@jbrowse/app-core 5.0.0-beta.1 → 5.0.0-beta.11

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 (75) hide show
  1. package/esm/AppSession/AppSessionMixin.d.ts +42 -316
  2. package/esm/Assemblies/AssembliesMixin.d.ts +172 -103
  3. package/esm/Assemblies/AssembliesMixin.js +13 -8
  4. package/esm/HistoryManagement/index.d.ts +6 -11
  5. package/esm/HistoryManagement/index.js +24 -28
  6. package/esm/JBrowseConfig/RootConfiguration.d.ts +80 -124
  7. package/esm/JBrowseConfig/RootConfiguration.js +5 -11
  8. package/esm/JBrowseConfig/defaultShareUrl.d.ts +1 -0
  9. package/esm/JBrowseConfig/defaultShareUrl.js +5 -0
  10. package/esm/JBrowseConfig/index.d.ts +89 -83
  11. package/esm/JBrowseConfig/index.js +6 -4
  12. package/esm/JBrowseModel/index.d.ts +93 -96
  13. package/esm/JBrowseModel/index.js +43 -43
  14. package/esm/JbApi/index.d.ts +2 -0
  15. package/esm/JbApi/index.js +1 -0
  16. package/esm/JbApi/jbApi.d.ts +2767 -0
  17. package/esm/JbApi/jbApi.js +1383 -0
  18. package/esm/RootMenu/index.d.ts +2 -11
  19. package/esm/RootMenu/index.js +0 -11
  20. package/esm/SessionSpec/index.d.ts +1 -1
  21. package/esm/SessionSpec/index.js +1 -1
  22. package/esm/SessionSpec/lgvUrlInit.js +5 -2
  23. package/esm/SessionSpec/loadSessionSpec.d.ts +56 -2
  24. package/esm/SessionSpec/loadSessionSpec.js +285 -123
  25. package/esm/SessionSpec/parseSessionSpecUrl.d.ts +2 -8
  26. package/esm/SessionSpec/parseSessionSpecUrl.js +2 -17
  27. package/esm/SessionSpec/types.d.ts +16 -12
  28. package/esm/WorkspaceLayout/WorkspaceContainer.js +4 -2
  29. package/esm/WorkspaceLayout/WorkspaceTab.js +2 -6
  30. package/esm/WorkspaceLayout/model.d.ts +25 -5
  31. package/esm/WorkspaceLayout/model.js +77 -18
  32. package/esm/WorkspaceLayout/spec.d.ts +40 -10
  33. package/esm/WorkspaceLayout/spec.js +81 -8
  34. package/esm/index.d.ts +4 -2
  35. package/esm/index.js +4 -1
  36. package/esm/menus.d.ts +15 -29
  37. package/esm/menus.js +76 -92
  38. package/esm/queryParams.d.ts +1 -1
  39. package/esm/queryParams.js +10 -9
  40. package/esm/ui/App/App.js +18 -11
  41. package/esm/ui/App/AppToolbar.js +23 -8
  42. package/esm/ui/App/ClassicViewsContainer.d.ts +2 -2
  43. package/esm/ui/App/DialogQueue.d.ts +2 -2
  44. package/esm/ui/App/DialogQueue.js +3 -3
  45. package/esm/ui/App/DrawerHeader.js +2 -3
  46. package/esm/ui/App/ThemeModeButton.d.ts +12 -0
  47. package/esm/ui/App/ThemeModeButton.js +34 -0
  48. package/esm/ui/App/ViewButtons.js +2 -2
  49. package/esm/ui/App/ViewContainer.js +1 -17
  50. package/esm/ui/App/ViewContainerTitle.js +15 -12
  51. package/esm/ui/App/ViewLauncher.js +1 -1
  52. package/esm/ui/App/ViewMenu.js +2 -2
  53. package/esm/ui/App/ViewStack.js +7 -1
  54. package/esm/ui/App/ViewsContainer.d.ts +2 -4
  55. package/esm/ui/App/ViewsContainer.js +3 -9
  56. package/esm/ui/App/index.d.ts +1 -1
  57. package/esm/ui/App/index.js +1 -1
  58. package/esm/ui/App/lazyParts.d.ts +32 -0
  59. package/esm/ui/App/lazyParts.js +8 -0
  60. package/esm/ui/App/preloadAppShell.d.ts +14 -0
  61. package/esm/ui/App/preloadAppShell.js +41 -0
  62. package/esm/ui/App/types.d.ts +12 -7
  63. package/esm/ui/App/useViewVisibility.d.ts +10 -9
  64. package/esm/ui/App/useViewVisibility.js +12 -11
  65. package/esm/ui/App/viewTitle.d.ts +10 -3
  66. package/esm/ui/App/viewTitle.js +13 -5
  67. package/esm/ui/index.d.ts +1 -1
  68. package/esm/ui/index.js +1 -1
  69. package/package.json +7 -7
  70. package/esm/ui/App/AppReadyMarker.d.ts +0 -34
  71. package/esm/ui/App/AppReadyMarker.js +0 -56
  72. package/esm/ui/App/DrawerControls.d.ts +0 -1
  73. package/esm/ui/App/DrawerControls.js +0 -1
  74. package/esm/ui/App/copyView.d.ts +0 -1
  75. package/esm/ui/App/copyView.js +0 -29
package/esm/AppSession/AppSessionMixin.d.ts CHANGED
@@ -42,7 +42,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
42
42
  error: unknown;
43
43
  loadingP: Promise<void> | undefined;
44
44
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
45
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
45
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
46
46
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
47
47
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
48
48
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -80,7 +80,6 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
80
80
  afterAttach(): void;
81
81
  } & {
82
82
  readonly initialized: boolean;
83
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
84
83
  readonly allRefNames: string[] | undefined;
85
84
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
86
85
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -98,6 +97,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
98
97
  getCanonicalRefName2(refName: string): string;
99
98
  isValidRefName(refName: string): boolean;
100
99
  } & {
100
+ getRefNamePosition(refName: string): number | undefined;
101
101
  getAliasesForRefName(refName: string): string[];
102
102
  getRefNameMapForAdapter(adapterConf: {
103
103
  [x: string]: unknown;
@@ -113,141 +113,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
113
113
  } | undefined;
114
114
  };
115
115
  } & {
116
- readonly assemblyNameMap: Record<string, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
117
- configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
118
- }> & {
119
- error: unknown;
120
- loadingP: Promise<void> | undefined;
121
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
122
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
123
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
124
- canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
125
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
126
- loadedGeneticCodes: Record<string, number> | undefined;
127
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
