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

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 (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/Tracks.d.ts CHANGED
@@ -3,6 +3,9 @@ import type { AnyConfiguration, AnyTrackConfig, TrackConfigEntry } from '@jbrows
3
3
  import type { IAnyStateTreeNode, Instance } from '@jbrowse/mobx-state-tree';
4
4
  /**
5
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  * #stateModel TracksManagerSessionMixin
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+ * Adds track configs to a session: looking one up by trackId among the
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+ * config's tracks, assembly sequences and connection tracks, and adding or
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+ * editing one.
6
9
  */
7
10
  export declare function TracksManagerSessionMixin(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<{
8
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  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -28,13 +31,13 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
28
31
  }, {
29
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  error: unknown;
30
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  loadingP: Promise<void> | undefined;
31
- 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>>;
32
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  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
33
- 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;
35
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  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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  loadedGeneticCodes: Record<string, number> | undefined;
37
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
40
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
38
41
  statusMessage: string | undefined;
39
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  statusProgress: number | undefined;
40
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  statusSource: string | undefined;
@@ -53,7 +56,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
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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;
55
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  } & {
56
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
59
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
57
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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>;
@@ -84,11 +87,12 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
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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: {
90
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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;
93
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
94
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  }, {
@@ -109,13 +113,13 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
109
113
  }> & {
110
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  error: unknown;
111
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  loadingP: Promise<void> | undefined;
112
- 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>>;
113
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  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
114
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
118
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
115
119
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
116
120
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
117
121
  loadedGeneticCodes: Record<string, number> | undefined;
118
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
122
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
119
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  statusMessage: string | undefined;
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  statusProgress: number | undefined;
121
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  statusSource: string | undefined;
@@ -134,7 +138,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
134
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  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
135
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  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
136
140
  } & {
137
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
141
+ 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[];
140
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  geneticCodes: Record<string, number>;
@@ -165,24 +169,25 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
165
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  getCanonicalRefName2(refName: string): string;
166
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  isValidRefName(refName: string): boolean;
167
171
  } & {
172
+ isCircularRefName(refName: string): boolean;
168
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  getRefNamePosition(refName: string): number | undefined;
169
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  getAliasesForRefName(refName: string): string[];
170
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  getRefNameMapForAdapter(adapterConf: {
171
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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>;
177
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
173
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  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
174
179
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
175
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  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
176
181
  }, {
177
182
  error: unknown;
178
183
  loadingP: Promise<void> | undefined;
179
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
184
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
180
185
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
181
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
186
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
182
187
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
183
188
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
184
189
  loadedGeneticCodes: Record<string, number> | undefined;
185
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
190
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
186
191
  statusMessage: string | undefined;
187
192
  statusProgress: number | undefined;
188
193
  statusSource: string | undefined;
@@ -201,7 +206,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
201
206
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
202
207
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
203
208
  } & {
204
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
209
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
205
210
  regions: import("@jbrowse/core/util").Region[];
206
211
