowerCaseRefNames: string[] | undefined;
858
- readonly allRefNamesWithLowerCase: string[] | undefined;
859
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
860
- readonly refNameColors: string[];
861
- } & {
862
- readonly refNames: string[] | undefined;
863
- } & {
864
- getCanonicalRefName(refName: string): string | undefined;
865
- getRefNameColor(refName: string): string | undefined;
866
- isValidRefName(refName: string): boolean;
867
- } & {
868
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
869
- regions: import("@jbrowse/core/util").Region[];
870
- refNameAliases: {
871
- [x: string]: string;
872
- };
873
- lowerCaseRefNameAliases: {
874
- [x: string]: string;
875
- };
876
- cytobands: import("@jbrowse/core/util").Feature[];
877
- }): void;
878
- setError(e: unknown): void;
879
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
880
- setRefNameAliases(aliases: {
881
- [x: string]: string;
882
- }, lowerCaseAliases: {
883
- [x: string]: string;
884
- }): void;
885
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
886
- setLoadingP(p?: Promise<void>): void;
887
- load(): Promise<void>;
888
- loadPre(): Promise<void>;
889
- } & {
890
- getAdapterMapEntry(adapterConf: {
891
- [x: string]: unknown;
892
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
893
- getRefNameMapForAdapter(adapterConf: {
894
- [x: string]: unknown;
895
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
896
- [x: string]: string;
897
- }>;
898
- getReverseRefNameMapForAdapter(adapterConf: {
899
- [x: string]: unknown;
900
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
901
- [x: string]: string;
902
- }>;
903
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
904
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
905
- }, {
906
- error: unknown;
907
- loadingP: Promise<void> | undefined;
908
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
909
- refNameAliases: {
910
- [x: string]: string;
911
- } | undefined;
912
- lowerCaseRefNameAliases: {
913
- [x: string]: string;
914
- } | undefined;
915
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
916
- } & {
917
- getConf(arg: string): any;
918
- } & {
919
- readonly initialized: boolean;
920
- readonly name: string;
921
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
922
- readonly aliases: string[];
923
- readonly displayName: string | undefined;
924
- hasName(name: string): boolean;
925
- readonly allAliases: string[];
926
- readonly allRefNames: string[] | undefined;
927
- readonly lowerCaseRefNames: string[] | undefined;
928
- readonly allRefNamesWithLowerCase: string[] | undefined;
929
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
930
- readonly refNameColors: string[];
931
- } & {
932
- readonly refNames: string[] | undefined;
933
- } & {
934
- getCanonicalRefName(refName: string): string | undefined;
935
- getRefNameColor(refName: string): string | undefined;
936
- isValidRefName(refName: string): boolean;
937
- } & {
938
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
939
- regions: import("@jbrowse/core/util").Region[];
940
- refNameAliases: {
941
- [x: string]: string;
942
- };
943
- lowerCaseRefNameAliases: {
944
- [x: string]: string;
945
- };
946
- cytobands: import("@jbrowse/core/util").Feature[];
947
- }): void;
948
- setError(e: unknown): void;
949
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
950
- setRefNameAliases(aliases: {
951
- [x: string]: string;
952
- }, lowerCaseAliases: {
953
- [x: string]: string;
954
- }): void;
955
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
956
- setLoadingP(p?: Promise<void>): void;
957
- load(): Promise<void>;
958
- loadPre(): Promise<void>;
959
- } & {
960
- getAdapterMapEntry(adapterConf: {
961
- [x: string]: unknown;
962
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
963
- getRefNameMapForAdapter(adapterConf: {
964
- [x: string]: unknown;
965
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
966
- [x: string]: string;
967
- }>;
968
- getReverseRefNameMapForAdapter(adapterConf: {
969
- [x: string]: unknown;
970
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
971
- [x: string]: string;
972
- }>;
973
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
974
- readonly assemblyNamesList: any[];
975
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
976
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
977
- } & {
978
- waitForAssembly(assemblyName: string): Promise<({
979
- configuration: any;
980
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
981
- error: unknown;
982
- loadingP: Promise<void> | undefined;
983
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
