@jbrowse/product-core 2.12.0 → 2.12.1

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 (30) hide show
  1. package/dist/RootModel/BaseRootModel.d.ts +14 -144
  2. package/dist/RootModel/BaseRootModel.js +2 -3
  3. package/dist/RootModel/FormatAbout.js +1 -2
  4. package/dist/RootModel/FormatDetails.js +1 -2
  5. package/dist/RootModel/HierarchicalConfig.js +1 -2
  6. package/dist/RootModel/InternetAccounts.js +1 -2
  7. package/dist/Session/BaseSession.d.ts +10 -8
  8. package/dist/Session/BaseSession.js +3 -4
  9. package/dist/Session/Connections.d.ts +29 -71
  10. package/dist/Session/Connections.js +2 -3
  11. package/dist/Session/DialogQueue.js +2 -3
  12. package/dist/Session/DrawerWidgets.js +2 -3
  13. package/dist/Session/MultipleViews.d.ts +84 -461
  14. package/dist/Session/MultipleViews.js +2 -3
  15. package/dist/Session/ReferenceManagement.js +2 -3
  16. package/dist/Session/SessionTracks.d.ts +69 -525
  17. package/dist/Session/SessionTracks.js +2 -3
  18. package/dist/Session/Themes.js +2 -3
  19. package/dist/Session/Tracks.d.ts +62 -535
  20. package/dist/Session/Tracks.js +2 -3
  21. package/dist/rpcWorker.js +1 -2
  22. package/dist/ui/AboutDialog.js +1 -2
  23. package/dist/ui/FileInfoPanel.js +1 -1
  24. package/esm/RootModel/BaseRootModel.d.ts +14 -144
  25. package/esm/Session/BaseSession.d.ts +10 -8
  26. package/esm/Session/Connections.d.ts +29 -71
  27. package/esm/Session/MultipleViews.d.ts +84 -461
  28. package/esm/Session/SessionTracks.d.ts +69 -525
  29. package/esm/Session/Tracks.d.ts +62 -535
  30. package/package.json +3 -3
package/esm/Session/MultipleViews.d.ts CHANGED
@@ -18,9 +18,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  drawerWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
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  widgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyType>;
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  activeWidgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>>;
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- minimized: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>; /**
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- * #action
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- */
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+ minimized: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  } & {
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  /**
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  * #property
@@ -73,14 +71,16 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  } & {
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  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
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  setError(e: unknown): void;
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- setRegions(regions: Region[]): 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 | undefined;
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  }, lcAliases: {
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  [x: string]: string | undefined;
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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> | undefined): void;
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+ setCytobands(cytobands: import("@jbrowse/core/util" /**
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+ * #action
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+ */).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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  } & {
@@ -135,14 +135,14 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  } & {
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  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
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  setError(e: unknown): void;
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- setRegions(regions: Region[]): 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 | undefined;
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  }, lcAliases: {
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  [x: string]: string | undefined;
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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> | undefined): 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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  } & {
@@ -167,7 +167,9 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  error: unknown;
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  loaded: boolean;
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  loadingP: Promise<void> | undefined;
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- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly" /**
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+ * #action
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+ */).BasicRegion[] | undefined;
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  refNameAliases: {
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  [x: string]: string | undefined;
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  } | undefined;
@@ -199,14 +201,14 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  } & {
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  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
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  setError(e: unknown): void;
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- setRegions(regions: Region[]): 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 | undefined;
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  }, lcAliases: {
