@jbrowse/product-core 5.0.0-beta.13 → 5.0.0-beta.14

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Files changed (47) hide show
  1. package/esm/RootModel/BaseRootModel.d.ts +88 -47
  2. package/esm/RootModel/BaseRootModel.js +45 -2
  3. package/esm/RootModel/HierarchicalConfig.d.ts +3 -1
  4. package/esm/RootModel/HierarchicalConfig.js +3 -1
  5. package/esm/RootModel/InternetAccounts.d.ts +2 -0
  6. package/esm/RootModel/InternetAccounts.js +2 -0
  7. package/esm/RootModel/PreferencesConfig.d.ts +4 -4
  8. package/esm/RootModel/PreferencesConfig.js +4 -4
  9. package/esm/RootModel/menuItems.d.ts +1 -2
  10. package/esm/RootModel/menuItems.js +3 -4
  11. package/esm/Session/BaseSession.d.ts +7 -5
  12. package/esm/Session/BaseSession.js +15 -5
  13. package/esm/Session/Connections.d.ts +3 -0
  14. package/esm/Session/Connections.js +3 -0
  15. package/esm/Session/DrawerWidgets.d.ts +2 -0
  16. package/esm/Session/DrawerWidgets.js +2 -0
  17. package/esm/Session/MultipleViews.d.ts +122 -96
  18. package/esm/Session/MultipleViews.js +5 -3
  19. package/esm/Session/Preferences.d.ts +122 -97
  20. package/esm/Session/Preferences.js +5 -4
  21. package/esm/Session/ReferenceManagement.d.ts +2 -0
  22. package/esm/Session/ReferenceManagement.js +2 -0
  23. package/esm/Session/SessionTracks.d.ts +119 -93
  24. package/esm/Session/SessionTracks.js +2 -0
  25. package/esm/Session/Themes.d.ts +7 -5
  26. package/esm/Session/Themes.js +15 -10
  27. package/esm/Session/TrackMenu.d.ts +4 -8
  28. package/esm/Session/TrackMenu.js +13 -7
  29. package/esm/Session/TrackMenuSessionMixin.js +7 -3
  30. package/esm/Session/Tracks.d.ts +120 -93
  31. package/esm/Session/Tracks.js +3 -0
  32. package/esm/Session/pluginExtraTrackItems.d.ts +2 -3
  33. package/esm/Session/pluginExtraTrackItems.js +1 -1
  34. package/esm/sessionMigrations/index.js +2 -2
  35. package/esm/siblingCast.d.ts +6 -0
  36. package/esm/siblingCast.js +7 -0
  37. package/esm/ui/AboutDialog.d.ts +3 -2
  38. package/esm/ui/AboutDialog.js +4 -2
  39. package/esm/ui/DescriptionPanel.js +4 -4
  40. package/esm/ui/Drawer.js +11 -15
  41. package/esm/ui/HeaderButtons.d.ts +1 -1
  42. package/esm/ui/HeaderButtons.js +3 -2
  43. package/esm/ui/PreferenceCheckbox.d.ts +3 -2
  44. package/esm/ui/PreferenceCheckbox.js +4 -2
  45. package/esm/ui/WidgetHeading.d.ts +2 -2
  46. package/esm/ui/WidgetHeading.js +3 -2
  47. package/package.json +6 -6
package/esm/Session/Preferences.d.ts CHANGED
@@ -2,10 +2,11 @@ import type PluginManager from '@jbrowse/core/PluginManager';
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2
  /**
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  * #stateModel PreferencesSessionMixin
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  *
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- * loads and persists user-preference overrides (the BaseSession
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- * `preferencesOverrides` volatile) to localStorage. Compose into products that
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- * let users edit preferences (web, desktop); embedded sessions omit it and
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- * resolve preferences from `configuration.preferences` admin defaults only.
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+ * Loads and saves a user's preference overrides (the BaseSession
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+ * `preferencesOverrides` volatile) in localStorage. Products that let users
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+ * edit preferences (web, desktop) compose it; embedded sessions omit it and
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+ * resolve preferences from the `configuration.preferences` admin defaults
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+ * only.
