@jbrowse/product-core 3.1.0 → 3.3.0

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 (15) hide show
  1. package/dist/RootModel/InternetAccounts.js +3 -1
  2. package/dist/Session/Connections.js +2 -2
  3. package/dist/Session/MultipleViews.d.ts +1671 -1
  4. package/dist/Session/ReferenceManagement.js +4 -4
  5. package/dist/Session/SessionTracks.d.ts +1671 -1
  6. package/dist/Session/Tracks.d.ts +1671 -1
  7. package/dist/Session/Tracks.js +2 -2
  8. package/esm/RootModel/InternetAccounts.js +3 -1
  9. package/esm/Session/Connections.js +2 -2
  10. package/esm/Session/MultipleViews.d.ts +1671 -1
  11. package/esm/Session/ReferenceManagement.js +4 -4
  12. package/esm/Session/SessionTracks.d.ts +1671 -1
  13. package/esm/Session/Tracks.d.ts +1671 -1
  14. package/esm/Session/Tracks.js +2 -2
  15. package/package.json +5 -5
package/esm/Session/MultipleViews.d.ts CHANGED
@@ -20,7 +20,1677 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
20
20
  selection: unknown;
21
21
  hovered: unknown;
22
22
  } & {
23
- readonly root: import("mobx-state-tree").TypeOrStateTreeNodeToStateTreeNode<ROOT_MODEL_TYPE>;
23
+ readonly root: {
24
+ jbrowse: any;
25
+ session: any;
26
+ sessionPath: string;
27
+ assemblyManager: {
28
+ assemblies: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
29
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
30
+ }, {
31
+ error: unknown;
32
+ loadingP: Promise<void> | undefined;
33
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
34
+ refNameAliases: {
35
+ [x: string]: string;
36
+ } | undefined;
37
+ lowerCaseRefNameAliases: {
38
+ [x: string]: string;
39
+ } | undefined;
40
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
41
+ } & {
42
+ getConf(arg: string): any;
43
+ } & {
44
+ readonly initialized: boolean;
45
+ readonly name: string;
46
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
47
+ readonly aliases: string[];
48
+ readonly displayName: string | undefined;
49
+ hasName(name: string): boolean;
50
+ readonly allAliases: string[];
51
+ readonly allRefNames: string[] | undefined;
52
+ readonly lowerCaseRefNames: string[] | undefined;
53
+ readonly allRefNamesWithLowerCase: string[] | undefined;
54
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
55
+ readonly refNameColors: string[];
56
+ } & {
57
+ readonly refNames: string[] | undefined;
58
+ } & {
59
+ getCanonicalRefName(refName: string): string | undefined;
60
+ getRefNameColor(refName: string): string | undefined;
61
+ isValidRefName(refName: string): boolean;
62
+ } & {
63
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
64
+ regions: import("@jbrowse/core/util").Region[];
65
+ refNameAliases: {
66
+ [x: string]: string;
67
+ };
68
+ lowerCaseRefNameAliases: {
69
+ [x: string]: string;
70
+ };
71
+ cytobands: import("@jbrowse/core/util").Feature[];
72
+ }): void;
73
+ setError(e: unknown): void;
74
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
75
+ setRefNameAliases(aliases: {
76
+ [x: string]: string;
77
+ }, lowerCaseAliases: {
78
+ [x: string]: string;
79
+ }): void;
80
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
81
+ setLoadingP(p?: Promise<void>): void;
82
+ load(): Promise<void>;
83
+ loadPre(): Promise<void>;
84
+ } & {
85
+ getAdapterMapEntry(adapterConf: {
86
+ [x: string]: unknown;
87
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
88
+ getRefNameMapForAdapter(adapterConf: {
89
+ [x: string]: unknown;
90
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
91
+ [x: string]: string;
92
+ }>;
93
+ getReverseRefNameMapForAdapter(adapterConf: {
94
+ [x: string]: unknown;
95
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
96
+ [x: string]: string;
97
+ }>;
98
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
99
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
100
+ }, {
101
+ error: unknown;
102
+ loadingP: Promise<void> | undefined;
103
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
104
+ refNameAliases: {