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  [x: string]: string | undefined;
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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> | undefined): 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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  } & {
@@ -261,14 +263,14 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  } & {
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  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
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  setError(e: unknown): void;
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- setRegions(regions: Region[]): 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 | undefined;
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  }, lcAliases: {
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  [x: string]: string | undefined;
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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> | undefined): 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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  } & {
@@ -325,14 +327,14 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  } & {
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  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
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  setError(e: unknown): void;
328
- setRegions(regions: Region[]): 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 | undefined;
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  }, lcAliases: {
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  [x: string]: string | undefined;
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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> | undefined): 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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  } & {
@@ -387,14 +389,14 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
387
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  } & {
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  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
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  setError(e: unknown): void;
390
- setRegions(regions: Region[]): 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 | undefined;
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  }, lcAliases: {
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  [x: string]: string | undefined;
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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> | undefined): 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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  } & {
@@ -413,11 +415,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  }>;
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
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  readonly assemblyNamesList: any[];
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- readonly assemblyList: ({
417
- [x: string]: any;
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- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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- setSubschema(slotName: string, data: unknown): any;
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- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
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+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
421
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  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
422
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  } & {
423
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  waitForAssembly(assemblyName: string): Promise<({
@@ -458,14 +456,14 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
458
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  } & {
459
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  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
460
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  setError(e: unknown): void;
461
- setRegions(regions: Region[]): void;
459
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
462
460
  setRefNameAliases(aliases: {
463
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  [x: string]: string | undefined;
464
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  }, lcAliases: {
465
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  [x: string]: string | undefined;
466
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  }): void;
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  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
468
- setLoadingP(p?: Promise<void> | undefined): void;
466
+ setLoadingP(p?: Promise<void>): void;
469
467
  load(): Promise<void>;
470
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  loadPre(): Promise<void>;
471
469
  } & {
@@ -520,14 +518,14 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
520
518
  } & {
521
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  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
522
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  setError(e: unknown): void;
523
- setRegions(regions: Region[]): void;
521
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
524
522
  setRefNameAliases(aliases: {
525
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  [x: string]: string | undefined;
526
524
  }, lcAliases: {
527
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  [x: string]: string | undefined;
528
526
  }): void;
529