  cytobands: import("@jbrowse/core/util").Feature[];
207
212
  geneticCodes: Record<string, number>;
@@ -232,11 +237,12 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
232
237
  getCanonicalRefName2(refName: string): string;
233
238
  isValidRefName(refName: string): boolean;
234
239
  } & {
240
+ isCircularRefName(refName: string): boolean;
235
241
  getRefNamePosition(refName: string): number | undefined;
236
242
  getAliasesForRefName(refName: string): string[];
237
243
  getRefNameMapForAdapter(adapterConf: {
238
244
  [x: string]: unknown;
239
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
245
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
240
246
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
241
247
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
242
248
  has(asmName: string): boolean;
@@ -245,13 +251,13 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
245
251
  }> & {
246
252
  error: unknown;
247
253
  loadingP: Promise<void> | undefined;
248
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
254
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
249
255
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
250
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
256
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
251
257
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
252
258
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
253
259
  loadedGeneticCodes: Record<string, number> | undefined;
254
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
260
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
255
261
  statusMessage: string | undefined;
256
262
  statusProgress: number | undefined;
257
263
  statusSource: string | undefined;
@@ -270,7 +276,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
270
276
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
271
277
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
272
278
  } & {
273
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
279
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
274
280
  regions: import("@jbrowse/core/util").Region[];
275
281
  cytobands: import("@jbrowse/core/util").Feature[];
276
282
  geneticCodes: Record<string, number>;
@@ -301,24 +307,25 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
301
307
  getCanonicalRefName2(refName: string): string;
302
308
  isValidRefName(refName: string): boolean;
303
309
  } & {
310
+ isCircularRefName(refName: string): boolean;
304
311
  getRefNamePosition(refName: string): number | undefined;
305
312
  getAliasesForRefName(refName: string): string[];
306
313
  getRefNameMapForAdapter(adapterConf: {
307
314
  [x: string]: unknown;
308
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
315
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
309
316
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
310
317
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
311
318
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
312
319
  }, {
313
320
  error: unknown;
314
321
  loadingP: Promise<void> | undefined;
315
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
322
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
316
323
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
317
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
324
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
318
325
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
319
326
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
320
327
  loadedGeneticCodes: Record<string, number> | undefined;
321
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
328
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
322
329
  statusMessage: string | undefined;
323
330
  statusProgress: number | undefined;
324
331
  statusSource: string | undefined;
@@ -337,7 +344,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
337
344
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
338
345
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
339
346
  } & {
340
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
347
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
341
348
  regions: import("@jbrowse/core/util").Region[];
342
349
  cytobands: import("@jbrowse/core/util").Feature[];
343
350
  geneticCodes: Record<string, number>;
@@ -368,11 +375,12 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
368
375
  getCanonicalRefName2(refName: string): string;
369
376
  isValidRefName(refName: string): boolean;
370
377
  } & {
378
+ isCircularRefName(refName: string): boolean;
371
379
  getRefNamePosition(refName: string): number | undefined;
372
380
  getAliasesForRefName(refName: string): string[];
373
381
  getRefNameMapForAdapter(adapterConf: {
374
382
  [x: string]: unknown;
375
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
383
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
376
384
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
377
385
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
378
386
  readonly assemblyNamesList: string[];
@@ -387,13 +395,13 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
387
395
  }> & {
388
396
  error: unknown;
389
397
  loadingP: Promise<void> | undefined;
390
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
398
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
391
399
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
392
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
400
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
393
401
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
394
402
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
395
403
  loadedGeneticCodes: Record<string, number> | undefined;
396
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
404
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
397
405
  statusMessage: string | undefined;
398
406
  statusProgress: number | undefined;
399
407
  statusSource: string | undefined;
@@ -412,7 +420,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
412
420
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
413
421
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
414
422
  } & {
415
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
423
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
416
424
  regions: import("@jbrowse/core/util").Region[];
417
425
  cytobands: import("@jbrowse/core/util").Feature[];
418
426
  geneticCodes: Record<string, number>;
@@ -443,24 +451,25 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
443
451
  getCanonicalRefName2(refName: string): string;
444
452
  isValidRefName(refName: string): boolean;
445
453
  } & {
454
+ isCircularRefName(refName: string): boolean;
446
455
  getRefNamePosition(refName: string): number | undefined;
447
456
  getAliasesForRefName(refName: string): string[];
448
457
  getRefNameMapForAdapter(adapterConf: {
449
458
  [x: string]: unknown;
450
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
459
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
