@jbrowse/app-core 5.0.0-beta.11 → 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 (78) hide show
  1. package/esm/AppSession/AppSessionMixin.d.ts +110 -92
  2. package/esm/Assemblies/AssembliesMixin.d.ts +30 -0
  3. package/esm/HistoryManagement/index.d.ts +2 -0
  4. package/esm/HistoryManagement/index.js +2 -0
  5. package/esm/JBrowseConfig/RootConfiguration.d.ts +4 -10
  6. package/esm/JBrowseConfig/RootConfiguration.js +5 -8
  7. package/esm/JBrowseConfig/index.d.ts +3 -11
  8. package/esm/JBrowseConfig/index.js +2 -3
  9. package/esm/JBrowseModel/index.d.ts +10 -9
  10. package/esm/JBrowseModel/index.js +8 -7
  11. package/esm/JbApi/jbApi.d.ts +2 -2
  12. package/esm/JbApi/jbApi.js +16 -11
  13. package/esm/RootMenu/index.d.ts +2 -0
  14. package/esm/RootMenu/index.js +2 -0
  15. package/esm/SessionSpec/index.d.ts +2 -2
  16. package/esm/SessionSpec/index.js +1 -1
  17. package/esm/SessionSpec/loadSessionSpec.js +2 -12
  18. package/esm/SessionSpec/parseSessionSpecUrl.d.ts +19 -0
  19. package/esm/SessionSpec/parseSessionSpecUrl.js +29 -0
  20. package/esm/WorkspaceLayout/LayoutRenderer.d.ts +0 -10
  21. package/esm/WorkspaceLayout/LayoutRenderer.js +34 -101
  22. package/esm/WorkspaceLayout/PanelView.js +19 -45
  23. package/esm/WorkspaceLayout/TabStrip.d.ts +2 -2
  24. package/esm/WorkspaceLayout/TabStrip.js +36 -104
  25. package/esm/WorkspaceLayout/WorkspaceContainer.d.ts +0 -9
  26. package/esm/WorkspaceLayout/WorkspaceContainer.js +9 -42
  27. package/esm/WorkspaceLayout/WorkspacePanelActions.d.ts +1 -16
  28. package/esm/WorkspaceLayout/WorkspacePanelActions.js +46 -51
  29. package/esm/WorkspaceLayout/WorkspaceTab.d.ts +3 -19
  30. package/esm/WorkspaceLayout/WorkspaceTab.js +12 -48
  31. package/esm/WorkspaceLayout/dropZone.d.ts +7 -37
  32. package/esm/WorkspaceLayout/dropZone.js +7 -44
  33. package/esm/WorkspaceLayout/model.d.ts +45 -120
  34. package/esm/WorkspaceLayout/model.js +145 -303
  35. package/esm/WorkspaceLayout/panelChrome.d.ts +4 -7
  36. package/esm/WorkspaceLayout/panelChrome.js +0 -2
  37. package/esm/WorkspaceLayout/spec.d.ts +10 -51
  38. package/esm/WorkspaceLayout/spec.js +12 -80
  39. package/esm/WorkspaceLayout/splitter.d.ts +3 -19
  40. package/esm/WorkspaceLayout/splitter.js +5 -21
  41. package/esm/WorkspaceLayout/tabName.d.ts +8 -0
  42. package/esm/WorkspaceLayout/tabName.js +14 -0
  43. package/esm/WorkspaceLayout/tree.d.ts +19 -79
  44. package/esm/WorkspaceLayout/tree.js +34 -131
  45. package/esm/WorkspaceLayout/useLayoutDrag.d.ts +4 -22
  46. package/esm/WorkspaceLayout/useLayoutDrag.js +55 -177
  47. package/esm/WorkspaceLayout/usePointerGesture.d.ts +24 -0
  48. package/esm/WorkspaceLayout/usePointerGesture.js +83 -0
  49. package/esm/WorkspaceLayout/workspaceTheme.d.ts +27 -0
  50. package/esm/WorkspaceLayout/workspaceTheme.js +37 -0
  51. package/esm/index.d.ts +5 -3
  52. package/esm/index.js +3 -2
  53. package/esm/queryParams.d.ts +2 -0
  54. package/esm/queryParams.js +16 -5
  55. package/esm/sessionSummary.d.ts +16 -0
  56. package/esm/sessionSummary.js +57 -0
  57. package/esm/ui/App/App.js +3 -0
  58. package/esm/ui/App/DrawerHeaderHelpDialog.d.ts +3 -2
  59. package/esm/ui/App/DrawerHeaderHelpDialog.js +4 -2
  60. package/esm/ui/App/JBrowseTabMenu.d.ts +3 -2
  61. package/esm/ui/App/JBrowseTabMenu.js +5 -3
  62. package/esm/ui/App/ThemeModeButton.d.ts +4 -5
  63. package/esm/ui/App/ThemeModeButton.js +22 -14
  64. package/esm/ui/App/ViewContainer.js +7 -1
  65. package/esm/ui/App/ViewMenu.js +69 -42
  66. package/esm/ui/App/ViewWrapper.js +2 -2
  67. package/esm/ui/App/ViewsContainer.js +3 -4
  68. package/esm/ui/App/lazyParts.d.ts +0 -5
  69. package/esm/ui/App/lazyParts.js +0 -1
  70. package/esm/ui/App/preloadAppShell.js +3 -6
  71. package/esm/ui/App/types.d.ts +3 -2
  72. package/esm/ui/App/viewTitle.d.ts +6 -1
  73. package/esm/ui/App/viewTitle.js +7 -2
  74. package/package.json +7 -7
  75. package/esm/WorkspaceLayout/dockviewTheme.d.ts +0 -69
  76. package/esm/WorkspaceLayout/dockviewTheme.js +0 -82
  77. package/esm/ui/App/ClassicViewsContainer.d.ts +0 -6
  78. package/esm/ui/App/ClassicViewsContainer.js +0 -22
package/esm/AppSession/AppSessionMixin.d.ts CHANGED
@@ -41,13 +41,13 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
41
41
  }, {
42
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  error: unknown;
43
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  loadingP: Promise<void> | undefined;
44
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
44
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
45
45
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
46
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
46
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
47
47
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
48
48
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
49
49
  loadedGeneticCodes: Record<string, number> | undefined;
50
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
50
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
51
51
  statusMessage: string | undefined;
52
52
  statusProgress: number | undefined;
53
53
  statusSource: string | undefined;
@@ -66,7 +66,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
66
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  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
67
67
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
68
68
  } & {
69
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
69
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
70
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  regions: import("@jbrowse/core/util").Region[];
71
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  cytobands: import("@jbrowse/core/util").Feature[];
72
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  geneticCodes: Record<string, number>;
@@ -97,11 +97,12 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
97
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  getCanonicalRefName2(refName: string): string;
98
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  isValidRefName(refName: string): boolean;
99
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  } & {
100
+ isCircularRefName(refName: string): boolean;
100