527
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
530
- setLoadingP(p?: Promise<void> | undefined): void;
528
+ setLoadingP(p?: Promise<void>): void;
531
529
  load(): Promise<void>;
532
530
  loadPre(): Promise<void>;
533
531
  } & {
@@ -548,7 +546,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  getRefNameMapForAdapter(adapterConf: {
549
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  [x: string]: unknown;
550
548
  }, assemblyName: string | undefined, opts: {
551
- signal?: AbortSignal | undefined;
549
+ signal?: AbortSignal;
552
550
  sessionId: string;
553
551
  }): Promise<{
554
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  [x: string]: string | undefined;
@@ -556,7 +554,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  getReverseRefNameMapForAdapter(adapterConf: {
557
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  [x: string]: unknown;
558
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  }, assemblyName: string | undefined, opts: {
559
- signal?: AbortSignal | undefined;
557
+ signal?: AbortSignal;
560
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  sessionId: string;
561
559
  }): Promise<{
562
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  [x: string]: string | undefined;
@@ -564,131 +562,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
564
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  isValidRefName(refName: string, assemblyName: string): boolean;
565
563
  } & {
566
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  afterAttach(): void;
567
- removeAssembly(asm: {
568
- configuration: any;
569
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
570
- error: unknown;
571
- loaded: boolean;
572
- loadingP: Promise<void> | undefined;
573
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
574
- refNameAliases: {
575
- [x: string]: string | undefined;
576
- } | undefined;
577
- lowerCaseRefNameAliases: {
578
- [x: string]: string | undefined;
579
- } | undefined;
580
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
581
- } & {
582
- getConf(arg: string): any;
583
- } & {
584
- readonly initialized: boolean;
585
- readonly name: string;
586
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
587
- readonly aliases: string[];
588
- readonly displayName: string | undefined;
589
- hasName(name: string): boolean;
590
- readonly allAliases: string[];
591
- readonly allRefNames: string[] | undefined;
592
- readonly lowerCaseRefNames: string[] | undefined;
593
- readonly allRefNamesWithLowerCase: string[] | undefined;
594
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
595
- readonly refNameColors: string[];
596
- } & {
597
- readonly refNames: string[] | undefined;
598
- } & {
599
- getCanonicalRefName(refName: string): string | undefined;
600
- getRefNameColor(refName: string): string | undefined;
601
- isValidRefName(refName: string): boolean;
602
- } & {
603
- setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
604
- setError(e: unknown): void;
605
- setRegions(regions: Region[]): void;
606
- setRefNameAliases(aliases: {
607
- [x: string]: string | undefined;
608
- }, lcAliases: {
609
- [x: string]: string | undefined;
610
- }): void;
611
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
612
- setLoadingP(p?: Promise<void> | undefined): void;
613
- load(): Promise<void>;
614
- loadPre(): Promise<void>;
615
- } & {
616
- getAdapterMapEntry(adapterConf: {
617
- [x: string]: unknown;
618
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
619
- getRefNameMapForAdapter(adapterConf: {
620
- [x: string]: unknown;
621
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
622
- [x: string]: string | undefined;
623
- }>;
624
- getReverseRefNameMapForAdapter(adapterConf: {
625
- [x: string]: unknown;
626
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
627
- [x: string]: string | undefined;
628
- }>;
629
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
630
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
631
- }, {
632
- error: unknown;
633
- loaded: boolean;
634
- loadingP: Promise<void> | undefined;
635
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
636
- refNameAliases: {
637
- [x: string]: string | undefined;
638
- } | undefined;
639
- lowerCaseRefNameAliases: {
640
- [x: string]: string | undefined;
641
- } | undefined;
642
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
643
- } & {
644
- getConf(arg: string): any;
645
- } & {
646
- readonly initialized: boolean;
647
- readonly name: string;
648
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
649
- readonly aliases: string[];
650
- readonly displayName: string | undefined;
651
- hasName(name: string): boolean;
652
- readonly allAliases: string[];
653
- readonly allRefNames: string[] | undefined;
654
- readonly lowerCaseRefNames: string[] | undefined;
655
- readonly allRefNamesWithLowerCase: string[] | undefined;
656
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
657
- readonly refNameColors: string[];
658
- } & {
659
- readonly refNames: string[] | undefined;
660
- } & {
661
- getCanonicalRefName(refName: string): string | undefined;
662
- getRefNameColor(refName: string): string | undefined;
663
- isValidRefName(refName: string): boolean;
664
- } & {
665
- setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
666
- setError(e: unknown): void;
667
- setRegions(regions: Region[]): void;
668
- setRefNameAliases(aliases: {
669
- [x: string]: string | undefined;
670
- }, lcAliases: {
671
- [x: string]: string | undefined;
672
- }): void;
673
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
674