105
+ [x: string]: string;
106
+ } | undefined;
107
+ lowerCaseRefNameAliases: {
108
+ [x: string]: string;
109
+ } | undefined;
110
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
111
+ } & {
112
+ getConf(arg: string): any;
113
+ } & {
114
+ readonly initialized: boolean;
115
+ readonly name: string;
116
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
117
+ readonly aliases: string[];
118
+ readonly displayName: string | undefined;
119
+ hasName(name: string): boolean;
120
+ readonly allAliases: string[];
121
+ readonly allRefNames: string[] | undefined;
122
+ readonly lowerCaseRefNames: string[] | undefined;
123
+ readonly allRefNamesWithLowerCase: string[] | undefined;
124
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
125
+ readonly refNameColors: string[];
126
+ } & {
127
+ readonly refNames: string[] | undefined;
128
+ } & {
129
+ getCanonicalRefName(refName: string): string | undefined;
130
+ getRefNameColor(refName: string): string | undefined;
131
+ isValidRefName(refName: string): boolean;
132
+ } & {
133
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
134
+ regions: import("@jbrowse/core/util").Region[];
135
+ refNameAliases: {
136
+ [x: string]: string;
137
+ };
138
+ lowerCaseRefNameAliases: {
139
+ [x: string]: string;
140
+ };
141
+ cytobands: import("@jbrowse/core/util").Feature[];
142
+ }): void;
143
+ setError(e: unknown): void;
144
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
145
+ setRefNameAliases(aliases: {
146
+ [x: string]: string;
147
+ }, lowerCaseAliases: {
148
+ [x: string]: string;
149
+ }): void;
150
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
151
+ setLoadingP(p?: Promise<void>): void;
152
+ load(): Promise<void>;
153
+ loadPre(): Promise<void>;
154
+ } & {
155
+ getAdapterMapEntry(adapterConf: {
156
+ [x: string]: unknown;
157
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
158
+ getRefNameMapForAdapter(adapterConf: {
159
+ [x: string]: unknown;
160
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
161
+ [x: string]: string;
162
+ }>;
163
+ getReverseRefNameMapForAdapter(adapterConf: {
164
+ [x: string]: unknown;
165
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
166
+ [x: string]: string;
167
+ }>;
168
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
169
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
170
+ readonly assemblyNameMap: Record<string, {
171
+ configuration: any;
172
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
173
+ error: unknown;
174
+ loadingP: Promise<void> | undefined;
175
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
176
+ refNameAliases: {
177
+ [x: string]: string;
178
+ } | undefined;
179
+ lowerCaseRefNameAliases: {
180
+ [x: string]: string;
181
+ } | undefined;
182
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
183
+ } & {
184
+ getConf(arg: string): any;
185
+ } & {
186
+ readonly initialized: boolean;
187
+ readonly name: string;
188
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
189
+ readonly aliases: string[];
190
+ readonly displayName: string | undefined;
191
+ hasName(name: string): boolean;
192
+ readonly allAliases: string[];
193
+ readonly allRefNames: string[] | undefined;
194
+ readonly lowerCaseRefNames: string[] | undefined;
195
+ readonly allRefNamesWithLowerCase: string[] | undefined;
196
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
197
+ readonly refNameColors: string[];
198
+ } & {
199
+ readonly refNames: string[] | undefined;
200
+ } & {
201
+ getCanonicalRefName(refName: string): string | undefined;
202
+ getRefNameColor(refName: string): string | undefined;
203
+ isValidRefName(refName: string): boolean;
204
+ } & {
205
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
206
+ regions: import("@jbrowse/core/util").Region[];
207
+ refNameAliases: {
208
+ [x: string]: string;
209
+ };
210
+ lowerCaseRefNameAliases: {
211
+ [x: string]: string;
212
+ };
213
+ cytobands: import("@jbrowse/core/util").Feature[];