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  getRefNamePosition(refName: string): number | undefined;
101
102
  getAliasesForRefName(refName: string): string[];
102
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  getRefNameMapForAdapter(adapterConf: {
103
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  [x: string]: unknown;
104
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
105
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
105
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  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
106
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
107
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  }> & {
@@ -122,13 +123,13 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
122
123
  }> & {
123
124
  error: unknown;
124
125
  loadingP: Promise<void> | undefined;
125
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
126
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
126
127
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
127
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
128
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
128
129
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
129
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  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
130
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  loadedGeneticCodes: Record<string, number> | undefined;
131
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
132
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
132
133
  statusMessage: string | undefined;
133
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  statusProgress: number | undefined;
134
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  statusSource: string | undefined;
@@ -147,7 +148,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
147
148
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
148
149
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
149
150
  } & {
150
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
151
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
151
152
  regions: import("@jbrowse/core/util").Region[];
152
153
  cytobands: import("@jbrowse/core/util").Feature[];
153
154
  geneticCodes: Record<string, number>;
@@ -178,24 +179,25 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
178
179
  getCanonicalRefName2(refName: string): string;
179
180
  isValidRefName(refName: string): boolean;
180
181
  } & {
182
+ isCircularRefName(refName: string): boolean;
181
183
  getRefNamePosition(refName: string): number | undefined;
182
184
  getAliasesForRefName(refName: string): string[];
183
185
  getRefNameMapForAdapter(adapterConf: {
184
186
  [x: string]: unknown;
185
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
187
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
186
188
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
187
189
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
188
190
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
189
191
  }, {
190
192
  error: unknown;
191
193
  loadingP: Promise<void> | undefined;
192
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
194
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
193
195
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
194
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
196
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
195
197
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
196
198
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
197
199
  loadedGeneticCodes: Record<string, number> | undefined;
198
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
200
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
199
201
  statusMessage: string | undefined;
200
202
  statusProgress: number | undefined;
201
203
  statusSource: string | undefined;
@@ -214,7 +216,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
214
216
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
215
217
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
216
218
  } & {
217
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
219
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
218
220
  regions: import("@jbrowse/core/util").Region[];
219
221
  cytobands: import("@jbrowse/core/util").Feature[];
220
222
  geneticCodes: Record<string, number>;
@@ -245,11 +247,12 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
245
247
  getCanonicalRefName2(refName: string): string;
246
248
  isValidRefName(refName: string): boolean;
247
249
  } & {
250
+ isCircularRefName(refName: string): boolean;
248
251
  getRefNamePosition(refName: string): number | undefined;
249
252
  getAliasesForRefName(refName: string): string[];
250
253
  getRefNameMapForAdapter(adapterConf: {
251
254
  [x: string]: unknown;
252
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
255
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
253
256
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
254
257
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
255
258
  has(asmName: string): boolean;
@@ -258,13 +261,13 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
258
261
  }> & {
259
262
  error: unknown;
260
263
  loadingP: Promise<void> | undefined;
261
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
264
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
262
265
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
263
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
266
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
264
267
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
265
268
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
266
269
  loadedGeneticCodes: Record<string, number> | undefined;
267
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
270
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
268
271
  statusMessage: string | undefined;
269
272
  statusProgress: number | undefined;
270
273
  statusSource: string | undefined;
@@ -283,7 +286,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
283
286
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
284
287
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
285
288
  } & {
286
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