- setLoadingP(p?: Promise<void> | undefined): void;
675
- load(): Promise<void>;
676
- loadPre(): Promise<void>;
677
- } & {
678
- getAdapterMapEntry(adapterConf: {
679
- [x: string]: unknown;
680
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
681
- getRefNameMapForAdapter(adapterConf: {
682
- [x: string]: unknown;
683
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
684
- [x: string]: string | undefined;
685
- }>;
686
- getReverseRefNameMapForAdapter(adapterConf: {
687
- [x: string]: unknown;
688
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
689
- [x: string]: string | undefined;
690
- }>;
691
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): void;
565
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
692
566
  addAssembly(configuration: any): void;
693
567
  replaceAssembly(idx: number, configuration: any): void;
694
568
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
@@ -730,14 +604,16 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
730
604
  } & {
731
605
  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
732
606
  setError(e: unknown): void;
733
- setRegions(regions: Region[]): void;
607
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
734
608
  setRefNameAliases(aliases: {
735
609
  [x: string]: string | undefined;
736
610
  }, lcAliases: {
737
611
  [x: string]: string | undefined;
738
612
  }): void;
739
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
740
- setLoadingP(p?: Promise<void> | undefined): void;
613
+ setCytobands(cytobands: import("@jbrowse/core/util" /**
614
+ * #action
615
+ */).Feature[]): void;
616
+ setLoadingP(p?: Promise<void>): void;
741
617
  load(): Promise<void>;
742
618
  loadPre(): Promise<void>;
743
619
  } & {
@@ -794,14 +670,14 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
794
670
  } & {
795
671
  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
796
672
  setError(e: unknown): void;
797
- setRegions(regions: Region[]): void;
673
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
798
674
  setRefNameAliases(aliases: {
799
675
  [x: string]: string | undefined;
800
676
  }, lcAliases: {
801
677
  [x: string]: string | undefined;
802
678
  }): void;
803
679
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
804
- setLoadingP(p?: Promise<void> | undefined): void;
680
+ setLoadingP(p?: Promise<void>): void;
805
681
  load(): Promise<void>;
806
682
  loadPre(): Promise<void>;
807
683
  } & {
@@ -856,14 +732,14 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
856
732
  } & {
857
733
  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
858
734
  setError(e: unknown): void;
859
- setRegions(regions: Region[]): void;
735
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
860
736
  setRefNameAliases(aliases: {
861
737
  [x: string]: string | undefined;
862
738
  }, lcAliases: {
863
739
  [x: string]: string | undefined;
864
740
  }): void;
865
741
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
866
- setLoadingP(p?: Promise<void> | undefined): void;
742
+ setLoadingP(p?: Promise<void>): void;
867
743
  load(): Promise<void>;
868
744
  loadPre(): Promise<void>;
869
745
  } & {
@@ -920,14 +796,14 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
920
796
  } & {
921
797
  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
922
798
  setError(e: unknown): void;
923
- setRegions(regions: Region[]): void;
799
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
924
800
  setRefNameAliases(aliases: {
925
801
  [x: string]: string | undefined;
926
802
  }, lcAliases: {
927
803
  [x: string]: string | undefined;
928
804
  }): void;
929
805
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
930
- setLoadingP(p?: Promise<void> | undefined): void;
806
+ setLoadingP(p?: Promise<void>): void;
931
807
  load(): Promise<void>;
932
808
  loadPre(): Promise<void>;
933
809
  } & {
@@ -982,14 +858,14 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
982
858
  } & {
983
859
  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
984
860
  setError(e: unknown): void;
985
- setRegions(regions: Region[]): void;
861
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
986
862
  setRefNameAliases(aliases: {
987
863
  [x: string]: string | undefined;
988
864
  }, lcAliases: {
989
865
  [x: string]: string | undefined;
990
866
  }): void;
991
867
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
992
- setLoadingP(p?: Promise<void> | undefined): void;
868
+ setLoadingP(p?: Promise<void>): void;
993
869
  load(): Promise<void>;
994
870
  loadPre(): Promise<void>;
995
871
  } & {
@@ -1008,11 +884,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1008
884
  }>;
1009
885
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1010
886
  readonly assemblyNamesList: any[];
1011
- readonly assemblyList: ({
1012
- [x: string]: any;
1013
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1014
- setSubschema(slotName: string, data: unknown): any;
1015
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
887
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1016
888
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1017
889
  } & {
1018
890
  waitForAssembly(assemblyName: string): Promise<({
@@ -1053,14 +925,14 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1053
925
  } & {
1054
926
  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
1055
927
  setError(e: unknown): void;
1056
- setRegions(regions: Region[]): void;
928
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1057
929
  setRefNameAliases(aliases: {
1058
930
  [x: string]: string | undefined;
1059
931
  }, lcAliases: {
1060
932
  [x: string]: string | undefined;