451
460
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
452
461
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
453
462
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
454
463
  }, {
455
464
  error: unknown;
456
465
  loadingP: Promise<void> | undefined;
457
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
466
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
458
467
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
459
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
468
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
460
469
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
461
470
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
462
471
  loadedGeneticCodes: Record<string, number> | undefined;
463
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
472
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
464
473
  statusMessage: string | undefined;
465
474
  statusProgress: number | undefined;
466
475
  statusSource: string | undefined;
@@ -479,7 +488,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
479
488
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
480
489
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
481
490
  } & {
482
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
491
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
483
492
  regions: import("@jbrowse/core/util").Region[];
484
493
  cytobands: import("@jbrowse/core/util").Feature[];
485
494
  geneticCodes: Record<string, number>;
@@ -510,11 +519,12 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
510
519
  getCanonicalRefName2(refName: string): string;
511
520
  isValidRefName(refName: string): boolean;
512
521
  } & {
522
+ isCircularRefName(refName: string): boolean;
513
523
  getRefNamePosition(refName: string): number | undefined;
514
524
  getAliasesForRefName(refName: string): string[];
515
525
  getRefNameMapForAdapter(adapterConf: {
516
526
  [x: string]: unknown;
517
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
527
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
518
528
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
519
529
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
520
530
  requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
@@ -522,13 +532,13 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
522
532
  }> & {
523
533
  error: unknown;
524
534
  loadingP: Promise<void> | undefined;
525
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
535
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
526
536
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
527
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
537
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
528
538
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
529
539
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
530
540
  loadedGeneticCodes: Record<string, number> | undefined;
531
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
541
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
532
542
  statusMessage: string | undefined;
533
543
  statusProgress: number | undefined;
534
544
  statusSource: string | undefined;
@@ -547,7 +557,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
547
557
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
548
558
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
549
559
  } & {
550
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
560
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
551
561
  regions: import("@jbrowse/core/util").Region[];
552
562
  cytobands: import("@jbrowse/core/util").Feature[];
553
563
  geneticCodes: Record<string, number>;
@@ -578,24 +588,25 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
578
588
  getCanonicalRefName2(refName: string): string;
579
589
  isValidRefName(refName: string): boolean;
580
590
  } & {
591
+ isCircularRefName(refName: string): boolean;
581
592
  getRefNamePosition(refName: string): number | undefined;
582
593
  getAliasesForRefName(refName: string): string[];
583
594
  getRefNameMapForAdapter(adapterConf: {
584
595
  [x: string]: unknown;
585
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
596
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
586
597
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
587
598
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
588
599
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
589
600
  }, {
590
601
  error: unknown;
591
602
  loadingP: Promise<void> | undefined;
592
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
603
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
593
604
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
594
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
605
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
595
606
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
596
607
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
597
608
  loadedGeneticCodes: Record<string, number> | undefined;
598
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
609
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
599
610
  statusMessage: string | undefined;
600
611
  statusProgress: number | undefined;
601
612
  statusSource: string | undefined;
@@ -614,7 +625,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
614
625
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
615
626
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
616
627
  } & {
617
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
628
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
618
629
  regions: import("@jbrowse/core/util").Region[];
619
630
  cytobands: import("@jbrowse/core/util").Feature[];
620
631
  geneticCodes: Record<string, number>;
@@ -645,16 +656,17 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
645
656
  getCanonicalRefName2(refName: string): string;
646
657
  isValidRefName(refName: string): boolean;
647
658
  } & {
659
+ isCircularRefName(refName: string): boolean;
648
660
  getRefNamePosition(refName: string): number | undefined;
649
661
  getAliasesForRefName(refName: string): string[];
650
662
  getRefNameMapForAdapter(adapterConf: {
651
663
  [x: string]: unknown;
652
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
664
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
653
665
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
654
666
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
655
667
  getRefNameMapForAdapter(adapterConf: {
656
668
  [x: string]: unknown;
657
- }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
669
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
658
670
  isValidRefName(refName: string, assemblyName: string): boolean;
659
671
  } & {
660
672
  afterAttach(): void;
@@ -667,8 +679,11 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
667
679
  error: unknown;
668
680
  textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
669
681
  pluginManager: PluginManager;
682