289
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
287
290
  regions: import("@jbrowse/core/util").Region[];
288
291
  cytobands: import("@jbrowse/core/util").Feature[];
289
292
  geneticCodes: Record<string, number>;
@@ -314,24 +317,25 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
314
317
  getCanonicalRefName2(refName: string): string;
315
318
  isValidRefName(refName: string): boolean;
316
319
  } & {
320
+ isCircularRefName(refName: string): boolean;
317
321
  getRefNamePosition(refName: string): number | undefined;
318
322
  getAliasesForRefName(refName: string): string[];
319
323
  getRefNameMapForAdapter(adapterConf: {
320
324
  [x: string]: unknown;
321
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
325
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
322
326
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
323
327
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
324
328
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
325
329
  }, {
326
330
  error: unknown;
327
331
  loadingP: Promise<void> | undefined;
328
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
332
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
329
333
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
330
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
334
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
331
335
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
332
336
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
333
337
  loadedGeneticCodes: Record<string, number> | undefined;
334
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
338
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
335
339
  statusMessage: string | undefined;
336
340
  statusProgress: number | undefined;
337
341
  statusSource: string | undefined;
@@ -350,7 +354,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
350
354
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
351
355
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
352
356
  } & {
353
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
357
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
354
358
  regions: import("@jbrowse/core/util").Region[];
355
359
  cytobands: import("@jbrowse/core/util").Feature[];
356
360
  geneticCodes: Record<string, number>;
@@ -381,11 +385,12 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
381
385
  getCanonicalRefName2(refName: string): string;
382
386
  isValidRefName(refName: string): boolean;
383
387
  } & {
388
+ isCircularRefName(refName: string): boolean;
384
389
  getRefNamePosition(refName: string): number | undefined;
385
390
  getAliasesForRefName(refName: string): string[];
386
391
  getRefNameMapForAdapter(adapterConf: {
387
392
  [x: string]: unknown;
388
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
393
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
389
394
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
390
395
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
391
396
  readonly assemblyNamesList: string[];
@@ -400,13 +405,13 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
400
405
  }> & {
401
406
  error: unknown;
402
407
  loadingP: Promise<void> | undefined;
403
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
408
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
404
409
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
405
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
410
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
406
411
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
407
412
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
408
413
  loadedGeneticCodes: Record<string, number> | undefined;
409
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
414
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
410
415
  statusMessage: string | undefined;
411
416
  statusProgress: number | undefined;
412
417
  statusSource: string | undefined;
@@ -425,7 +430,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
425
430
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
426
431
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
427
432
  } & {
428
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
433
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
429
434
  regions: import("@jbrowse/core/util").Region[];
430
435
  cytobands: import("@jbrowse/core/util").Feature[];
431
436
  geneticCodes: Record<string, number>;
@@ -456,24 +461,25 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
456
461
  getCanonicalRefName2(refName: string): string;
457
462
  isValidRefName(refName: string): boolean;
458
463
  } & {
464
+ isCircularRefName(refName: string): boolean;
459
465
  getRefNamePosition(refName: string): number | undefined;
460
466
  getAliasesForRefName(refName: string): string[];
461
467
  getRefNameMapForAdapter(adapterConf: {
462
468
  [x: string]: unknown;
463
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
469
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
464
470
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
465
471
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
466
472
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
467
473
  }, {
468
474
  error: unknown;
469
475
  loadingP: Promise<void> | undefined;
470
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
476
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
471
477
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
472
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
478
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
473
479
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
474
480
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
475
481
  loadedGeneticCodes: Record<string, number> | undefined;
476
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
482
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
477
483
  statusMessage: string | undefined;
478
484
  statusProgress: number | undefined;
479
485
  statusSource: string | undefined;
@@ -492,7 +498,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
492
498
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
493
499
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
494
500
  } & {
495
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