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  */
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  export declare function PreferencesSessionMixin(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<{
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  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -31,13 +32,13 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
31
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  }, {
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  error: unknown;
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  loadingP: Promise<void> | undefined;
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- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
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+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
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  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
36
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
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+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
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  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
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  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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  loadedGeneticCodes: Record<string, number> | undefined;
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- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
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+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
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  statusMessage: string | undefined;
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  statusProgress: number | undefined;
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  statusSource: string | undefined;
@@ -56,7 +57,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
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  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
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  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
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  } & {
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- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
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+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
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  regions: import("@jbrowse/core/util").Region[];
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  cytobands: import("@jbrowse/core/util").Feature[];
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  geneticCodes: Record<string, number>;
@@ -87,11 +88,12 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
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  getCanonicalRefName2(refName: string): string;
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  isValidRefName(refName: string): boolean;
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  } & {
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+ isCircularRefName(refName: string): boolean;
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  getRefNamePosition(refName: string): number | undefined;
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  getAliasesForRefName(refName: string): string[];
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  getRefNameMapForAdapter(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").RefNameAliases>;
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+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
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  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
96
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
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  }, {
@@ -112,13 +114,13 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
112
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  }> & {
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  error: unknown;
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  loadingP: Promise<void> | undefined;
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- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
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+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
116
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  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
117
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
119
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
118
120
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
119
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  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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  loadedGeneticCodes: Record<string, number> | undefined;
121
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
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+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
122
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  statusMessage: string | undefined;
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  statusProgress: number | undefined;
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  statusSource: string | undefined;
@@ -137,7 +139,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
137
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  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
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  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
139
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  } & {
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- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
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+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
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  regions: import("@jbrowse/core/util").Region[];
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  cytobands: import("@jbrowse/core/util").Feature[];
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  geneticCodes: Record<string, number>;
@@ -168,24 +170,25 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
168
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  getCanonicalRefName2(refName: string): string;
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  isValidRefName(refName: string): boolean;
170
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  } & {
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+ isCircularRefName(refName: string): boolean;
171
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  getRefNamePosition(refName: string): number | undefined;
172
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  getAliasesForRefName(refName: string): string[];
173
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  getRefNameMapForAdapter(adapterConf: {
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  [x: string]: unknown;
175
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
178
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
176
179
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
177