+ detachDisposers: (() => void)[];
670
683
  } & {
671
684
  setError(error: unknown): void;
685
+ addDetachDisposer(disposer: () => void): void;
686
+ detach(): void;
672
687
  setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
673
688
  setDefaultSession(): void;
674
689
  setSessionPath(path: string): void;
@@ -683,13 +698,13 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
683
698
  }, {
684
699
  error: unknown;
685
700
  loadingP: Promise<void> | undefined;
686
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
701
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
687
702
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
688
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
703
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
689
704
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
690
705
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
691
706
  loadedGeneticCodes: Record<string, number> | undefined;
692
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
707
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
693
708
  statusMessage: string | undefined;
694
709
  statusProgress: number | undefined;
695
710
  statusSource: string | undefined;
@@ -708,7 +723,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
708
723
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
709
724
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
710
725
  } & {
711
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
726
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
712
727
  regions: import("@jbrowse/core/util").Region[];
713
728
  cytobands: import("@jbrowse/core/util").Feature[];
714
729
  geneticCodes: Record<string, number>;
@@ -739,11 +754,12 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
739
754
  getCanonicalRefName2(refName: string): string;
740
755
  isValidRefName(refName: string): boolean;
741
756
  } & {
757
+ isCircularRefName(refName: string): boolean;
742
758
  getRefNamePosition(refName: string): number | undefined;
743
759
  getAliasesForRefName(refName: string): string[];
744
760
  getRefNameMapForAdapter(adapterConf: {
745
761
  [x: string]: unknown;
746
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
762
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
747
763
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
748
764
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
749
765
  }, {
@@ -764,13 +780,13 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
764
780
  }> & {
765
781
  error: unknown;
766
782
  loadingP: Promise<void> | undefined;
767
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
783
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
768
784
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
769
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
785
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
770
786
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
771
787
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
772
788
  loadedGeneticCodes: Record<string, number> | undefined;
773
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
789
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
774
790
  statusMessage: string | undefined;
775
791
  statusProgress: number | undefined;
776
792
  statusSource: string | undefined;
@@ -789,7 +805,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
789
805
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
790
806
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
791
807
  } & {
792
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
808
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
793
809
  regions: import("@jbrowse/core/util").Region[];
794
810
  cytobands: import("@jbrowse/core/util").Feature[];
795
811
  geneticCodes: Record<string, number>;
@@ -820,24 +836,25 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
820
836
  getCanonicalRefName2(refName: string): string;
821
837
  isValidRefName(refName: string): boolean;
822
838
  } & {
839
+ isCircularRefName(refName: string): boolean;
823
840
  getRefNamePosition(refName: string): number | undefined;
824
841
  getAliasesForRefName(refName: string): string[];
825
842
  getRefNameMapForAdapter(adapterConf: {
826
843
  [x: string]: unknown;
827
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
844
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
828
845
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
829
846
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
830
847
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
831
848
  }, {
832
849
  error: unknown;
833
850
  loadingP: Promise<void> | undefined;
834
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
851
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
835
852
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
836
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
853
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
837
854
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
838
855
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
839
856
  loadedGeneticCodes: Record<string, number> | undefined;
840
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
857
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
841
858
  statusMessage: string | undefined;
842
859
  statusProgress: number | undefined;
843
860
  statusSource: string | undefined;
@@ -856,7 +873,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
856
873
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
857
874
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
858
875
  } & {
859
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
876
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
860
877
  regions: import("@jbrowse/core/util").Region[];
861
878
  cytobands: import("@jbrowse/core/util").Feature[];
862
879
  geneticCodes: Record<string, number>;
@@ -887,11 +904,12 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
887
904
  getCanonicalRefName2(refName: string): string;
888
905
  isValidRefName(refName: string): boolean;
889
906
  } & {
907
+ isCircularRefName(refName: string): boolean;
890
908
  getRefNamePosition(refName: string): number | undefined;
891
909
  getAliasesForRefName(refName: string): string[];
892
910
  getRefNameMapForAdapter(adapterConf: {
893
911
  [x: string]: unknown;
894
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
912
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
895
913
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
896
914
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
897
915
  has(asmName: string): boolean;
@@ -900,13 +918,13 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
900
918
  }> & {
901
919
  error: unknown;
902
920
  loadingP: Promise<void> | undefined;
903
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
921
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
904
922
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
905
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