984
- refNameAliases: {
985
- [x: string]: string;
986
- } | undefined;
987
- lowerCaseRefNameAliases: {
988
- [x: string]: string;
989
- } | undefined;
990
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
991
- } & {
992
- getConf(arg: string): any;
993
- } & {
994
- readonly initialized: boolean;
995
- readonly name: string;
996
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
997
- readonly aliases: string[];
998
- readonly displayName: string | undefined;
999
- hasName(name: string): boolean;
1000
- readonly allAliases: string[];
1001
- readonly allRefNames: string[] | undefined;
1002
- readonly lowerCaseRefNames: string[] | undefined;
1003
- readonly allRefNamesWithLowerCase: string[] | undefined;
1004
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1005
- readonly refNameColors: string[];
1006
- } & {
1007
- readonly refNames: string[] | undefined;
1008
- } & {
1009
- getCanonicalRefName(refName: string): string | undefined;
1010
- getRefNameColor(refName: string): string | undefined;
1011
- isValidRefName(refName: string): boolean;
1012
- } & {
1013
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1014
- regions: import("@jbrowse/core/util").Region[];
1015
- refNameAliases: {
1016
- [x: string]: string;
1017
- };
1018
- lowerCaseRefNameAliases: {
1019
- [x: string]: string;
1020
- };
1021
- cytobands: import("@jbrowse/core/util").Feature[];
1022
- }): void;
1023
- setError(e: unknown): void;
1024
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1025
- setRefNameAliases(aliases: {
1026
- [x: string]: string;
1027
- }, lowerCaseAliases: {
1028
- [x: string]: string;
1029
- }): void;
1030
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1031
- setLoadingP(p?: Promise<void>): void;
1032
- load(): Promise<void>;
1033
- loadPre(): Promise<void>;
1034
- } & {
1035
- getAdapterMapEntry(adapterConf: {
1036
- [x: string]: unknown;
1037
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1038
- getRefNameMapForAdapter(adapterConf: {
1039
- [x: string]: unknown;
1040
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1041
- [x: string]: string;
1042
- }>;
1043
- getReverseRefNameMapForAdapter(adapterConf: {
1044
- [x: string]: unknown;
1045
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1046
- [x: string]: string;
1047
- }>;
1048
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1049
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1050
- }, {
1051
- error: unknown;
1052
- loadingP: Promise<void> | undefined;
1053
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1054
- refNameAliases: {
1055
- [x: string]: string;
1056
- } | undefined;
1057
- lowerCaseRefNameAliases: {
1058
- [x: string]: string;
1059
- } | undefined;
1060
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1061
- } & {
1062
- getConf(arg: string): any;
1063
- } & {
1064
- readonly initialized: boolean;
1065
- readonly name: string;
1066
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1067
- readonly aliases: string[];
1068
- readonly displayName: string | undefined;
1069
- hasName(name: string): boolean;
1070
- readonly allAliases: string[];
1071
- readonly allRefNames: string[] | undefined;
1072
- readonly lowerCaseRefNames: string[] | undefined;
1073
- readonly allRefNamesWithLowerCase: string[] | undefined;
1074
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1075
- readonly refNameColors: string[];
1076
- } & {
1077
- readonly refNames: string[] | undefined;
1078
- } & {
1079
- getCanonicalRefName(refName: string): string | undefined;
1080
- getRefNameColor(refName: string): string | undefined;
1081
- isValidRefName(refName: string): boolean;
1082
- } & {
1083
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1084
- regions: import("@jbrowse/core/util").Region[];
1085
- refNameAliases: {
1086
- [x: string]: string;
1087
- };
1088
- lowerCaseRefNameAliases: {
1089
- [x: string]: string;
1090
- };
1091
- cytobands: import("@jbrowse/core/util").Feature[];
1092
- }): void;
1093
- setError(e: unknown): void;
1094
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1095
- setRefNameAliases(aliases: {
1096
- [x: string]: string;
1097
- }, lowerCaseAliases: {
1098
- [x: string]: string;
1099
- }): void;
1100
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1101
- setLoadingP(p?: Promise<void>): void;
1102
- load(): Promise<void>;
1103
- loadPre(): Promise<void>;
1104
- } & {
1105
- getAdapterMapEntry(adapterConf: {
1106
- [x: string]: unknown;
1107
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1108
- getRefNameMapForAdapter(adapterConf: {
1109
- [x: string]: unknown;
1110
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1111