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  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
178
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  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
179
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  }, {
180
183
  error: unknown;
181
184
  loadingP: Promise<void> | undefined;
182
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
185
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
183
186
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
184
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
187
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
185
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  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
186
189
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
187
190
  loadedGeneticCodes: Record<string, number> | undefined;
188
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
191
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
189
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  statusMessage: string | undefined;
190
193
  statusProgress: number | undefined;
191
194
  statusSource: string | undefined;
@@ -204,7 +207,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
204
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  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
205
208
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
206
209
  } & {
207
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
210
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
208
211
  regions: import("@jbrowse/core/util").Region[];
209
212
  cytobands: import("@jbrowse/core/util").Feature[];
210
213
  geneticCodes: Record<string, number>;
@@ -235,11 +238,12 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
235
238
  getCanonicalRefName2(refName: string): string;
236
239
  isValidRefName(refName: string): boolean;
237
240
  } & {
241
+ isCircularRefName(refName: string): boolean;
238
242
  getRefNamePosition(refName: string): number | undefined;
239
243
  getAliasesForRefName(refName: string): string[];
240
244
  getRefNameMapForAdapter(adapterConf: {
241
245
  [x: string]: unknown;
242
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
246
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
243
247
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
244
248
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
245
249
  has(asmName: string): boolean;
@@ -248,13 +252,13 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
248
252
  }> & {
249
253
  error: unknown;
250
254
  loadingP: Promise<void> | undefined;
251
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
255
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
252
256
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
253
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
257
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
254
258
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
255
259
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
256
260
  loadedGeneticCodes: Record<string, number> | undefined;
257
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
261
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
258
262
  statusMessage: string | undefined;
259
263
  statusProgress: number | undefined;
260
264
  statusSource: string | undefined;
@@ -273,7 +277,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
273
277
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
274
278
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
275
279
  } & {
276
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
280
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
277
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  regions: import("@jbrowse/core/util").Region[];
278
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  cytobands: import("@jbrowse/core/util").Feature[];
279
283
  geneticCodes: Record<string, number>;
@@ -304,24 +308,25 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
304
308
  getCanonicalRefName2(refName: string): string;
305
309
  isValidRefName(refName: string): boolean;
306
310
  } & {
311
+ isCircularRefName(refName: string): boolean;
307
312
  getRefNamePosition(refName: string): number | undefined;
308
313
  getAliasesForRefName(refName: string): string[];
309
314
  getRefNameMapForAdapter(adapterConf: {
310
315
  [x: string]: unknown;
311
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
316
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
312
317
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
313
318
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
314
319
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
315
320
  }, {
316
321
  error: unknown;
317
322
  loadingP: Promise<void> | undefined;
318
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
323
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
319
324
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
320
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
325
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
321
326
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
322
327
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
323
328
  loadedGeneticCodes: Record<string, number> | undefined;
324
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
329
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
325
330
  statusMessage: string | undefined;
326
331
  statusProgress: number | undefined;
327
332
  statusSource: string | undefined;
@@ -340,7 +345,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
340
345
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
341
346
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
342
347
  } & {
343
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
348
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
344
349
  regions: import("@jbrowse/core/util").Region[];
345
350
  cytobands: import("@jbrowse/core/util").Feature[];
346
351
  geneticCodes: Record<string, number>;
@@ -371,11 +376,12 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
371
376
  getCanonicalRefName2(refName: string): string;
372
377
  isValidRefName(refName: string): boolean;
373
378
  } & {
379
+ isCircularRefName(refName: string): boolean;
374
380
  getRefNamePosition(refName: string): number | undefined;
375
381
  getAliasesForRefName(refName: string): string[];
376
382
  getRefNameMapForAdapter(adapterConf: {
377
383
  [x: string]: unknown;
378
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
384
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
379
385
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
380
386
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
381
387
  readonly assemblyNamesList: string[];
@@ -390,13 +396,13 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
390
396
  }> & {
391
397
  error: unknown;
392
398
  loadingP: Promise<void> | undefined;
393
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
399
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
394
400
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
395
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
401
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
396
402
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
397
403
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
398
404