128
- statusMessage: string | undefined;
129
- statusProgress: number | undefined;
130
- statusSource: string | undefined;
131
- refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
132
- } & {
133
- getConf(arg: string): any;
134
- } & {
135
- readonly name: string;
136
- readonly aliases: string[];
137
- readonly displayName: string;
138
- readonly refNameColors: string[];
139
- } & {
140
- readonly allAliases: string[];
141
- hasName(name: string): boolean;
142
- } & {
143
- setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
144
- setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
145
- } & {
146
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
147
- regions: import("@jbrowse/core/util").Region[];
148
- cytobands: import("@jbrowse/core/util").Feature[];
149
- geneticCodes: Record<string, number>;
150
- }): void;
151
- setError(e: unknown): void;
152
- setLoadingP(p?: Promise<void>): void;
153
- loadPre(): Promise<void>;
154
- } & {
155
- load(): Promise<void>;
156
- } & {
157
- afterAttach(): void;
158
- } & {
159
- readonly initialized: boolean;
160
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
161
- readonly allRefNames: string[] | undefined;
162
- readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
163
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
164
- } & {
165
- readonly refNames: string[] | undefined;
166
- } & {
167
- readonly refNameToIndex: Map<string, number> | undefined;
168
- } & {
169
- getCanonicalRefName(refName: string): string | undefined;
170
- getRefNameColor(refName: string): string | undefined;
171
- getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
172
- getGeneticCodeId(refName: string): number;
173
- getSeqAdapterRefName(canonicalRefName: string): string;
174
- } & {
175
- getCanonicalRefName2(refName: string): string;
176
- isValidRefName(refName: string): boolean;
177
- } & {
178
- getAliasesForRefName(refName: string): string[];
179
- getRefNameMapForAdapter(adapterConf: {
180
- [x: string]: unknown;
181
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
182
- getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
183
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
184
- configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
185
- }, {
186
- error: unknown;
187
- loadingP: Promise<void> | undefined;
188
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
189
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
190
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
191
- canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
192
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
193
- loadedGeneticCodes: Record<string, number> | undefined;
194
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
195
- statusMessage: string | undefined;
196
- statusProgress: number | undefined;
197
- statusSource: string | undefined;
198
- refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
199
- } & {
200
- getConf(arg: string): any;
201
- } & {
202
- readonly name: string;
203
- readonly aliases: string[];
204
- readonly displayName: string;
205
- readonly refNameColors: string[];
206
- } & {
207
- readonly allAliases: string[];
208
- hasName(name: string): boolean;
209
- } & {
210
- setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
211
- setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
212
- } & {
213
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
214
- regions: import("@jbrowse/core/util").Region[];
215
- cytobands: import("@jbrowse/core/util").Feature[];
216
- geneticCodes: Record<string, number>;
217
- }): void;
218
- setError(e: unknown): void;
219
- setLoadingP(p?: Promise<void>): void;
220
- loadPre(): Promise<void>;
221
- } & {
222
- load(): Promise<void>;
223
- } & {
224
- afterAttach(): void;
225
- } & {
226
- readonly initialized: boolean;
227
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
228
- readonly allRefNames: string[] | undefined;
229
- readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
230
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
231
- } & {
232
- readonly refNames: string[] | undefined;
233
- } & {
234
- readonly refNameToIndex: Map<string, number> | undefined;
235
- } & {
236
- getCanonicalRefName(refName: string): string | undefined;
237
- getRefNameColor(refName: string): string | undefined;
238
- getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
239
- getGeneticCodeId(refName: string): number;
240
- getSeqAdapterRefName(canonicalRefName: string): string;
241
- } & {
242
- getCanonicalRefName2(refName: string): string;
243
- isValidRefName(refName: string): boolean;
244
- } & {
245
- getAliasesForRefName(refName: string): string[];
246
- getRefNameMapForAdapter(adapterConf: {
247
- [x: string]: unknown;
248
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
249
- getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
250
- }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
116
+ readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
251
117
  } & {
252
118
  getCanonicalAssemblyName(asmName: string): string | undefined;
253
119
  getDisplayName(asmName: string): string;
@@ -257,7 +123,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
257
123
  error: unknown;
258
124
  loadingP: Promise<void> | undefined;
259
125
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
260
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
126
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
261
127
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
262
128
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
263
129
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -295,7 +161,6 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
295
161
  afterAttach(): void;
296
162
  } & {
297
163
  readonly initialized: boolean;