1061
933
  }): void;
1062
934
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1063
- setLoadingP(p?: Promise<void> | undefined): void;
935
+ setLoadingP(p?: Promise<void>): void;
1064
936
  load(): Promise<void>;
1065
937
  loadPre(): Promise<void>;
1066
938
  } & {
@@ -1115,14 +987,14 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1115
987
  } & {
1116
988
  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
1117
989
  setError(e: unknown): void;
1118
- setRegions(regions: Region[]): void;
990
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1119
991
  setRefNameAliases(aliases: {
1120
992
  [x: string]: string | undefined;
1121
993
  }, lcAliases: {
1122
994
  [x: string]: string | undefined;
1123
995
  }): void;
1124
996
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1125
- setLoadingP(p?: Promise<void> | undefined): void;
997
+ setLoadingP(p?: Promise<void>): void;
1126
998
  load(): Promise<void>;
1127
999
  loadPre(): Promise<void>;
1128
1000
  } & {
@@ -1143,7 +1015,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1143
1015
  getRefNameMapForAdapter(adapterConf: {
1144
1016
  [x: string]: unknown;
1145
1017
  }, assemblyName: string | undefined, opts: {
1146
- signal?: AbortSignal | undefined;
1018
+ signal?: AbortSignal;
1147
1019
  sessionId: string;
1148
1020
  }): Promise<{
1149
1021
  [x: string]: string | undefined;
@@ -1151,7 +1023,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1151
1023
  getReverseRefNameMapForAdapter(adapterConf: {
1152
1024
  [x: string]: unknown;
1153
1025
  }, assemblyName: string | undefined, opts: {
1154
- signal?: AbortSignal | undefined;
1026
+ signal?: AbortSignal;
1155
1027
  sessionId: string;
1156
1028
  }): Promise<{
1157
1029
  [x: string]: string | undefined;
@@ -1159,131 +1031,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1159
1031
  isValidRefName(refName: string, assemblyName: string): boolean;
1160
1032
  } & {
1161
1033
  afterAttach(): void;
1162
- removeAssembly(asm: {
1163
- configuration: any;
1164
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1165
- error: unknown;
1166
- loaded: boolean;
1167
- loadingP: Promise<void> | undefined;
1168
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1169
- refNameAliases: {
1170
- [x: string]: string | undefined;
1171
- } | undefined;
1172
- lowerCaseRefNameAliases: {
1173
- [x: string]: string | undefined;
1174
- } | undefined;
1175
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1176
- } & {
1177
- getConf(arg: string): any;
1178
- } & {
1179
- readonly initialized: boolean;
1180
- readonly name: string;
1181
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1182
- readonly aliases: string[];
1183
- readonly displayName: string | undefined;
1184
- hasName(name: string): boolean;
1185
- readonly allAliases: string[];
1186
- readonly allRefNames: string[] | undefined;
1187
- readonly lowerCaseRefNames: string[] | undefined;
1188
- readonly allRefNamesWithLowerCase: string[] | undefined;
1189
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1190
- readonly refNameColors: string[];
1191
- } & {
1192
- readonly refNames: string[] | undefined;
1193
- } & {
1194
- getCanonicalRefName(refName: string): string | undefined;
1195
- getRefNameColor(refName: string): string | undefined;
1196
- isValidRefName(refName: string): boolean;
1197
- } & {
1198
- setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
1199
- setError(e: unknown): void;
1200
- setRegions(regions: Region[]): void;
1201
- setRefNameAliases(aliases: {
1202
- [x: string]: string | undefined;
1203
- }, lcAliases: {
1204
- [x: string]: string | undefined;
1205
- }): void;
1206
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1207
- setLoadingP(p?: Promise<void> | undefined): void;
1208
- load(): Promise<void>;
1209
- loadPre(): Promise<void>;
1210
- } & {
1211
- getAdapterMapEntry(adapterConf: {
1212
- [x: string]: unknown;
1213
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1214
- getRefNameMapForAdapter(adapterConf: {
1215
- [x: string]: unknown;
1216
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1217
- [x: string]: string | undefined;
1218
- }>;
1219
- getReverseRefNameMapForAdapter(adapterConf: {
1220
- [x: string]: unknown;
1221
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1222
- [x: string]: string | undefined;
1223
- }>;
1224
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1225
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1226
- }, {
1227
- error: unknown;
1228
- loaded: boolean;
1229
- loadingP: Promise<void> | undefined;
1230
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1231
- refNameAliases: {
1232
- [x: string]: string | undefined;
1233
- } | undefined;
1234
- lowerCaseRefNameAliases: {
1235
- [x: string]: string | undefined;
1236
- } | undefined;
1237
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1238
- } & {
1239
- getConf(arg: string): any;
1240
- } & {
1241
- readonly initialized: boolean;
1242
- readonly name: string;
1243
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1244
- readonly aliases: string[];
1245
- readonly displayName: string | undefined;
1246
- hasName(name: string): boolean;
1247
- readonly allAliases: string[];
1248
- readonly allRefNames: string[] | undefined;
1249
- readonly lowerCaseRefNames: string[] | undefined;
1250
- readonly allRefNamesWithLowerCase: string[] | undefined;
1251
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1252
- readonly refNameColors: string[];
1253
- } & {
1254
- readonly refNames: string[] | undefined;
1255
- } & {
1256
- getCanonicalRefName(refName: string): string | undefined;