501
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
496
502
  regions: import("@jbrowse/core/util").Region[];
497
503
  cytobands: import("@jbrowse/core/util").Feature[];
498
504
  geneticCodes: Record<string, number>;
@@ -523,11 +529,12 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
523
529
  getCanonicalRefName2(refName: string): string;
524
530
  isValidRefName(refName: string): boolean;
525
531
  } & {
532
+ isCircularRefName(refName: string): boolean;
526
533
  getRefNamePosition(refName: string): number | undefined;
527
534
  getAliasesForRefName(refName: string): string[];
528
535
  getRefNameMapForAdapter(adapterConf: {
529
536
  [x: string]: unknown;
530
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
537
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
531
538
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
532
539
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
533
540
  requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
@@ -535,13 +542,13 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
535
542
  }> & {
536
543
  error: unknown;
537
544
  loadingP: Promise<void> | undefined;
538
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
545
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
539
546
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
540
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
547
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
541
548
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
542
549
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
543
550
  loadedGeneticCodes: Record<string, number> | undefined;
544
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
551
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
545
552
  statusMessage: string | undefined;
546
553
  statusProgress: number | undefined;
547
554
  statusSource: string | undefined;
@@ -560,7 +567,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
560
567
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
561
568
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
562
569
  } & {
563
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
570
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
564
571
  regions: import("@jbrowse/core/util").Region[];
565
572
  cytobands: import("@jbrowse/core/util").Feature[];
566
573
  geneticCodes: Record<string, number>;
@@ -591,24 +598,25 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
591
598
  getCanonicalRefName2(refName: string): string;
592
599
  isValidRefName(refName: string): boolean;
593
600
  } & {
601
+ isCircularRefName(refName: string): boolean;
594
602
  getRefNamePosition(refName: string): number | undefined;
595
603
  getAliasesForRefName(refName: string): string[];
596
604
  getRefNameMapForAdapter(adapterConf: {
597
605
  [x: string]: unknown;
598
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
606
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
599
607
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
600
608
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
601
609
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
602
610
  }, {
603
611
  error: unknown;
604
612
  loadingP: Promise<void> | undefined;
605
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
613
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
606
614
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
607
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
615
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
608
616
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
609
617
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
610
618
  loadedGeneticCodes: Record<string, number> | undefined;
611
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
619
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
612
620
  statusMessage: string | undefined;
613
621
  statusProgress: number | undefined;
614
622
  statusSource: string | undefined;
@@ -627,7 +635,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
627
635
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
628
636
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
629
637
  } & {
630
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
638
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
631
639
  regions: import("@jbrowse/core/util").Region[];
632
640
  cytobands: import("@jbrowse/core/util").Feature[];
633
641
  geneticCodes: Record<string, number>;
@@ -658,16 +666,17 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
658
666
  getCanonicalRefName2(refName: string): string;
659
667
  isValidRefName(refName: string): boolean;
660
668
  } & {
669
+ isCircularRefName(refName: string): boolean;
661
670
  getRefNamePosition(refName: string): number | undefined;
662
671
  getAliasesForRefName(refName: string): string[];
663
672
  getRefNameMapForAdapter(adapterConf: {
664
673
  [x: string]: unknown;
665
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
674
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
666
675
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
667
676
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
668
677
  getRefNameMapForAdapter(adapterConf: {
669
678
  [x: string]: unknown;
670
- }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
679
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
671
680
  isValidRefName(refName: string, assemblyName: string): boolean;
672
681
  } & {
673
682
  afterAttach(): void;
@@ -679,13 +688,13 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
679
688
  }, {
680
689
  error: unknown;
681
690
  loadingP: Promise<void> | undefined;
682
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
691
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
683
692
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
684
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
693
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
685
694
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
686
695
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
687
696
  loadedGeneticCodes: Record<string, number> | undefined;
688
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
697
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
689
698