214
+ }): void;
215
+ setError(e: unknown): void;
216
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
217
+ setRefNameAliases(aliases: {
218
+ [x: string]: string;
219
+ }, lowerCaseAliases: {
220
+ [x: string]: string;
221
+ }): void;
222
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
223
+ setLoadingP(p?: Promise<void>): void;
224
+ load(): Promise<void>;
225
+ loadPre(): Promise<void>;
226
+ } & {
227
+ getAdapterMapEntry(adapterConf: {
228
+ [x: string]: unknown;
229
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
230
+ getRefNameMapForAdapter(adapterConf: {
231
+ [x: string]: unknown;
232
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
233
+ [x: string]: string;
234
+ }>;
235
+ getReverseRefNameMapForAdapter(adapterConf: {
236
+ [x: string]: unknown;
237
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
238
+ [x: string]: string;
239
+ }>;
240
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
241
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
242
+ }, {
243
+ error: unknown;
244
+ loadingP: Promise<void> | undefined;
245
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
246
+ refNameAliases: {
247
+ [x: string]: string;
248
+ } | undefined;
249
+ lowerCaseRefNameAliases: {
250
+ [x: string]: string;
251
+ } | undefined;
252
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
253
+ } & {
254
+ getConf(arg: string): any;
255
+ } & {
256
+ readonly initialized: boolean;
257
+ readonly name: string;
258
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
259
+ readonly aliases: string[];
260
+ readonly displayName: string | undefined;
261
+ hasName(name: string): boolean;
262
+ readonly allAliases: string[];
263
+ readonly allRefNames: string[] | undefined;
264
+ readonly lowerCaseRefNames: string[] | undefined;
265
+ readonly allRefNamesWithLowerCase: string[] | undefined;
266
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
267
+ readonly refNameColors: string[];
268
+ } & {
269
+ readonly refNames: string[] | undefined;
270
+ } & {
271
+ getCanonicalRefName(refName: string): string | undefined;
272
+ getRefNameColor(refName: string): string | undefined;
273
+ isValidRefName(refName: string): boolean;
274
+ } & {
275
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
276
+ regions: import("@jbrowse/core/util").Region[];
277
+ refNameAliases: {
278
+ [x: string]: string;
279
+ };
280
+ lowerCaseRefNameAliases: {
281
+ [x: string]: string;
282
+ };
283
+ cytobands: import("@jbrowse/core/util").Feature[];
284
+ }): void;
285
+ setError(e: unknown): void;
286
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
287
+ setRefNameAliases(aliases: {
288
+ [x: string]: string;
289
+ }, lowerCaseAliases: {
290
+ [x: string]: string;
291
+ }): void;
292
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
293
+ setLoadingP(p?: Promise<void>): void;
294
+ load(): Promise<void>;
295
+ loadPre(): Promise<void>;
296
+ } & {
297
+ getAdapterMapEntry(adapterConf: {
298
+ [x: string]: unknown;
299
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
300
+ getRefNameMapForAdapter(adapterConf: {
301
+ [x: string]: unknown;
302
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
303
+ [x: string]: string;
304
+ }>;
305
+ getReverseRefNameMapForAdapter(adapterConf: {
306
+ [x: string]: unknown;
307
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
308
+ [x: string]: string;
309
+ }>;
310
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
311
+ } & {
312
+ get(asmName: string): ({
313
+ configuration: any;
314
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
315
+ error: unknown;
316
+ loadingP: Promise<void> | undefined;
317
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
318
+ refNameAliases: {
319
+ [x: string]: string;
320
+ } | undefined;
321
+ lowerCaseRefNameAliases: {
322
+ [x: string]: string;
323
+ } | undefined;
324
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
325
+ } & {
326
+ getConf(arg: string): any;