- [x: string]: string;
1112
- }>;
1113
- getReverseRefNameMapForAdapter(adapterConf: {
1114
- [x: string]: unknown;
1115
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1116
- [x: string]: string;
1117
- }>;
1118
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1119
- getRefNameMapForAdapter(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
- getReverseRefNameMapForAdapter(adapterConf: {
1128
- [x: string]: unknown;
1129
- }, assemblyName: string | undefined, opts: {
1130
- stopToken?: string;
1131
- sessionId: string;
1132
- }): Promise<{
1133
- [x: string]: string;
1134
- } | undefined>;
1135
- isValidRefName(refName: string, assemblyName: string): boolean;
1136
- } & {
1137
- afterAttach(): void;
1138
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1139
- addAssembly(configuration: any): void;
1140
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
1141
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1142
- rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1143
- adminMode: boolean;
1144
- error: unknown;
1145
- textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1146
- pluginManager: PluginManager;
1147
- } & {
1148
- setError(error: unknown): void;
1149
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1150
- setDefaultSession(): void;
1151
- setSessionPath(path: string): void;
1152
- renameCurrentSession(newName: string): void;
1153
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1154
- jbrowse: import("mobx-state-tree").IAnyType;
1155
- session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
1156
- sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1157
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1158
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1159
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1160
- }, {
1161
- error: unknown;
1162
- loadingP: Promise<void> | undefined;
1163
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1164
- refNameAliases: {
1165
- [x: string]: string;
1166
- } | undefined;
1167
- lowerCaseRefNameAliases: {
1168
- [x: string]: string;
1169
- } | undefined;
1170
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1171
- } & {
1172
- getConf(arg: string): any;
1173
- } & {
1174
- readonly initialized: boolean;
1175
- readonly name: string;
1176
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1177
- readonly aliases: string[];
1178
- readonly displayName: string | undefined;
1179
- hasName(name: string): boolean;
1180
- readonly allAliases: string[];
1181
- readonly allRefNames: string[] | undefined;
1182
- readonly lowerCaseRefNames: string[] | undefined;
1183
- readonly allRefNamesWithLowerCase: string[] | undefined;
1184
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1185
- readonly refNameColors: string[];
1186
- } & {
1187
- readonly refNames: string[] | undefined;
1188
- } & {
1189
- getCanonicalRefName(refName: string): string | undefined;
1190
- getRefNameColor(refName: string): string | undefined;
1191
- isValidRefName(refName: string): boolean;
1192
- } & {
1193
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1194
- regions: import("@jbrowse/core/util").Region[];
1195
- refNameAliases: {
1196
- [x: string]: string;
1197
- };
1198
- lowerCaseRefNameAliases: {
1199
- [x: string]: string;
1200
- };
1201
- cytobands: import("@jbrowse/core/util").Feature[];
1202
- }): void;
1203
- setError(e: unknown): void;
1204
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1205
- setRefNameAliases(aliases: {
1206
- [x: string]: string;
1207
- }, lowerCaseAliases: {
1208
- [x: string]: string;
1209
- }): void;
1210
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1211
- setLoadingP(p?: Promise<void>): void;
1212
- load(): Promise<void>;
1213
- loadPre(): Promise<void>;
1214
- } & {
1215
- getAdapterMapEntry(adapterConf: {
1216
- [x: string]: unknown;
1217
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1218
- getRefNameMapForAdapter(adapterConf: {
1219
- [x: string]: unknown;
1220
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1221
- [x: string]: string;
1222
- }>;
1223
- getReverseRefNameMapForAdapter(adapterConf: {
1224
- [x: string]: unknown;
1225
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1226
- [x: string]: string;
1227
- }>;
1228
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1229
- }, {
1230
- readonly assemblyNameMap: Record<string, {
1231
- configuration: any;
1232
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1233
- error: unknown;
1234
- loadingP: Promise<void> | undefined;
1235
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1236
- refNameAliases: {