  statusMessage: string | undefined;
690
699
  statusProgress: number | undefined;
691
700
  statusSource: string | undefined;
@@ -704,7 +713,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
704
713
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
705
714
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
706
715
  } & {
707
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
716
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
708
717
  regions: import("@jbrowse/core/util").Region[];
709
718
  cytobands: import("@jbrowse/core/util").Feature[];
710
719
  geneticCodes: Record<string, number>;
@@ -735,11 +744,12 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
735
744
  getCanonicalRefName2(refName: string): string;
736
745
  isValidRefName(refName: string): boolean;
737
746
  } & {
747
+ isCircularRefName(refName: string): boolean;
738
748
  getRefNamePosition(refName: string): number | undefined;
739
749
  getAliasesForRefName(refName: string): string[];
740
750
  getRefNameMapForAdapter(adapterConf: {
741
751
  [x: string]: unknown;
742
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
752
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
743
753
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
744
754
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
745
755
  }, {
@@ -760,13 +770,13 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
760
770
  }> & {
761
771
  error: unknown;
762
772
  loadingP: Promise<void> | undefined;
763
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
773
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
764
774
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
765
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
775
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
766
776
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
767
777
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
768
778
  loadedGeneticCodes: Record<string, number> | undefined;
769
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
779
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
770
780
  statusMessage: string | undefined;
771
781
  statusProgress: number | undefined;
772
782
  statusSource: string | undefined;
@@ -785,7 +795,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
785
795
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
786
796
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
787
797
  } & {
788
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
798
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
789
799
  regions: import("@jbrowse/core/util").Region[];
790
800
  cytobands: import("@jbrowse/core/util").Feature[];
791
801
  geneticCodes: Record<string, number>;
@@ -816,24 +826,25 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
816
826
  getCanonicalRefName2(refName: string): string;
817
827
  isValidRefName(refName: string): boolean;
818
828
  } & {
829
+ isCircularRefName(refName: string): boolean;
819
830
  getRefNamePosition(refName: string): number | undefined;
820
831
  getAliasesForRefName(refName: string): string[];
821
832
  getRefNameMapForAdapter(adapterConf: {
822
833
  [x: string]: unknown;
823
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
834
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
824
835
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
825
836
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
826
837
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
827
838
  }, {
828
839
  error: unknown;
829
840
  loadingP: Promise<void> | undefined;
830
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
841
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
831
842
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
832
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
843
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
833
844
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
834
845
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
835
846
  loadedGeneticCodes: Record<string, number> | undefined;
836
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
847
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
837
848
  statusMessage: string | undefined;
838
849
  statusProgress: number | undefined;
839
850
  statusSource: string | undefined;
@@ -852,7 +863,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
852
863
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
853
864
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
854
865
  } & {
855
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
866
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
856
867
  regions: import("@jbrowse/core/util").Region[];
857
868
  cytobands: import("@jbrowse/core/util").Feature[];
858
869
  geneticCodes: Record<string, number>;
@@ -883,11 +894,12 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
883
894
  getCanonicalRefName2(refName: string): string;
884
895
  isValidRefName(refName: string): boolean;
885
896
  } & {
897
+ isCircularRefName(refName: string): boolean;
886
898
  getRefNamePosition(refName: string): number | undefined;
887
899
  getAliasesForRefName(refName: string): string[];
888
900
  getRefNameMapForAdapter(adapterConf: {
889
901
  [x: string]: unknown;
890
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
902
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
891
903
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
892
904
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
893
905
  has(asmName: string): boolean;
@@ -896,13 +908,13 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
896
908
  }> & {
897
909
  error: unknown;
898
910
  loadingP: Promise<void> | undefined;
899
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
911
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
900
912
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
901
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
913
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
902
914
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
903
915
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
904
916
  loadedGeneticCodes: Record<string, number> | undefined;
905
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
917