298
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
299
164
  readonly allRefNames: string[] | undefined;
300
165
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
301
166
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -313,6 +178,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
313
178
  getCanonicalRefName2(refName: string): string;
314
179
  isValidRefName(refName: string): boolean;
315
180
  } & {
181
+ getRefNamePosition(refName: string): number | undefined;
316
182
  getAliasesForRefName(refName: string): string[];
317
183
  getRefNameMapForAdapter(adapterConf: {
318
184
  [x: string]: unknown;
@@ -324,7 +190,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
324
190
  error: unknown;
325
191
  loadingP: Promise<void> | undefined;
326
192
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
327
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
193
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
328
194
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
329
195
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
330
196
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -362,7 +228,6 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
362
228
  afterAttach(): void;
363
229
  } & {
364
230
  readonly initialized: boolean;
365
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
366
231
  readonly allRefNames: string[] | undefined;
367
232
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
368
233
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -380,6 +245,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
380
245
  getCanonicalRefName2(refName: string): string;
381
246
  isValidRefName(refName: string): boolean;
382
247
  } & {
248
+ getRefNamePosition(refName: string): number | undefined;
383
249
  getAliasesForRefName(refName: string): string[];
384
250
  getRefNameMapForAdapter(adapterConf: {
385
251
  [x: string]: unknown;
@@ -393,7 +259,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
393
259
  error: unknown;
394
260
  loadingP: Promise<void> | undefined;
395
261
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
396
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
262
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
397
263
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
398
264
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
399
265
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -431,7 +297,6 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
431
297
  afterAttach(): void;
432
298
  } & {
433
299
  readonly initialized: boolean;
434
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
435
300
  readonly allRefNames: string[] | undefined;
436
301
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
437
302
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -449,6 +314,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
449
314
  getCanonicalRefName2(refName: string): string;
450
315
  isValidRefName(refName: string): boolean;
451
316
  } & {
317
+ getRefNamePosition(refName: string): number | undefined;
452
318
  getAliasesForRefName(refName: string): string[];
453
319
  getRefNameMapForAdapter(adapterConf: {
454
320
  [x: string]: unknown;
@@ -460,7 +326,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
460
326
  error: unknown;
461
327
  loadingP: Promise<void> | undefined;
462
328
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
463
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
329
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
464
330
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
465
331
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
466
332
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -498,7 +364,6 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
498
364
  afterAttach(): void;
499
365
  } & {
500
366
  readonly initialized: boolean;
501
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
502
367
  readonly allRefNames: string[] | undefined;
503
368
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
504
369
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -516,6 +381,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
516
381
  getCanonicalRefName2(refName: string): string;
517
382
  isValidRefName(refName: string): boolean;
518
383
  } & {
384
+ getRefNamePosition(refName: string): number | undefined;
519
385
  getAliasesForRefName(refName: string): string[];
520
386
  getRefNameMapForAdapter(adapterConf: {
521
387
  [x: string]: unknown;
@@ -523,11 +389,8 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
523
389
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
524
390
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
525
391
  readonly assemblyNamesList: string[];
526
- readonly configuredAssemblyNames: Set<string>;
527
- readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
528
- setSubschema(slotName: string, data: Record<string, unknown>): any;
529
- setSlot(slotName: string, value: unknown): void;
530
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
392
+ readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
393
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
531
394
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
532
395
  } & {
533
396
  settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -538,7 +401,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
538
401
  error: unknown;
539
402
  loadingP: Promise<void> | undefined;
540
403
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
541
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
404
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
542
405
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
543
406
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
544
407