1237
- [x: string]: string;
1238
- } | undefined;
1239
- lowerCaseRefNameAliases: {
1240
- [x: string]: string;
1241
- } | undefined;
1242
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1243
- } & {
1244
- getConf(arg: string): any;
1245
- } & {
1246
- readonly initialized: boolean;
1247
- readonly name: string;
1248
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1249
- readonly aliases: string[];
1250
- readonly displayName: string | undefined;
1251
- hasName(name: string): boolean;
1252
- readonly allAliases: string[];
1253
- readonly allRefNames: string[] | undefined;
1254
- readonly lowerCaseRefNames: string[] | undefined;
1255
- readonly allRefNamesWithLowerCase: string[] | undefined;
1256
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1257
- readonly refNameColors: string[];
1258
- } & {
1259
- readonly refNames: string[] | undefined;
1260
- } & {
1261
- getCanonicalRefName(refName: string): string | undefined;
1262
- getRefNameColor(refName: string): string | undefined;
1263
- isValidRefName(refName: string): boolean;
1264
- } & {
1265
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1266
- regions: import("@jbrowse/core/util").Region[];
1267
- refNameAliases: {
1268
- [x: string]: string;
1269
- };
1270
- lowerCaseRefNameAliases: {
1271
- [x: string]: string;
1272
- };
1273
- cytobands: import("@jbrowse/core/util").Feature[];
1274
- }): void;
1275
- setError(e: unknown): void;
1276
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1277
- setRefNameAliases(aliases: {
1278
- [x: string]: string;
1279
- }, lowerCaseAliases: {
1280
- [x: string]: string;
1281
- }): void;
1282
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1283
- setLoadingP(p?: Promise<void>): void;
1284
- load(): Promise<void>;
1285
- loadPre(): Promise<void>;
1286
- } & {
1287
- getAdapterMapEntry(adapterConf: {
1288
- [x: string]: unknown;
1289
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1290
- getRefNameMapForAdapter(adapterConf: {
1291
- [x: string]: unknown;
1292
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1293
- [x: string]: string;
1294
- }>;
1295
- getReverseRefNameMapForAdapter(adapterConf: {
1296
- [x: string]: unknown;
1297
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1298
- [x: string]: string;
1299
- }>;
1300
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1301
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1302
- }, {
1303
- error: unknown;
1304
- loadingP: Promise<void> | undefined;
1305
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1306
- refNameAliases: {
1307
- [x: string]: string;
1308
- } | undefined;
1309
- lowerCaseRefNameAliases: {
1310
- [x: string]: string;
1311
- } | undefined;
1312
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1313
- } & {
1314
- getConf(arg: string): any;
1315
- } & {
1316
- readonly initialized: boolean;
1317
- readonly name: string;
1318
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1319
- readonly aliases: string[];
1320
- readonly displayName: string | undefined;
1321
- hasName(name: string): boolean;
1322
- readonly allAliases: string[];
1323
- readonly allRefNames: string[] | undefined;
1324
- readonly lowerCaseRefNames: string[] | undefined;
1325
- readonly allRefNamesWithLowerCase: string[] | undefined;
1326
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1327
- readonly refNameColors: string[];
1328
- } & {
1329
- readonly refNames: string[] | undefined;
1330
- } & {
1331
- getCanonicalRefName(refName: string): string | undefined;
1332
- getRefNameColor(refName: string): string | undefined;
1333
- isValidRefName(refName: string): boolean;
1334
- } & {
1335
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1336
- regions: import("@jbrowse/core/util").Region[];
1337
- refNameAliases: {
1338
- [x: string]: string;
1339
- };
1340
- lowerCaseRefNameAliases: {
1341
- [x: string]: string;
1342
- };
1343
- cytobands: import("@jbrowse/core/util").Feature[];
1344
- }): void;
1345
- setError(e: unknown): void;
1346
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1347
- setRefNameAliases(aliases: {
1348
- [x: string]: string;
1349
- }, lowerCaseAliases: {
1350
- [x: string]: string;
1351
- }): void;
1352
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1353
- setLoadingP(p?: Promise<void>): void;
1354
- load(): Promise<void>;
1355
- loadPre(): Promise<void>;
1356
- } & {
1357
- getAdapterMapEntry(adapterConf: {
1358
- [x: string]: unknown;
1359
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1360
- getRefNameMapForAdapter(adapterConf: {
1361
- [x: string]: unknown;
1362
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1363