  loadedGeneticCodes: Record<string, number> | undefined;
399
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
405
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
400
406
  statusMessage: string | undefined;
401
407
  statusProgress: number | undefined;
402
408
  statusSource: string | undefined;
@@ -415,7 +421,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
415
421
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
416
422
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
417
423
  } & {
418
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
424
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
419
425
  regions: import("@jbrowse/core/util").Region[];
420
426
  cytobands: import("@jbrowse/core/util").Feature[];
421
427
  geneticCodes: Record<string, number>;
@@ -446,24 +452,25 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
446
452
  getCanonicalRefName2(refName: string): string;
447
453
  isValidRefName(refName: string): boolean;
448
454
  } & {
455
+ isCircularRefName(refName: string): boolean;
449
456
  getRefNamePosition(refName: string): number | undefined;
450
457
  getAliasesForRefName(refName: string): string[];
451
458
  getRefNameMapForAdapter(adapterConf: {
452
459
  [x: string]: unknown;
453
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
460
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
454
461
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
455
462
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
456
463
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
457
464
  }, {
458
465
  error: unknown;
459
466
  loadingP: Promise<void> | undefined;
460
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
467
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
461
468
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
462
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
469
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
463
470
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
464
471
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
465
472
  loadedGeneticCodes: Record<string, number> | undefined;
466
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
473
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
467
474
  statusMessage: string | undefined;
468
475
  statusProgress: number | undefined;
469
476
  statusSource: string | undefined;
@@ -482,7 +489,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
482
489
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
483
490
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
484
491
  } & {
485
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
492
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
486
493
  regions: import("@jbrowse/core/util").Region[];
487
494
  cytobands: import("@jbrowse/core/util").Feature[];
488
495
  geneticCodes: Record<string, number>;
@@ -513,11 +520,12 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
513
520
  getCanonicalRefName2(refName: string): string;
514
521
  isValidRefName(refName: string): boolean;
515
522
  } & {
523
+ isCircularRefName(refName: string): boolean;
516
524
  getRefNamePosition(refName: string): number | undefined;
517
525
  getAliasesForRefName(refName: string): string[];
518
526
  getRefNameMapForAdapter(adapterConf: {
519
527
  [x: string]: unknown;
520
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
528
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
521
529
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
522
530
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
523
531
  requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
@@ -525,13 +533,13 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
525
533
  }> & {
526
534
  error: unknown;
527
535
  loadingP: Promise<void> | undefined;
528
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
536
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
529
537
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
530
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
538
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
531
539
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
532
540
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
533
541
  loadedGeneticCodes: Record<string, number> | undefined;
534
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
542
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
535
543
  statusMessage: string | undefined;
536
544
  statusProgress: number | undefined;
537
545
  statusSource: string | undefined;
@@ -550,7 +558,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
550
558
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
551
559
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
552
560
  } & {
553
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
561
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
554
562
  regions: import("@jbrowse/core/util").Region[];
555
563
  cytobands: import("@jbrowse/core/util").Feature[];
556
564
  geneticCodes: Record<string, number>;
@@ -581,24 +589,25 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
581
589
  getCanonicalRefName2(refName: string): string;
582
590
  isValidRefName(refName: string): boolean;
583
591
  } & {
592
+ isCircularRefName(refName: string): boolean;
584
593
  getRefNamePosition(refName: string): number | undefined;
585
594
  getAliasesForRefName(refName: string): string[];
586
595
  getRefNameMapForAdapter(adapterConf: {
587
596
  [x: string]: unknown;
588
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
597
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
589
598
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
590
599
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
591
600
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
592
601
  }, {
593
602
  error: unknown;
594
603
  loadingP: Promise<void> | undefined;
595
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
604
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
596
605
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
597
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
606
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
598
607
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
599
608
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
600
609
  loadedGeneticCodes: Record<string, number> | undefined;
601
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
610
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
602
611
  statusMessage: string | undefined;
603
612
  statusProgress: number | undefined;
604
613
  statusSource: string | undefined;
@@ -617,7 +626,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
617
626
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
618
627
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
619
628
  } & {
620
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
629
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
621
630
  regions: import("@jbrowse/core/util").Region[];
622
631
  cytobands: import("@jbrowse/core/util").Feature[];
623
632
  geneticCodes: Record<string, number>;
@@ -648,16 +657,17 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
648
657
  getCanonicalRefName2(refName: string): string;
649
658
  isValidRefName(refName: string): boolean;
650
659
  } & {
660
+ isCircularRefName(refName: string): boolean;