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
906
918
  statusMessage: string | undefined;
907
919
  statusProgress: number | undefined;
908
920
  statusSource: string | undefined;
@@ -921,7 +933,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
921
933
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
922
934
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
923
935
  } & {
924
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
936
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
925
937
  regions: import("@jbrowse/core/util").Region[];
926
938
  cytobands: import("@jbrowse/core/util").Feature[];
927
939
  geneticCodes: Record<string, number>;
@@ -952,24 +964,25 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
952
964
  getCanonicalRefName2(refName: string): string;
953
965
  isValidRefName(refName: string): boolean;
954
966
  } & {
967
+ isCircularRefName(refName: string): boolean;
955
968
  getRefNamePosition(refName: string): number | undefined;
956
969
  getAliasesForRefName(refName: string): string[];
957
970
  getRefNameMapForAdapter(adapterConf: {
958
971
  [x: string]: unknown;
959
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
972
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
960
973
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
961
974
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
962
975
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
963
976
  }, {
964
977
  error: unknown;
965
978
  loadingP: Promise<void> | undefined;
966
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
979
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
967
980
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
968
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
981
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
969
982
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
970
983
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
971
984
  loadedGeneticCodes: Record<string, number> | undefined;
972
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
985
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
973
986
  statusMessage: string | undefined;
974
987
  statusProgress: number | undefined;
975
988
  statusSource: string | undefined;
@@ -988,7 +1001,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
988
1001
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
989
1002
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
990
1003
  } & {
991
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1004
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
992
1005
  regions: import("@jbrowse/core/util").Region[];
993
1006
  cytobands: import("@jbrowse/core/util").Feature[];
994
1007
  geneticCodes: Record<string, number>;
@@ -1019,11 +1032,12 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1019
1032
  getCanonicalRefName2(refName: string): string;
1020
1033
  isValidRefName(refName: string): boolean;
1021
1034
  } & {
1035
+ isCircularRefName(refName: string): boolean;
1022
1036
  getRefNamePosition(refName: string): number | undefined;
1023
1037
  getAliasesForRefName(refName: string): string[];
1024
1038
  getRefNameMapForAdapter(adapterConf: {
1025
1039
  [x: string]: unknown;
1026
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1040
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1027
1041
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1028
1042
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1029
1043
  readonly assemblyNamesList: string[];
@@ -1038,13 +1052,13 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1038
1052
  }> & {
1039
1053
  error: unknown;
1040
1054
  loadingP: Promise<void> | undefined;
1041
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1055
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1042
1056
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1043
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1057
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1044
1058
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1045
1059
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1046
1060
  loadedGeneticCodes: Record<string, number> | undefined;
1047
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1061
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1048
1062
  statusMessage: string | undefined;
1049
1063
  statusProgress: number | undefined;
1050
1064
  statusSource: string | undefined;
@@ -1063,7 +1077,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1063
1077
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1064
1078
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1065
1079
  } & {
1066
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1080
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1067
1081
  regions: import("@jbrowse/core/util").Region[];
1068
1082
  cytobands: import("@jbrowse/core/util").Feature[];
1069
1083
  geneticCodes: Record<string, number>;
@@ -1094,24 +1108,25 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1094
1108
  getCanonicalRefName2(refName: string): string;
1095
1109
  isValidRefName(refName: string): boolean;
1096
1110
  } & {
1111
+ isCircularRefName(refName: string): boolean;
1097
1112
  getRefNamePosition(refName: string): number | undefined;
1098
1113
  getAliasesForRefName(refName: string): string[];
1099
1114
  getRefNameMapForAdapter(adapterConf: {
1100
1115
  [x: string]: unknown;
1101
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1116
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1102
1117
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1103
1118
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1104
1119
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1105
1120
  }, {
1106
1121
  error: unknown;
1107
1122
  loadingP: Promise<void> | undefined;
1108
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1123
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1109
1124
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1110
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1125
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1111
1126
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1112
1127
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1113
1128
  loadedGeneticCodes: Record<string, number> | undefined;