1257
- getRefNameColor(refName: string): string | undefined;
1258
- isValidRefName(refName: string): boolean;
1259
- } & {
1260
- setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
1261
- setError(e: unknown): void;
1262
- setRegions(regions: Region[]): void;
1263
- setRefNameAliases(aliases: {
1264
- [x: string]: string | undefined;
1265
- }, lcAliases: {
1266
- [x: string]: string | undefined;
1267
- }): void;
1268
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1269
- setLoadingP(p?: Promise<void> | undefined): void;
1270
- load(): Promise<void>;
1271
- loadPre(): Promise<void>;
1272
- } & {
1273
- getAdapterMapEntry(adapterConf: {
1274
- [x: string]: unknown;
1275
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1276
- getRefNameMapForAdapter(adapterConf: {
1277
- [x: string]: unknown;
1278
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1279
- [x: string]: string | undefined;
1280
- }>;
1281
- getReverseRefNameMapForAdapter(adapterConf: {
1282
- [x: string]: unknown;
1283
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1284
- [x: string]: string | undefined;
1285
- }>;
1286
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): void;
1034
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1287
1035
  addAssembly(configuration: any): void;
1288
1036
  replaceAssembly(idx: number, configuration: any): void;
1289
1037
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
@@ -1295,7 +1043,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1295
1043
  pluginManager: PluginManager;
1296
1044
  } & {
1297
1045
  setError(error: unknown): void;
1298
- setSession(sessionSnapshot?: any): void;
1046
+ setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1299
1047
  setDefaultSession(): void;
1300
1048
  setSessionPath(path: string): void;
1301
1049
  renameCurrentSession(newName: string): void;
@@ -1342,14 +1090,14 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1342
1090
  } & {
1343
1091
  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
1344
1092
  setError(e: unknown): void;
1345
- setRegions(regions: Region[]): void;
1093
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1346
1094
  setRefNameAliases(aliases: {
1347
1095
  [x: string]: string | undefined;
1348
1096
  }, lcAliases: {
1349
1097
  [x: string]: string | undefined;
1350
1098
  }): void;
1351
1099
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1352
- setLoadingP(p?: Promise<void> | undefined): void;
1100
+ setLoadingP(p?: Promise<void>): void;
1353
1101
  load(): Promise<void>;
1354
1102
  loadPre(): Promise<void>;
1355
1103
  } & {
@@ -1406,14 +1154,14 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1406
1154
  } & {
1407
1155
  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
1408
1156
  setError(e: unknown): void;
1409
- setRegions(regions: Region[]): void;
1157
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1410
1158
  setRefNameAliases(aliases: {
1411
1159
  [x: string]: string | undefined;
1412
1160
  }, lcAliases: {
1413
1161
  [x: string]: string | undefined;
1414
1162
  }): void;
1415
1163
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1416
- setLoadingP(p?: Promise<void> | undefined): void;
1164
+ setLoadingP(p?: Promise<void>): void;
1417
1165
  load(): Promise<void>;
1418
1166
  loadPre(): Promise<void>;
1419
1167
  } & {
@@ -1468,14 +1216,14 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1468
1216
  } & {
1469
1217
  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
1470
1218
  setError(e: unknown): void;
1471
- setRegions(regions: Region[]): void;
1219
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1472
1220
  setRefNameAliases(aliases: {
1473
1221
  [x: string]: string | undefined;
1474
1222
  }, lcAliases: {
1475
1223
  [x: string]: string | undefined;
1476
1224
  }): void;
1477
1225
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1478
- setLoadingP(p?: Promise<void> | undefined): void;
1226
+ setLoadingP(p?: Promise<void>): void;
1479
1227
  load(): Promise<void>;
1480
1228
  loadPre(): Promise<void>;
1481
1229
  } & {
@@ -1532,14 +1280,14 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1532
1280
  } & {
1533
1281
  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
1534
1282
  setError(e: unknown): void;
1535
- setRegions(regions: Region[]): void;
1283
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1536
1284
  setRefNameAliases(aliases: {
1537
1285
  [x: string]: string | undefined;
1538
1286
  }, lcAliases: {
1539
1287
  [x: string]: string | undefined;
1540
1288
  }): void;
1541
1289
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1542
- setLoadingP(p?: Promise<void> | undefined): void;
1290
+ setLoadingP(p?: Promise<void>): void;
1543
1291
  load(): Promise<void>;
1544
1292
  loadPre(): Promise<void>;
1545
1293
  } & {
@@ -1594,14 +1342,14 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1594
1342
  } & {
1595
1343
  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
1596
1344
  setError(e: unknown): void;
1597
- setRegions(regions: Region[]): void;
1345
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1598
1346
  setRefNameAliases(aliases: {
1599
1347
  [x: string]: string | undefined;
1600
1348
  }, lcAliases: {
1601
1349
  [x: string]: string | undefined;
1602
1350
  }): void;
1603
1351
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1604
- setLoadingP(p?: Promise<void> | undefined): void;
1352
+ setLoadingP(p?: Promise<void>): void;
1605
1353
  load(): Promise<void>;
1606
1354
  loadPre(): Promise<void>;
1607
1355
  } & {
@@ -1620,11 +1368,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1620