- [x: string]: string;
1364
- }>;
1365
- getReverseRefNameMapForAdapter(adapterConf: {
1366
- [x: string]: unknown;
1367
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1368
- [x: string]: string;
1369
- }>;
1370
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
1371
- } & {
1372
- get(asmName: string): ({
1373
- configuration: any;
1374
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1375
- error: unknown;
1376
- loadingP: Promise<void> | undefined;
1377
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1378
- refNameAliases: {
1379
- [x: string]: string;
1380
- } | undefined;
1381
- lowerCaseRefNameAliases: {
1382
- [x: string]: string;
1383
- } | undefined;
1384
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1385
- } & {
1386
- getConf(arg: string): any;
1387
- } & {
1388
- readonly initialized: boolean;
1389
- readonly name: string;
1390
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1391
- readonly aliases: string[];
1392
- readonly displayName: string | undefined;
1393
- hasName(name: string): boolean;
1394
- readonly allAliases: string[];
1395
- readonly allRefNames: string[] | undefined;
1396
- readonly lowerCaseRefNames: string[] | undefined;
1397
- readonly allRefNamesWithLowerCase: string[] | undefined;
1398
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1399
- readonly refNameColors: string[];
1400
- } & {
1401
- readonly refNames: string[] | undefined;
1402
- } & {
1403
- getCanonicalRefName(refName: string): string | undefined;
1404
- getRefNameColor(refName: string): string | undefined;
1405
- isValidRefName(refName: string): boolean;
1406
- } & {
1407
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1408
- regions: import("@jbrowse/core/util").Region[];
1409
- refNameAliases: {
1410
- [x: string]: string;
1411
- };
1412
- lowerCaseRefNameAliases: {
1413
- [x: string]: string;
1414
- };
1415
- cytobands: import("@jbrowse/core/util").Feature[];
1416
- }): void;
1417
- setError(e: unknown): void;
1418
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1419
- setRefNameAliases(aliases: {
1420
- [x: string]: string;
1421
- }, lowerCaseAliases: {
1422
- [x: string]: string;
1423
- }): void;
1424
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1425
- setLoadingP(p?: Promise<void>): void;
1426
- load(): Promise<void>;
1427
- loadPre(): Promise<void>;
1428
- } & {
1429
- getAdapterMapEntry(adapterConf: {
1430
- [x: string]: unknown;
1431
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1432
- getRefNameMapForAdapter(adapterConf: {
1433
- [x: string]: unknown;
1434
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1435
- [x: string]: string;
1436
- }>;
1437
- getReverseRefNameMapForAdapter(adapterConf: {
1438
- [x: string]: unknown;
1439
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1440
- [x: string]: string;
1441
- }>;
1442
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1443
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1444
- }, {
1445
- error: unknown;
1446
- loadingP: Promise<void> | undefined;
1447
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1448
- refNameAliases: {
1449
- [x: string]: string;
1450
- } | undefined;
1451
- lowerCaseRefNameAliases: {
1452
- [x: string]: string;
1453
- } | undefined;
1454
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1455
- } & {
1456
- getConf(arg: string): any;
1457
- } & {
1458
- readonly initialized: boolean;
1459
- readonly name: string;
1460
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1461
- readonly aliases: string[];
1462
- readonly displayName: string | undefined;
1463
- hasName(name: string): boolean;
1464
- readonly allAliases: string[];
1465
- readonly allRefNames: string[] | undefined;
1466
- readonly lowerCaseRefNames: string[] | undefined;
1467
- readonly allRefNamesWithLowerCase: string[] | undefined;
1468
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1469
- readonly refNameColors: string[];
1470
- } & {
1471
- readonly refNames: string[] | undefined;
1472
- } & {
1473
- getCanonicalRefName(refName: string): string | undefined;
1474
- getRefNameColor(refName: string): string | undefined;
1475
- isValidRefName(refName: string): boolean;
1476
- } & {
1477
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1478
- regions: import("@jbrowse/core/util").Region[];
1479
- refNameAliases: {
1480
- [x: string]: string;
1481
- };
1482
- lowerCaseRefNameAliases: {
1483
- [x: string]: string;
1484
- };
1485
- cytobands: import("@jbrowse/core/util").Feature[];
1486
- }): void;
1487
- setError(e: unknown): void;
1488
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1489