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -576,7 +439,6 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
576
439
  afterAttach(): void;
577
440
  } & {
578
441
  readonly initialized: boolean;
579
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
580
442
  readonly allRefNames: string[] | undefined;
581
443
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
582
444
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -594,6 +456,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
594
456
  getCanonicalRefName2(refName: string): string;
595
457
  isValidRefName(refName: string): boolean;
596
458
  } & {
459
+ getRefNamePosition(refName: string): number | undefined;
597
460
  getAliasesForRefName(refName: string): string[];
598
461
  getRefNameMapForAdapter(adapterConf: {
599
462
  [x: string]: unknown;
@@ -605,7 +468,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
605
468
  error: unknown;
606
469
  loadingP: Promise<void> | undefined;
607
470
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
608
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
471
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
609
472
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
610
473
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
611
474
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -643,7 +506,6 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
643
506
  afterAttach(): void;
644
507
  } & {
645
508
  readonly initialized: boolean;
646
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
647
509
  readonly allRefNames: string[] | undefined;
648
510
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
649
511
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -661,6 +523,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
661
523
  getCanonicalRefName2(refName: string): string;
662
524
  isValidRefName(refName: string): boolean;
663
525
  } & {
526
+ getRefNamePosition(refName: string): number | undefined;
664
527
  getAliasesForRefName(refName: string): string[];
665
528
  getRefNameMapForAdapter(adapterConf: {
666
529
  [x: string]: unknown;
@@ -673,7 +536,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
673
536
  error: unknown;
674
537
  loadingP: Promise<void> | undefined;
675
538
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
676
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
539
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
677
540
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
678
541
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
679
542
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -711,7 +574,6 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
711
574
  afterAttach(): void;
712
575
  } & {
713
576
  readonly initialized: boolean;
714
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
715
577
  readonly allRefNames: string[] | undefined;
716
578
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
717
579
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -729,6 +591,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
729
591
  getCanonicalRefName2(refName: string): string;
730
592
  isValidRefName(refName: string): boolean;
731
593
  } & {
594
+ getRefNamePosition(refName: string): number | undefined;
732
595
  getAliasesForRefName(refName: string): string[];
733
596
  getRefNameMapForAdapter(adapterConf: {
734
597
  [x: string]: unknown;
@@ -740,7 +603,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
740
603
  error: unknown;
741
604
  loadingP: Promise<void> | undefined;
742
605
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
743
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
606
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
744
607
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
745
608
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
746
609
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -778,7 +641,6 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
778
641
  afterAttach(): void;
779
642
  } & {
780
643
  readonly initialized: boolean;
781
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
782
644
  readonly allRefNames: string[] | undefined;
783
645
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
784
646
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -796,6 +658,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
796
658
  getCanonicalRefName2(refName: string): string;
797
659
  isValidRefName(refName: string): boolean;
798
660
  } & {
661
+ getRefNamePosition(refName: string): number | undefined;
799
662
  getAliasesForRefName(refName: string): string[];
800
663
  getRefNameMapForAdapter(adapterConf: {
801
664
  [x: string]: unknown;
@@ -817,7 +680,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
817
680
  error: unknown;
818
681
  loadingP: Promise<void> | undefined;
819
682
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
820
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
683
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
821
684
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
822
685
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
823
686
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -855,7 +718,6 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
855
718
  afterAttach(): void;
856
719
  } & {
857
720
  readonly initialized: boolean;
858
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
859
721
  readonly allRefNames: string[] | undefined;
860
722
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
861
723
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -873,6 +735,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
873
735
  getCanonicalRefName2(refName: string): string;
874
736
  isValidRefName(refName: string): boolean;
875
737
  } & {
738
+ getRefNamePosition(refName: string): number | undefined;
876
739