1368
  }>;
1621
1369
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1622
1370
  readonly assemblyNamesList: any[];
1623
- readonly assemblyList: ({
1624
- [x: string]: any;
1625
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1626
- setSubschema(slotName: string, data: unknown): any;
1627
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
1371
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1628
1372
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1629
1373
  } & {
1630
1374
  waitForAssembly(assemblyName: string): Promise<({
@@ -1665,14 +1409,14 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1665
1409
  } & {
1666
1410
  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
1667
1411
  setError(e: unknown): void;
1668
- setRegions(regions: Region[]): void;
1412
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1669
1413
  setRefNameAliases(aliases: {
1670
1414
  [x: string]: string | undefined;
1671
1415
  }, lcAliases: {
1672
1416
  [x: string]: string | undefined;
1673
1417
  }): void;
1674
1418
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1675
- setLoadingP(p?: Promise<void> | undefined): void;
1419
+ setLoadingP(p?: Promise<void>): void;
1676
1420
  load(): Promise<void>;
1677
1421
  loadPre(): Promise<void>;
1678
1422
  } & {
@@ -1727,14 +1471,14 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1727
1471
  } & {
1728
1472
  setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
1729
1473
  setError(e: unknown): void;
1730
- setRegions(regions: Region[]): void;
1474
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1731
1475
  setRefNameAliases(aliases: {
1732
1476
  [x: string]: string | undefined;
1733
1477
  }, lcAliases: {
1734
1478
  [x: string]: string | undefined;
1735
1479
  }): void;
1736
1480
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1737
- setLoadingP(p?: Promise<void> | undefined): void;
1481
+ setLoadingP(p?: Promise<void>): void;
1738
1482
  load(): Promise<void>;
1739
1483
  loadPre(): Promise<void>;
1740
1484
  } & {
@@ -1755,7 +1499,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1755
1499
  getRefNameMapForAdapter(adapterConf: {
1756
1500
  [x: string]: unknown;
1757
1501
  }, assemblyName: string | undefined, opts: {
1758
- signal?: AbortSignal | undefined;
1502
+ signal?: AbortSignal;
1759
1503
  sessionId: string;
1760
1504
  }): Promise<{
1761
1505
  [x: string]: string | undefined;
@@ -1763,7 +1507,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1763
1507
  getReverseRefNameMapForAdapter(adapterConf: {
1764
1508
  [x: string]: unknown;
1765
1509
  }, assemblyName: string | undefined, opts: {
1766
- signal?: AbortSignal | undefined;
1510
+ signal?: AbortSignal;
1767
1511
  sessionId: string;
1768
1512
  }): Promise<{
1769
1513
  [x: string]: string | undefined;
@@ -1771,131 +1515,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1771
1515
  isValidRefName(refName: string, assemblyName: string): boolean;
1772
1516
  } & {
1773
1517
  afterAttach(): void;
1774
- removeAssembly(asm: {
1775
- configuration: any;
1776
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1777
- error: unknown;
1778
- loaded: boolean;
1779
- loadingP: Promise<void> | undefined;
1780
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1781
- refNameAliases: {
1782
- [x: string]: string | undefined;
1783
- } | undefined;
1784
- lowerCaseRefNameAliases: {
1785
- [x: string]: string | undefined;
1786
- } | undefined;
1787
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1788
- } & {
1789
- getConf(arg: string): any;
1790
- } & {
1791
- readonly initialized: boolean;
1792
- readonly name: string;
1793
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1794
- readonly aliases: string[];
1795
- readonly displayName: string | undefined;
1796
- hasName(name: string): boolean;
1797
- readonly allAliases: string[];
1798
- readonly allRefNames: string[] | undefined;
1799
- readonly lowerCaseRefNames: string[] | undefined;
1800
- readonly allRefNamesWithLowerCase: string[] | undefined;
1801
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1802
- readonly refNameColors: string[];
1803
- } & {
1804
- readonly refNames: string[] | undefined;
1805
- } & {
1806
- getCanonicalRefName(refName: string): string | undefined;
1807
- getRefNameColor(refName: string): string | undefined;
1808
- isValidRefName(refName: string): boolean;
1809
- } & {
1810
- setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
1811
- setError(e: unknown): void;
1812
- setRegions(regions: Region[]): void;
1813
- setRefNameAliases(aliases: {
1814
- [x: string]: string | undefined;
1815
- }, lcAliases: {
1816
- [x: string]: string | undefined;
1817
- }): void;
1818
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1819
- setLoadingP(p?: Promise<void> | undefined): void;
1820
- load(): Promise<void>;
1821
- loadPre(): Promise<void>;
1822
- } & {
1823
- getAdapterMapEntry(adapterConf: {
1824
- [x: string]: unknown;
1825
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1826
- getRefNameMapForAdapter(adapterConf: {
1827
- [x: string]: unknown;
1828
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1829
- [x: string]: string | undefined;
1830
- }>;
1831
- getReverseRefNameMapForAdapter(adapterConf: {
1832
- [x: string]: unknown;
1833
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1834
- [x: string]: string | undefined;
1835
- }>;
1836
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1837
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1838
- }, {
1839
- error: unknown;
1840
- loaded: boolean;
1841
- loadingP: Promise<void> | undefined;