- setRefNameAliases(aliases: {
1490
- [x: string]: string;
1491
- }, lowerCaseAliases: {
1492
- [x: string]: string;
1493
- }): void;
1494
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1495
- setLoadingP(p?: Promise<void>): void;
1496
- load(): Promise<void>;
1497
- loadPre(): Promise<void>;
1498
- } & {
1499
- getAdapterMapEntry(adapterConf: {
1500
- [x: string]: unknown;
1501
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1502
- getRefNameMapForAdapter(adapterConf: {
1503
- [x: string]: unknown;
1504
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1505
- [x: string]: string;
1506
- }>;
1507
- getReverseRefNameMapForAdapter(adapterConf: {
1508
- [x: string]: unknown;
1509
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1510
- [x: string]: string;
1511
- }>;
1512
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1513
- readonly assemblyNamesList: any[];
1514
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1515
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1516
- } & {
1517
- waitForAssembly(assemblyName: string): Promise<({
1518
- configuration: any;
1519
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1520
- error: unknown;
1521
- loadingP: Promise<void> | undefined;
1522
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1523
- refNameAliases: {
1524
- [x: string]: string;
1525
- } | undefined;
1526
- lowerCaseRefNameAliases: {
1527
- [x: string]: string;
1528
- } | undefined;
1529
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1530
- } & {
1531
- getConf(arg: string): any;
1532
- } & {
1533
- readonly initialized: boolean;
1534
- readonly name: string;
1535
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1536
- readonly aliases: string[];
1537
- readonly displayName: string | undefined;
1538
- hasName(name: string): boolean;
1539
- readonly allAliases: string[];
1540
- readonly allRefNames: string[] | undefined;
1541
- readonly lowerCaseRefNames: string[] | undefined;
1542
- readonly allRefNamesWithLowerCase: string[] | undefined;
1543
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1544
- readonly refNameColors: string[];
1545
- } & {
1546
- readonly refNames: string[] | undefined;
1547
- } & {
1548
- getCanonicalRefName(refName: string): string | undefined;
1549
- getRefNameColor(refName: string): string | undefined;
1550
- isValidRefName(refName: string): boolean;
1551
- } & {
1552
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1553
- regions: import("@jbrowse/core/util").Region[];
1554
- refNameAliases: {
1555
- [x: string]: string;
1556
- };
1557
- lowerCaseRefNameAliases: {
1558
- [x: string]: string;
1559
- };
1560
- cytobands: import("@jbrowse/core/util").Feature[];
1561
- }): void;
1562
- setError(e: unknown): void;
1563
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1564
- setRefNameAliases(aliases: {
1565
- [x: string]: string;
1566
- }, lowerCaseAliases: {
1567
- [x: string]: string;
1568
- }): void;
1569
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1570
- setLoadingP(p?: Promise<void>): void;
1571
- load(): Promise<void>;
1572
- loadPre(): Promise<void>;
1573
- } & {
1574
- getAdapterMapEntry(adapterConf: {
1575
- [x: string]: unknown;
1576
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1577
- getRefNameMapForAdapter(adapterConf: {
1578
- [x: string]: unknown;
1579
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1580
- [x: string]: string;
1581
- }>;
1582
- getReverseRefNameMapForAdapter(adapterConf: {
1583
- [x: string]: unknown;
1584
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1585
- [x: string]: string;
1586
- }>;
1587
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1588
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1589
- }, {
1590
- error: unknown;
1591
- loadingP: Promise<void> | undefined;
1592
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1593
- refNameAliases: {
1594
- [x: string]: string;
1595
- } | undefined;
1596
- lowerCaseRefNameAliases: {
1597
- [x: string]: string;
1598
- } | undefined;
1599
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1600
- } & {
1601
- getConf(arg: string): any;
1602
- } & {
1603
- readonly initialized: boolean;
1604
- readonly name: string;
1605
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1606
- readonly aliases: string[];
1607
- readonly displayName: string | undefined;
1608
- hasName(name: string): boolean;
1609
- readonly allAliases: string[];
1610
- readonly allRefNames: string[] | undefined;
1611
- readonly lowerCaseRefNames: string[] | undefined;
1612
- readonly allRefNamesWithLowerCase: string[] | undefined;
1613
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1614