  getAliasesForRefName(refName: string): string[];
877
740
  getRefNameMapForAdapter(adapterConf: {
878
741
  [x: string]: unknown;
@@ -888,141 +751,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
888
751
  } | undefined;
889
752
  };
890
753
  } & {
891
- readonly assemblyNameMap: Record<string, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
892
- configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
893
- }> & {
894
- error: unknown;
895
- loadingP: Promise<void> | undefined;
896
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
897
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
898
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
899
- canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
900
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
901
- loadedGeneticCodes: Record<string, number> | undefined;
902
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
903
- statusMessage: string | undefined;
904
- statusProgress: number | undefined;
905
- statusSource: string | undefined;
906
- refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
907
- } & {
908
- getConf(arg: string): any;
909
- } & {
910
- readonly name: string;
911
- readonly aliases: string[];
912
- readonly displayName: string;
913
- readonly refNameColors: string[];
914
- } & {
915
- readonly allAliases: string[];
916
- hasName(name: string): boolean;
917
- } & {
918
- setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
919
- setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
920
- } & {
921
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
922
- regions: import("@jbrowse/core/util").Region[];
923
- cytobands: import("@jbrowse/core/util").Feature[];
924
- geneticCodes: Record<string, number>;
925
- }): void;
926
- setError(e: unknown): void;
927
- setLoadingP(p?: Promise<void>): void;
928
- loadPre(): Promise<void>;
929
- } & {
930
- load(): Promise<void>;
931
- } & {
932
- afterAttach(): void;
933
- } & {
934
- readonly initialized: boolean;
935
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
936
- readonly allRefNames: string[] | undefined;
937
- readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
938
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
939
- } & {
940
- readonly refNames: string[] | undefined;
941
- } & {
942
- readonly refNameToIndex: Map<string, number> | undefined;
943
- } & {
944
- getCanonicalRefName(refName: string): string | undefined;
945
- getRefNameColor(refName: string): string | undefined;
946
- getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
947
- getGeneticCodeId(refName: string): number;
948
- getSeqAdapterRefName(canonicalRefName: string): string;
949
- } & {
950
- getCanonicalRefName2(refName: string): string;
951
- isValidRefName(refName: string): boolean;
952
- } & {
953
- getAliasesForRefName(refName: string): string[];
954
- getRefNameMapForAdapter(adapterConf: {
955
- [x: string]: unknown;
956
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
957
- getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
958
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
959
- configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
960
- }, {
961
- error: unknown;
962
- loadingP: Promise<void> | undefined;
963
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
964
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
965
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
966
- canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
967
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
968
- loadedGeneticCodes: Record<string, number> | undefined;
969
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
970
- statusMessage: string | undefined;
971
- statusProgress: number | undefined;
972
- statusSource: string | undefined;
973
- refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
974
- } & {
975
- getConf(arg: string): any;
976
- } & {
977
- readonly name: string;
978
- readonly aliases: string[];
979
- readonly displayName: string;
980
- readonly refNameColors: string[];
981
- } & {
982
- readonly allAliases: string[];
983
- hasName(name: string): boolean;
984
- } & {
985
- setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
986
- setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
987
- } & {
988
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
989
- regions: import("@jbrowse/core/util").Region[];
990
- cytobands: import("@jbrowse/core/util").Feature[];
991
- geneticCodes: Record<string, number>;
992
- }): void;
993
- setError(e: unknown): void;
994
- setLoadingP(p?: Promise<void>): void;
995
- loadPre(): Promise<void>;
996
- } & {
997
- load(): Promise<void>;
998
- } & {
999
- afterAttach(): void;
1000
- } & {
1001
- readonly initialized: boolean;
1002
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1003
- readonly allRefNames: string[] | undefined;
1004
- readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1005
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1006
- } & {
1007
- readonly refNames: string[] | undefined;
1008
- } & {
1009
- readonly refNameToIndex: Map<string, number> | undefined;
1010
- } & {
1011
- getCanonicalRefName(refName: string): string | undefined;
1012
- getRefNameColor(refName: string): string | undefined;
1013
- getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1014
- getGeneticCodeId(refName: string): number;
1015
- getSeqAdapterRefName(canonicalRefName: string): string;
1016
- } & {
1017
- getCanonicalRefName2(refName: string): string;
1018
- isValidRefName(refName: string): boolean;
1019
- } & {
1020
- getAliasesForRefName(refName: string): string[];
1021
- getRefNameMapForAdapter(adapterConf: {
1022
- [x: string]: unknown;
1023
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1024
- getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1025