651
661
  getRefNamePosition(refName: string): number | undefined;
652
662
  getAliasesForRefName(refName: string): string[];
653
663
  getRefNameMapForAdapter(adapterConf: {
654
664
  [x: string]: unknown;
655
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
665
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
656
666
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
657
667
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
658
668
  getRefNameMapForAdapter(adapterConf: {
659
669
  [x: string]: unknown;
660
- }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
670
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
661
671
  isValidRefName(refName: string, assemblyName: string): boolean;
662
672
  } & {
663
673
  afterAttach(): void;
@@ -670,8 +680,11 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
670
680
  error: unknown;
671
681
  textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
672
682
  pluginManager: PluginManager;
683
+ detachDisposers: (() => void)[];
673
684
  } & {
674
685
  setError(error: unknown): void;
686
+ addDetachDisposer(disposer: () => void): void;
687
+ detach(): void;
675
688
  setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
676
689
  setDefaultSession(): void;
677
690
  setSessionPath(path: string): void;
@@ -686,13 +699,13 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
686
699
  }, {
687
700
  error: unknown;
688
701
  loadingP: Promise<void> | undefined;
689
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
702
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
690
703
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
691
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
704
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
692
705
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
693
706
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
694
707
  loadedGeneticCodes: Record<string, number> | undefined;
695
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
708
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
696
709
  statusMessage: string | undefined;
697
710
  statusProgress: number | undefined;
698
711
  statusSource: string | undefined;
@@ -711,7 +724,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
711
724
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
712
725
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
713
726
  } & {
714
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
727
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
715
728
  regions: import("@jbrowse/core/util").Region[];
716
729
  cytobands: import("@jbrowse/core/util").Feature[];
717
730
  geneticCodes: Record<string, number>;
@@ -742,11 +755,12 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
742
755
  getCanonicalRefName2(refName: string): string;
743
756
  isValidRefName(refName: string): boolean;
744
757
  } & {
758
+ isCircularRefName(refName: string): boolean;
745
759
  getRefNamePosition(refName: string): number | undefined;
746
760
  getAliasesForRefName(refName: string): string[];
747
761
  getRefNameMapForAdapter(adapterConf: {
748
762
  [x: string]: unknown;
749
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
763
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
750
764
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
751
765
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
752
766
  }, {
@@ -767,13 +781,13 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
767
781
  }> & {
768
782
  error: unknown;
769
783
  loadingP: Promise<void> | undefined;
770
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
784
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
771
785
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
772
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
786
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
773
787
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
774
788
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
775
789
  loadedGeneticCodes: Record<string, number> | undefined;
776
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
790
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
777
791
  statusMessage: string | undefined;
778
792
  statusProgress: number | undefined;
779
793
  statusSource: string | undefined;
@@ -792,7 +806,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
792
806
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
793
807
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
794
808
  } & {
795
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
809
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
796
810
  regions: import("@jbrowse/core/util").Region[];
797
811
  cytobands: import("@jbrowse/core/util").Feature[];
798
812
  geneticCodes: Record<string, number>;
@@ -823,24 +837,25 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
823
837
  getCanonicalRefName2(refName: string): string;
824
838
  isValidRefName(refName: string): boolean;
825
839
  } & {
840
+ isCircularRefName(refName: string): boolean;
826
841
  getRefNamePosition(refName: string): number | undefined;
827
842
  getAliasesForRefName(refName: string): string[];
828
843
  getRefNameMapForAdapter(adapterConf: {
829
844
  [x: string]: unknown;
830
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
845
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
831
846
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
832
847
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
833
848
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
834
849
  }, {
835
850
  error: unknown;
836
851
  loadingP: Promise<void> | undefined;
837
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
852
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
838
853
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
839
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
854
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
840
855
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
841
856
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
842
857
  loadedGeneticCodes: Record<string, number> | undefined;
843
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
858
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
844
859
  statusMessage: string | undefined;
845
860
  statusProgress: number | undefined;
846
861
  statusSource: string | undefined;
@@ -859,7 +874,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
859
874
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
860
875
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
861
876
  } & {
862
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
877
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
863
878
  regions: import("@jbrowse/core/util").Region[];
864
879
  cytobands: import("@jbrowse/core/util").Feature[];
865
880
  geneticCodes: Record<string, number>;
@@ -890,11 +905,12 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
890
905
  getCanonicalRefName2(refName: string): string;
891
906
  isValidRefName(refName: string): boolean;
892
907
  } & {
908
+ isCircularRefName(refName: string): boolean;
893
909
  getRefNamePosition(refName: string): number | undefined;
894
910
  getAliasesForRefName(refName: string): string[];
895
911
  getRefNameMapForAdapter(adapterConf: {
896
912
  [x: string]: unknown;