1114
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1129
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1115
1130
  statusMessage: string | undefined;
1116
1131
  statusProgress: number | undefined;
1117
1132
  statusSource: string | undefined;
@@ -1130,7 +1145,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1130
1145
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1131
1146
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1132
1147
  } & {
1133
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1148
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1134
1149
  regions: import("@jbrowse/core/util").Region[];
1135
1150
  cytobands: import("@jbrowse/core/util").Feature[];
1136
1151
  geneticCodes: Record<string, number>;
@@ -1161,11 +1176,12 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1161
1176
  getCanonicalRefName2(refName: string): string;
1162
1177
  isValidRefName(refName: string): boolean;
1163
1178
  } & {
1179
+ isCircularRefName(refName: string): boolean;
1164
1180
  getRefNamePosition(refName: string): number | undefined;
1165
1181
  getAliasesForRefName(refName: string): string[];
1166
1182
  getRefNameMapForAdapter(adapterConf: {
1167
1183
  [x: string]: unknown;
1168
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1184
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1169
1185
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1170
1186
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
1171
1187
  requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
@@ -1173,13 +1189,13 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1173
1189
  }> & {
1174
1190
  error: unknown;
1175
1191
  loadingP: Promise<void> | undefined;
1176
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1192
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1177
1193
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1178
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1194
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1179
1195
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1180
1196
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1181
1197
  loadedGeneticCodes: Record<string, number> | undefined;
1182
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1198
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1183
1199
  statusMessage: string | undefined;
1184
1200
  statusProgress: number | undefined;
1185
1201
  statusSource: string | undefined;
@@ -1198,7 +1214,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1198
1214
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1199
1215
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1200
1216
  } & {
1201
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1217
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1202
1218
  regions: import("@jbrowse/core/util").Region[];
1203
1219
  cytobands: import("@jbrowse/core/util").Feature[];
1204
1220
  geneticCodes: Record<string, number>;
@@ -1229,24 +1245,25 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1229
1245
  getCanonicalRefName2(refName: string): string;
1230
1246
  isValidRefName(refName: string): boolean;
1231
1247
  } & {
1248
+ isCircularRefName(refName: string): boolean;
1232
1249
  getRefNamePosition(refName: string): number | undefined;
1233
1250
  getAliasesForRefName(refName: string): string[];
1234
1251
  getRefNameMapForAdapter(adapterConf: {
1235
1252
  [x: string]: unknown;
1236
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1253
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1237
1254
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1238
1255
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1239
1256
  configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1240
1257
  }, {
1241
1258
  error: unknown;
1242
1259
  loadingP: Promise<void> | undefined;
1243
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1260
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>>;
1244
1261
  regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1245
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1262
+ refNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1246
1263
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1247
1264
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1248
1265
  loadedGeneticCodes: Record<string, number> | undefined;
1249
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1266
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases | undefined;
1250
1267
  statusMessage: string | undefined;
1251
1268
  statusProgress: number | undefined;
1252
1269
  statusSource: string | undefined;
@@ -1265,7 +1282,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1265
1282
  setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1266
1283
  setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1267
1284
  } & {
1268
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1285
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/refNameMaps").RefNameMaps & {
1269
1286
  regions: import("@jbrowse/core/util").Region[];
1270
1287
  cytobands: import("@jbrowse/core/util").Feature[];
1271
1288
  geneticCodes: Record<string, number>;
@@ -1296,16 +1313,17 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1296
1313
  getCanonicalRefName2(refName: string): string;
1297
1314
  isValidRefName(refName: string): boolean;
1298
1315
  } & {
1316
+ isCircularRefName(refName: string): boolean;
1299
1317
  getRefNamePosition(refName: string): number | undefined;
1300
1318
  getAliasesForRefName(refName: string): string[];
1301
1319
  getRefNameMapForAdapter(adapterConf: {
1302
1320
  [x: string]: unknown;
1303
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1321
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1304
1322
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1305
1323
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
1306
1324
  getRefNameMapForAdapter(adapterConf: {
1307
1325
  [x: string]: unknown;
1308
- }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1326
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/refNameMaps").RefNameAliases>;
1309
1327
  isValidRefName(refName: string, assemblyName: string): boolean;
1310
1328
  } & {
1311
1329
  afterAttach(): void;