- }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
754
+ readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
1026
755
  } & {
1027
756
  getCanonicalAssemblyName(asmName: string): string | undefined;
1028
757
  getDisplayName(asmName: string): string;
@@ -1032,7 +761,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1032
761
  error: unknown;
1033
762
  loadingP: Promise<void> | undefined;
1034
763
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1035
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
764
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1036
765
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1037
766
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1038
767
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1070,7 +799,6 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1070
799
  afterAttach(): void;
1071
800
  } & {
1072
801
  readonly initialized: boolean;
1073
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1074
802
  readonly allRefNames: string[] | undefined;
1075
803
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1076
804
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1088,6 +816,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1088
816
  getCanonicalRefName2(refName: string): string;
1089
817
  isValidRefName(refName: string): boolean;
1090
818
  } & {
819
+ getRefNamePosition(refName: string): number | undefined;
1091
820
  getAliasesForRefName(refName: string): string[];
1092
821
  getRefNameMapForAdapter(adapterConf: {
1093
822
  [x: string]: unknown;
@@ -1099,7 +828,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1099
828
  error: unknown;
1100
829
  loadingP: Promise<void> | undefined;
1101
830
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1102
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
831
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1103
832
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1104
833
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1105
834
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1137,7 +866,6 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1137
866
  afterAttach(): void;
1138
867
  } & {
1139
868
  readonly initialized: boolean;
1140
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1141
869
  readonly allRefNames: string[] | undefined;
1142
870
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1143
871
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1155,6 +883,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1155
883
  getCanonicalRefName2(refName: string): string;
1156
884
  isValidRefName(refName: string): boolean;
1157
885
  } & {
886
+ getRefNamePosition(refName: string): number | undefined;
1158
887
  getAliasesForRefName(refName: string): string[];
1159
888
  getRefNameMapForAdapter(adapterConf: {
1160
889
  [x: string]: unknown;
@@ -1168,7 +897,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1168
897
  error: unknown;
1169
898
  loadingP: Promise<void> | undefined;
1170
899
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1171
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
900
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1172
901
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1173
902
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1174
903
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1206,7 +935,6 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1206
935
  afterAttach(): void;
1207
936
  } & {
1208
937
  readonly initialized: boolean;
1209
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1210
938
  readonly allRefNames: string[] | undefined;
1211
939
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1212
940
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1224,6 +952,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1224
952
  getCanonicalRefName2(refName: string): string;
1225
953
  isValidRefName(refName: string): boolean;
1226
954
  } & {
955
+ getRefNamePosition(refName: string): number | undefined;
1227
956
  getAliasesForRefName(refName: string): string[];
1228
957
  getRefNameMapForAdapter(adapterConf: {
1229
958
  [x: string]: unknown;
@@ -1235,7 +964,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1235
964
  error: unknown;
1236
965
  loadingP: Promise<void> | undefined;
1237
966
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1238
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
967
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1239
968
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1240
969
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1241
970
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1273,7 +1002,6 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1273
1002
  afterAttach(): void;
1274
1003
  } & {
1275
1004
  readonly initialized: boolean;
1276
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1277
1005
  readonly allRefNames: string[] | undefined;
1278
1006
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1279
1007
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1291,6 +1019,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1291
1019
  getCanonicalRefName2(refName: string): string;
1292
1020
  isValidRefName(refName: string): boolean;
1293
1021
  } & {
1022
+ getRefNamePosition(refName: string): number | undefined;
1294
1023
  getAliasesForRefName(refName: string): string[];
1295
1024
  getRefNameMapForAdapter(adapterConf: {
1296
1025
  [x: string]: unknown;
@@ -1298,11 +1027,8 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1298
1027
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1299
1028
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1300
1029
  readonly assemblyNamesList: string[];
1301
- readonly configuredAssemblyNames: Set<string>;
1302
- readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
1303
- setSubschema(slotName: string, data: Record<string, unknown>): any;
1304
- setSlot(slotName: string, value: unknown): void;
1305
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
1030
+ readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
1031
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1306
1032
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1307
1033
  } & {
1308
1034
  settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -1313,7 +1039,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1313
1039
  error: unknown;
1314
1040
  loadingP: Promise<void> | undefined;
1315
1041
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1316
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1042
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1317
1043
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1318
1044
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1319
1045
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1351,7 +1077,6 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1351
1077
  afterAttach(): void;
1352
1078
  } & {
1353
1079
  readonly initialized: boolean;
1354
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1355
1080
  readonly allRefNames: string[] | undefined;
1356
1081
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1357
1082
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1369,6 +1094,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1369
1094
  getCanonicalRefName2(refName: string): string;
1370
1095
  isValidRefName(refName: string): boolean;
1371
1096
  } & {
1097
+ getRefNamePosition(refName: string): number | undefined;
1372
1098
  getAliasesForRefName(refName: string): string[];
1373
1099
  getRefNameMapForAdapter(adapterConf: {
1374
1100
  [x: string]: unknown;
@@ -1380,7 +1106,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1380
1106
  error: unknown;
1381
1107
  loadingP: Promise<void> | undefined;
1382
1108
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1383
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1109
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1384
1110
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1385
1111
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1386
1112
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1418,7 +1144,6 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1418
1144
  afterAttach(): void;
1419
1145
  } & {
1420
1146
  readonly initialized: boolean;
1421
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1422
1147
  readonly allRefNames: string[] | undefined;
1423
1148
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1424
1149
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1436,6 +1161,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1436
1161
  getCanonicalRefName2(refName: string): string;
1437
1162
  isValidRefName(refName: string): boolean;
1438
1163
  } & {
1164
+ getRefNamePosition(refName: string): number | undefined;
1439
1165
  getAliasesForRefName(refName: string): string[];
1440
1166
  getRefNameMapForAdapter(adapterConf: {
1441
1167
  [x: string]: unknown;
@@ -1448,7 +1174,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1448
1174
  error: unknown;
1449
1175
  loadingP: Promise<void> | undefined;
1450
1176
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1451
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1177
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1452
1178
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1453
1179
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1454
1180
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1486,7 +1212,6 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1486
1212
  afterAttach(): void;
1487
1213
  } & {
1488
1214
  readonly initialized: boolean;
1489
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1490
1215
  readonly allRefNames: string[] | undefined;
1491
1216
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1492
1217
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1504,6 +1229,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1504
1229
  getCanonicalRefName2(refName: string): string;
1505
1230
  isValidRefName(refName: string): boolean;
1506
1231
  } & {
1232
+ getRefNamePosition(refName: string): number | undefined;
1507
1233
  getAliasesForRefName(refName: string): string[];
1508
1234
  getRefNameMapForAdapter(adapterConf: {
1509
1235
  [x: string]: unknown;
@@ -1515,7 +1241,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1515
1241
  error: unknown;
1516
1242
  loadingP: Promise<void> | undefined;
1517
1243
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1518
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1244
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1519
1245
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1520
1246
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1521
1247
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1553,7 +1279,6 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1553
1279
  afterAttach(): void;
1554
1280
  } & {
1555
1281
  readonly initialized: boolean;
1556
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1557
1282
  readonly allRefNames: string[] | undefined;
1558
1283
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1559
1284
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1571,6 +1296,7 @@ export declare function AppSessionMixin(_pluginManager: PluginManager): import("
1571
1296
  getCanonicalRefName2(refName: string): string;
1572
1297
  isValidRefName(refName: string): boolean;
1573
1298
  } & {
1299
+ getRefNamePosition(refName: string): number | undefined;
1574
1300
  getAliasesForRefName(refName: string): string[];
1575
1301
  getRefNameMapForAdapter(adapterConf: {
1576
1302
  [x: string]: unknown;