897
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
913
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
898
914
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
899
915
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
900
916
  has(asmName: string): boolean;
@@ -903,13 +919,13 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
903
919
  }> & {
904
920
  error: unknown;
905
921
  loadingP: Promise<void> | undefined;
906
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
922
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
907
923
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
908
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
924
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
909
925
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
910
926
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
911
927
  loadedGeneticCodes: Record<string, number> | undefined;
912
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
928
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
913
929
  statusMessage: string | undefined;
914
930
  statusProgress: number | undefined;
915
931
  statusSource: string | undefined;
@@ -928,7 +944,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
928
944
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
929
945
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
930
946
  } & {
931
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
947
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
932
948
  regions: import("@jbrowse/core/util").Region[];
933
949
  cytobands: import("@jbrowse/core/util").Feature[];
934
950
  geneticCodes: Record<string, number>;
@@ -959,24 +975,25 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
959
975
  getCanonicalRefName2(refName: string): string;
960
976
  isValidRefName(refName: string): boolean;
961
977
  } & {
978
+ isCircularRefName(refName: string): boolean;
962
979
  getRefNamePosition(refName: string): number | undefined;
963
980
  getAliasesForRefName(refName: string): string[];
964
981
  getRefNameMapForAdapter(adapterConf: {
965
982
  [x: string]: unknown;
966
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
983
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
967
984
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
968
985
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
969
986
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
970
987
  }, {
971
988
  error: unknown;
972
989
  loadingP: Promise<void> | undefined;
973
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
990
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
974
991
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
975
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
992
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
976
993
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
977
994
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
978
995
  loadedGeneticCodes: Record<string, number> | undefined;
979
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
996
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
980
997
  statusMessage: string | undefined;
981
998
  statusProgress: number | undefined;
982
999
  statusSource: string | undefined;
@@ -995,7 +1012,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
995
1012
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
996
1013
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
997
1014
  } & {
998
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1015
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
999
1016
  regions: import("@jbrowse/core/util").Region[];
1000
1017
  cytobands: import("@jbrowse/core/util").Feature[];
1001
1018
  geneticCodes: Record<string, number>;
@@ -1026,11 +1043,12 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
1026
1043
  getCanonicalRefName2(refName: string): string;
1027
1044
  isValidRefName(refName: string): boolean;
1028
1045
  } & {
1046
+ isCircularRefName(refName: string): boolean;
1029
1047
  getRefNamePosition(refName: string): number | undefined;
1030
1048
  getAliasesForRefName(refName: string): string[];
1031
1049
  getRefNameMapForAdapter(adapterConf: {
1032
1050
  [x: string]: unknown;
1033
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1051
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1034
1052
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1035
1053
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1036
1054
  readonly assemblyNamesList: string[];
@@ -1045,13 +1063,13 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
1045
1063
  }> & {
1046
1064
  error: unknown;
1047
1065
  loadingP: Promise<void> | undefined;
1048
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1066
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1049
1067
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1050
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1068
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1051
1069
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1052
1070
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1053
1071
  loadedGeneticCodes: Record<string, number> | undefined;
1054
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1072
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1055
1073
  statusMessage: string | undefined;
1056
1074
  statusProgress: number | undefined;
1057
1075
  statusSource: string | undefined;
@@ -1070,7 +1088,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
1070
1088
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1071
1089
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1072
1090
  } & {
1073
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1091
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1074
1092
  regions: import("@jbrowse/core/util").Region[];
1075
1093
  cytobands: import("@jbrowse/core/util").Feature[];
1076
1094
  geneticCodes: Record<string, number>;
@@ -1101,24 +1119,25 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
1101
1119
  getCanonicalRefName2(refName: string): string;
1102
1120
  isValidRefName(refName: string): boolean;
1103
1121
  } & {
1122
+ isCircularRefName(refName: string): boolean;
1104
1123
  getRefNamePosition(refName: string): number | undefined;
1105
1124
  getAliasesForRefName(refName: string): string[];
1106
1125
  getRefNameMapForAdapter(adapterConf: {
1107
1126
  [x: string]: unknown;
1108
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1127
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1109
1128
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1110
1129
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1111
1130
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1112
1131
  }, {
1113
1132
  error: unknown;
1114
1133
  loadingP: Promise<void> | undefined;
1115
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1134
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1116
1135
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1117
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1136
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1118
1137
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1119
1138
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1120
1139
  loadedGeneticCodes: Record<string, number> | undefined;
1121