1842
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1843
- refNameAliases: {
1844
- [x: string]: string | undefined;
1845
- } | undefined;
1846
- lowerCaseRefNameAliases: {
1847
- [x: string]: string | undefined;
1848
- } | undefined;
1849
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1850
- } & {
1851
- getConf(arg: string): any;
1852
- } & {
1853
- readonly initialized: boolean;
1854
- readonly name: string;
1855
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1856
- readonly aliases: string[];
1857
- readonly displayName: string | undefined;
1858
- hasName(name: string): boolean;
1859
- readonly allAliases: string[];
1860
- readonly allRefNames: string[] | undefined;
1861
- readonly lowerCaseRefNames: string[] | undefined;
1862
- readonly allRefNamesWithLowerCase: string[] | undefined;
1863
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1864
- readonly refNameColors: string[];
1865
- } & {
1866
- readonly refNames: string[] | undefined;
1867
- } & {
1868
- getCanonicalRefName(refName: string): string | undefined;
1869
- getRefNameColor(refName: string): string | undefined;
1870
- isValidRefName(refName: string): boolean;
1871
- } & {
1872
- setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
1873
- setError(e: unknown): void;
1874
- setRegions(regions: Region[]): void;
1875
- setRefNameAliases(aliases: {
1876
- [x: string]: string | undefined;
1877
- }, lcAliases: {
1878
- [x: string]: string | undefined;
1879
- }): void;
1880
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1881
- setLoadingP(p?: Promise<void> | undefined): void;
1882
- load(): Promise<void>;
1883
- loadPre(): Promise<void>;
1884
- } & {
1885
- getAdapterMapEntry(adapterConf: {
1886
- [x: string]: unknown;
1887
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1888
- getRefNameMapForAdapter(adapterConf: {
1889
- [x: string]: unknown;
1890
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1891
- [x: string]: string | undefined;
1892
- }>;
1893
- getReverseRefNameMapForAdapter(adapterConf: {
1894
- [x: string]: unknown;
1895
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1896
- [x: string]: string | undefined;
1897
- }>;
1898
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): void;
1518
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1899
1519
  addAssembly(configuration: any): void;
1900
1520
  replaceAssembly(idx: number, configuration: any): void;
1901
1521
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
@@ -1907,20 +1527,24 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1907
1527
  pluginManager: PluginManager;
1908
1528
  } & {
1909
1529
  setError(error: unknown): void;
1910
- setSession(sessionSnapshot?: any): void;
1530
+ setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1911
1531
  setDefaultSession(): void;
1912
1532
  setSessionPath(path: string): void;
1913
1533
  renameCurrentSession(newName: string): void;
1914
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
1915
- * #action
1916
- */
1534
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1917
1535
  } & {
1918
1536
  readonly jbrowse: any;
1919
1537
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1920
1538
  readonly configuration: {
1921
1539
  [x: string]: any;
1922
1540
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1923
- setSubschema(slotName: string, data: unknown): any;
1541
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1542
+ [x: string]: any;
1543
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1544
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1545
+ [x: string]: any;
1546
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1547
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1924
1548
  } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1925
1549
  readonly adminMode: boolean;
1926
1550
  readonly textSearchManager: import("@jbrowse/core/util").TextSearchManager;
@@ -1928,7 +1552,13 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1928
1552
  readonly assemblies: ({
1929
1553
  [x: string]: any;
1930
1554
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1931
- setSubschema(slotName: string, data: unknown): any;
1555
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1556
+ [x: string]: any;
1557
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1558
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1559
+ [x: string]: any;
1560
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1561
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1932
1562
  } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1933
1563
  aliases: {
1934
1564
  type: string;
@@ -1961,9 +1591,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1961
1591
  readonly visibleWidget: any;
1962
1592
  } & {
1963
1593
  setDrawerPosition(arg: string): void;
1964
- /**
1965
- * #action
1966
- */
1967
1594
  updateDrawerWidth(drawerWidth: number): number;
1968
1595
  resizeDrawer(distance: number): number;
1969
1596
  addWidget(typeName: string, id: string, initialState?: {}, conf?: unknown): any;
@@ -1973,11 +1600,7 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
1973
1600
  minimizeWidgetDrawer(): void;
1974
1601
  showWidgetDrawer(): void;
1975
1602
  hideAllWidgets(): void;
1976
- editConfiguration(configuration: {
1977
- [x: string]: any;
1978
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1979
- setSubschema(slotName: string, data: unknown): any;
1980
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>): void;
1603
+ editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1981
1604
  afterAttach(): void;
1982
1605
  } & {
1983
1606
  /**