923
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
906
924
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
907
925
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
908
926
  loadedGeneticCodes: Record<string, number> | undefined;
909
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
927
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
910
928
  statusMessage: string | undefined;
911
929
  statusProgress: number | undefined;
912
930
  statusSource: string | undefined;
@@ -925,7 +943,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
925
943
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
926
944
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
927
945
  } & {
928
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
946
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
929
947
  regions: import("@jbrowse/core/util").Region[];
930
948
  cytobands: import("@jbrowse/core/util").Feature[];
931
949
  geneticCodes: Record<string, number>;
@@ -956,24 +974,25 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
956
974
  getCanonicalRefName2(refName: string): string;
957
975
  isValidRefName(refName: string): boolean;
958
976
  } & {
977
+ isCircularRefName(refName: string): boolean;
959
978
  getRefNamePosition(refName: string): number | undefined;
960
979
  getAliasesForRefName(refName: string): string[];
961
980
  getRefNameMapForAdapter(adapterConf: {
962
981
  [x: string]: unknown;
963
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
982
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
964
983
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
965
984
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
966
985
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
967
986
  }, {
968
987
  error: unknown;
969
988
  loadingP: Promise<void> | undefined;
970
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
989
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
971
990
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
972
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
991
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
973
992
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
974
993
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
975
994
  loadedGeneticCodes: Record<string, number> | undefined;
976
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
995
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
977
996
  statusMessage: string | undefined;
978
997
  statusProgress: number | undefined;
979
998
  statusSource: string | undefined;
@@ -992,7 +1011,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
992
1011
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
993
1012
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
994
1013
  } & {
995
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1014
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
996
1015
  regions: import("@jbrowse/core/util").Region[];
997
1016
  cytobands: import("@jbrowse/core/util").Feature[];
998
1017
  geneticCodes: Record<string, number>;
@@ -1023,11 +1042,12 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
1023
1042
  getCanonicalRefName2(refName: string): string;
1024
1043
  isValidRefName(refName: string): boolean;
1025
1044
  } & {
1045
+ isCircularRefName(refName: string): boolean;
1026
1046
  getRefNamePosition(refName: string): number | undefined;
1027
1047
  getAliasesForRefName(refName: string): string[];
1028
1048
  getRefNameMapForAdapter(adapterConf: {
1029
1049
  [x: string]: unknown;
1030
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1050
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1031
1051
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1032
1052
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1033
1053
  readonly assemblyNamesList: string[];
@@ -1042,13 +1062,13 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
1042
1062
  }> & {
1043
1063
  error: unknown;
1044
1064
  loadingP: Promise<void> | undefined;
1045
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1065
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1046
1066
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1047
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1067
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1048
1068
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1049
1069
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1050
1070
  loadedGeneticCodes: Record<string, number> | undefined;
1051
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1071
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1052
1072
  statusMessage: string | undefined;
1053
1073
  statusProgress: number | undefined;
1054
1074
  statusSource: string | undefined;
@@ -1067,7 +1087,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
1067
1087
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1068
1088
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1069
1089
  } & {
1070
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1090
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1071
1091
  regions: import("@jbrowse/core/util").Region[];
1072
1092
  cytobands: import("@jbrowse/core/util").Feature[];
1073
1093
  geneticCodes: Record<string, number>;
@@ -1098,24 +1118,25 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
1098
1118
  getCanonicalRefName2(refName: string): string;
1099
1119
  isValidRefName(refName: string): boolean;
1100
1120
  } & {
1121
+ isCircularRefName(refName: string): boolean;
1101
1122
  getRefNamePosition(refName: string): number | undefined;
1102
1123
  getAliasesForRefName(refName: string): string[];
1103
1124
  getRefNameMapForAdapter(adapterConf: {
1104
1125
  [x: string]: unknown;
1105
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1126
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1106
1127
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1107
1128
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1108
1129
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1109
1130
  }, {
1110
1131
  error: unknown;
1111
1132
  loadingP: Promise<void> | undefined;
1112
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1133
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1113
1134
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1114
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1135
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1115
1136
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1116
1137
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1117
1138
  loadedGeneticCodes: Record<string, number> | undefined;
1118
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1139
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1119
1140
  statusMessage: string | undefined;
1120
1141
  statusProgress: number | undefined;
1121
1142
  statusSource: string | undefined;
@@ -1134,7 +1155,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
1134
1155