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1140
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1122
1141
  statusMessage: string | undefined;
1123
1142
  statusProgress: number | undefined;
1124
1143
  statusSource: string | undefined;
@@ -1137,7 +1156,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
1137
1156
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1138
1157
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1139
1158
  } & {
1140
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1159
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1141
1160
  regions: import("@jbrowse/core/util").Region[];
1142
1161
  cytobands: import("@jbrowse/core/util").Feature[];
1143
1162
  geneticCodes: Record<string, number>;
@@ -1168,11 +1187,12 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
1168
1187
  getCanonicalRefName2(refName: string): string;
1169
1188
  isValidRefName(refName: string): boolean;
1170
1189
  } & {
1190
+ isCircularRefName(refName: string): boolean;
1171
1191
  getRefNamePosition(refName: string): number | undefined;
1172
1192
  getAliasesForRefName(refName: string): string[];
1173
1193
  getRefNameMapForAdapter(adapterConf: {
1174
1194
  [x: string]: unknown;
1175
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1195
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1176
1196
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1177
1197
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
1178
1198
  requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
@@ -1180,13 +1200,13 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
1180
1200
  }> & {
1181
1201
  error: unknown;
1182
1202
  loadingP: Promise<void> | undefined;
1183
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1203
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1184
1204
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1185
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1205
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1186
1206
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1187
1207
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1188
1208
  loadedGeneticCodes: Record<string, number> | undefined;
1189
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1209
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1190
1210
  statusMessage: string | undefined;
1191
1211
  statusProgress: number | undefined;
1192
1212
  statusSource: string | undefined;
@@ -1205,7 +1225,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
1205
1225
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1206
1226
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1207
1227
  } & {
1208
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1228
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1209
1229
  regions: import("@jbrowse/core/util").Region[];
1210
1230
  cytobands: import("@jbrowse/core/util").Feature[];
1211
1231
  geneticCodes: Record<string, number>;
@@ -1236,24 +1256,25 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
1236
1256
  getCanonicalRefName2(refName: string): string;
1237
1257
  isValidRefName(refName: string): boolean;
1238
1258
  } & {
1259
+ isCircularRefName(refName: string): boolean;
1239
1260
  getRefNamePosition(refName: string): number | undefined;
1240
1261
  getAliasesForRefName(refName: string): string[];
1241
1262
  getRefNameMapForAdapter(adapterConf: {
1242
1263
  [x: string]: unknown;
1243
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1264
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1244
1265
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1245
1266
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1246
1267
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1247
1268
  }, {
1248
1269
  error: unknown;
1249
1270
  loadingP: Promise<void> | undefined;
1250
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1271
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1251
1272
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1252
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1273
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1253
1274
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1254
1275
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1255
1276
  loadedGeneticCodes: Record<string, number> | undefined;
1256
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1277
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1257
1278
  statusMessage: string | undefined;
1258
1279
  statusProgress: number | undefined;
1259
1280
  statusSource: string | undefined;
@@ -1272,7 +1293,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
1272
1293
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1273
1294
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1274
1295
  } & {
1275
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1296
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1276
1297
  regions: import("@jbrowse/core/util").Region[];
1277
1298
  cytobands: import("@jbrowse/core/util").Feature[];
1278
1299
  geneticCodes: Record<string, number>;
@@ -1303,16 +1324,17 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
1303
1324
  getCanonicalRefName2(refName: string): string;
1304
1325
  isValidRefName(refName: string): boolean;
1305
1326
  } & {
1327
+ isCircularRefName(refName: string): boolean;
1306
1328
  getRefNamePosition(refName: string): number | undefined;
1307
1329
  getAliasesForRefName(refName: string): string[];
1308
1330
  getRefNameMapForAdapter(adapterConf: {
1309
1331
  [x: string]: unknown;
1310
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1332
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1311
1333
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1312
1334
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
1313
1335
  getRefNameMapForAdapter(adapterConf: {
1314
1336
  [x: string]: unknown;
1315
- }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1337
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1316
1338
  isValidRefName(refName: string, assemblyName: string): boolean;
1317
1339
  } & {
1318
1340
  afterAttach(): void;
@@ -1325,8 +1347,11 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
1325
1347
  error: unknown;
1326
1348
  textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1327
1349
  pluginManager: PluginManager;
1350
+ detachDisposers: (() => void)[];
1328
1351
  } & {
1329
1352
  setError(error: unknown): void;
1353
+ addDetachDisposer(disposer: () => void): void;
1354
+ detach(): void;
1330
1355
  setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
1331
1356
  setDefaultSession(): void;
1332
1357
  setSessionPath(path: string): void;
@@ -1368,7 +1393,7 @@ export declare function PreferencesSessionMixin(pluginManager: PluginManager): i
1368
1393
  setName(str: string): void;
1369
1394
  setFocusedViewId(viewId: string | undefined): void;
1370
1395
  removeActiveDialog(): void;
1371
- queueDialog(doneCallback: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
1396
+ queueDialog<T extends import("@jbrowse/core/util").DialogComponentType>(callback: (doneCallback: () => void) => [T, import("react").ComponentProps<T>]): void;
1372
1397
  removeDialog(entry: [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
1373
1398
  } & {
1374
1399
  snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;