- readonly refNameColors: string[];
1615
- } & {
1616
- readonly refNames: string[] | undefined;
1617
- } & {
1618
- getCanonicalRefName(refName: string): string | undefined;
1619
- getRefNameColor(refName: string): string | undefined;
1620
- isValidRefName(refName: string): boolean;
1621
- } & {
1622
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1623
- regions: import("@jbrowse/core/util").Region[];
1624
- refNameAliases: {
1625
- [x: string]: string;
1626
- };
1627
- lowerCaseRefNameAliases: {
1628
- [x: string]: string;
1629
- };
1630
- cytobands: import("@jbrowse/core/util").Feature[];
1631
- }): void;
1632
- setError(e: unknown): void;
1633
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1634
- setRefNameAliases(aliases: {
1635
- [x: string]: string;
1636
- }, lowerCaseAliases: {
1637
- [x: string]: string;
1638
- }): void;
1639
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1640
- setLoadingP(p?: Promise<void>): void;
1641
- load(): Promise<void>;
1642
- loadPre(): Promise<void>;
1643
- } & {
1644
- getAdapterMapEntry(adapterConf: {
1645
- [x: string]: unknown;
1646
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1647
- getRefNameMapForAdapter(adapterConf: {
1648
- [x: string]: unknown;
1649
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1650
- [x: string]: string;
1651
- }>;
1652
- getReverseRefNameMapForAdapter(adapterConf: {
1653
- [x: string]: unknown;
1654
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1655
- [x: string]: string;
1656
- }>;
1657
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1658
- getRefNameMapForAdapter(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
- getReverseRefNameMapForAdapter(adapterConf: {
1667
- [x: string]: unknown;
1668
- }, assemblyName: string | undefined, opts: {
1669
- stopToken?: string;
1670
- sessionId: string;
1671
- }): Promise<{
1672
- [x: string]: string;
1673
- } | undefined>;
1674
- isValidRefName(refName: string, assemblyName: string): boolean;
1675
- } & {
1676
- afterAttach(): void;
1677
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1678
- addAssembly(configuration: any): void;
1679
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
1680
- }, {
1681
- rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1682
- adminMode: boolean;
1683
- error: unknown;
1684
- textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1685
- pluginManager: PluginManager;
1686
- } & {
1687
- setError(error: unknown): void;
1688
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1689
- setDefaultSession(): void;
1690
- setSessionPath(path: string): void;
1691
- renameCurrentSession(newName: string): void;
1692
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
22
+ readonly root: import("mobx-state-tree").TypeOrStateTreeNodeToStateTreeNode<ROOT_MODEL_TYPE>;
1693
23
  } & {
1694
24
  readonly jbrowse: any;
1695
25
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1707,40 +37,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1707
37
  readonly adminMode: boolean;
1708
38
  readonly textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1709
39
  } & {
1710
- readonly assemblies: ({
1711
- [x: string]: any;
1712
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1713
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1714
- [x: string]: any;
1715
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1716
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1717
- [x: string]: any;
1718
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1719
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1720
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1721
- aliases: {
1722
- type: string;
1723
- defaultValue: never[];
1724
- description: string;
1725
- };
1726
- sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1727
- refNameColors: {
1728
- type: string;
1729
- defaultValue: never[];
1730
- description: string;
1731
- };
1732
- refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1733
- adapter: import("mobx-state-tree").IAnyModelType;
1734
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
1735
- cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1736
- adapter: import("mobx-state-tree").IAnyModelType;
1737
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
1738
- displayName: {
1739
- type: string;
1740
- defaultValue: string;
1741
- description: string;
1742
- };
1743
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name">>>)[];
40
+ readonly assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
1744
41
  } & {
1745
42
  setSelection(thing: unknown): void;
1746
43
  clearSelection(): void;