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1135
1156
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1136
1157
  } & {
1137
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1158
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1138
1159
  regions: import("@jbrowse/core/util").Region[];
1139
1160
  cytobands: import("@jbrowse/core/util").Feature[];
1140
1161
  geneticCodes: Record<string, number>;
@@ -1165,11 +1186,12 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
1165
1186
  getCanonicalRefName2(refName: string): string;
1166
1187
  isValidRefName(refName: string): boolean;
1167
1188
  } & {
1189
+ isCircularRefName(refName: string): boolean;
1168
1190
  getRefNamePosition(refName: string): number | undefined;
1169
1191
  getAliasesForRefName(refName: string): string[];
1170
1192
  getRefNameMapForAdapter(adapterConf: {
1171
1193
  [x: string]: unknown;
1172
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1194
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1173
1195
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1174
1196
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
1175
1197
  requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
@@ -1177,13 +1199,13 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
1177
1199
  }> & {
1178
1200
  error: unknown;
1179
1201
  loadingP: Promise<void> | undefined;
1180
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1202
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1181
1203
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1182
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1204
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1183
1205
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1184
1206
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1185
1207
  loadedGeneticCodes: Record<string, number> | undefined;
1186
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1208
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1187
1209
  statusMessage: string | undefined;
1188
1210
  statusProgress: number | undefined;
1189
1211
  statusSource: string | undefined;
@@ -1202,7 +1224,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
1202
1224
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1203
1225
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1204
1226
  } & {
1205
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1227
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1206
1228
  regions: import("@jbrowse/core/util").Region[];
1207
1229
  cytobands: import("@jbrowse/core/util").Feature[];
1208
1230
  geneticCodes: Record<string, number>;
@@ -1233,24 +1255,25 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
1233
1255
  getCanonicalRefName2(refName: string): string;
1234
1256
  isValidRefName(refName: string): boolean;
1235
1257
  } & {
1258
+ isCircularRefName(refName: string): boolean;
1236
1259
  getRefNamePosition(refName: string): number | undefined;
1237
1260
  getAliasesForRefName(refName: string): string[];
1238
1261
  getRefNameMapForAdapter(adapterConf: {
1239
1262
  [x: string]: unknown;
1240
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1263
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1241
1264
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1242
1265
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1243
1266
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1244
1267
  }, {
1245
1268
  error: unknown;
1246
1269
  loadingP: Promise<void> | undefined;
1247
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1270
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1248
1271
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1249
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1272
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1250
1273
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1251
1274
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1252
1275
  loadedGeneticCodes: Record<string, number> | undefined;
1253
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1276
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1254
1277
  statusMessage: string | undefined;
1255
1278
  statusProgress: number | undefined;
1256
1279
  statusSource: string | undefined;
@@ -1269,7 +1292,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
1269
1292
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1270
1293
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1271
1294
  } & {
1272
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1295
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1273
1296
  regions: import("@jbrowse/core/util").Region[];
1274
1297
  cytobands: import("@jbrowse/core/util").Feature[];
1275
1298
  geneticCodes: Record<string, number>;
@@ -1300,16 +1323,17 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
1300
1323
  getCanonicalRefName2(refName: string): string;
1301
1324
  isValidRefName(refName: string): boolean;
1302
1325
  } & {
1326
+ isCircularRefName(refName: string): boolean;
1303
1327
  getRefNamePosition(refName: string): number | undefined;
1304
1328
  getAliasesForRefName(refName: string): string[];
1305
1329
  getRefNameMapForAdapter(adapterConf: {
1306
1330
  [x: string]: unknown;
1307
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1331
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1308
1332
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1309
1333
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
1310
1334
  getRefNameMapForAdapter(adapterConf: {
1311
1335
  [x: string]: unknown;
1312
- }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1336
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1313
1337
  isValidRefName(refName: string, assemblyName: string): boolean;
1314
1338
  } & {
1315
1339
  afterAttach(): void;
@@ -1322,8 +1346,11 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
1322
1346
  error: unknown;
1323
1347
  textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1324
1348
  pluginManager: PluginManager;
1349
+ detachDisposers: (() => void)[];
1325
1350
  } & {
1326
1351
  setError(error: unknown): void;
1352
+ addDetachDisposer(disposer: () => void): void;
1353
+ detach(): void;
1327
1354
  setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
1328
1355
  setDefaultSession(): void;
1329
1356
  setSessionPath(path: string): void;
@@ -1365,7 +1392,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
1365
1392
  setName(str: string): void;
1366
1393
  setFocusedViewId(viewId: string | undefined): void;
1367
1394
  removeActiveDialog(): void;
1368
- queueDialog(doneCallback: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
1395
+ queueDialog<T extends import("@jbrowse/core/util").DialogComponentType>(callback: (doneCallback: () => void) => [T, import("react").ComponentProps<T>]): void;
1369
1396
  removeDialog(entry: [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
1370
1397
  } & {
1371
1398
  snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;