327
+ } & {
328
+ readonly initialized: boolean;
329
+ readonly name: string;
330
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
331
+ readonly aliases: string[];
332
+ readonly displayName: string | undefined;
333
+ hasName(name: string): boolean;
334
+ readonly allAliases: string[];
335
+ readonly allRefNames: string[] | undefined;
336
+ readonly lowerCaseRefNames: string[] | undefined;
337
+ readonly allRefNamesWithLowerCase: string[] | undefined;
338
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
339
+ readonly refNameColors: string[];
340
+ } & {
341
+ readonly refNames: string[] | undefined;
342
+ } & {
343
+ getCanonicalRefName(refName: string): string | undefined;
344
+ getRefNameColor(refName: string): string | undefined;
345
+ isValidRefName(refName: string): boolean;
346
+ } & {
347
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
348
+ regions: import("@jbrowse/core/util").Region[];
349
+ refNameAliases: {
350
+ [x: string]: string;
351
+ };
352
+ lowerCaseRefNameAliases: {
353
+ [x: string]: string;
354
+ };
355
+ cytobands: import("@jbrowse/core/util").Feature[];
356
+ }): void;
357
+ setError(e: unknown): void;
358
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
359
+ setRefNameAliases(aliases: {
360
+ [x: string]: string;
361
+ }, lowerCaseAliases: {
362
+ [x: string]: string;
363
+ }): void;
364
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
365
+ setLoadingP(p?: Promise<void>): void;
366
+ load(): Promise<void>;
367
+ loadPre(): Promise<void>;
368
+ } & {
369
+ getAdapterMapEntry(adapterConf: {
370
+ [x: string]: unknown;
371
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
372
+ getRefNameMapForAdapter(adapterConf: {
373
+ [x: string]: unknown;
374
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
375
+ [x: string]: string;
376
+ }>;
377
+ getReverseRefNameMapForAdapter(adapterConf: {
378
+ [x: string]: unknown;
379
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
380
+ [x: string]: string;
381
+ }>;
382
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
383
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
384
+ }, {
385
+ error: unknown;
386
+ loadingP: Promise<void> | undefined;
387
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
388
+ refNameAliases: {
389
+ [x: string]: string;
390
+ } | undefined;
391
+ lowerCaseRefNameAliases: {
392
+ [x: string]: string;
393
+ } | undefined;
394
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
395
+ } & {
396
+ getConf(arg: string): any;
397
+ } & {
398
+ readonly initialized: boolean;
399
+ readonly name: string;
400
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
401
+ readonly aliases: string[];
402
+ readonly displayName: string | undefined;
403
+ hasName(name: string): boolean;
404
+ readonly allAliases: string[];
405
+ readonly allRefNames: string[] | undefined;
406
+ readonly lowerCaseRefNames: string[] | undefined;
407
+ readonly allRefNamesWithLowerCase: string[] | undefined;
408
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
409
+ readonly refNameColors: string[];
410
+ } & {
411
+ readonly refNames: string[] | undefined;
412
+ } & {
413
+ getCanonicalRefName(refName: string): string | undefined;
414
+ getRefNameColor(refName: string): string | undefined;
415
+ isValidRefName(refName: string): boolean;
416
+ } & {
417
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
418
+ regions: import("@jbrowse/core/util").Region[];
419
+ refNameAliases: {
420
+ [x: string]: string;
421
+ };
422
+ lowerCaseRefNameAliases: {
423
+ [x: string]: string;
424
+ };
425
+ cytobands: import("@jbrowse/core/util").Feature[];
426
+ }): void;
427
+ setError(e: unknown): void;
428
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
429
+ setRefNameAliases(aliases: {
430
+ [x: string]: string;
431
+ }, lowerCaseAliases: {
432
+ [x: string]: string;
433
+ }): void;
434
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
435
+ setLoadingP(p?: Promise<void>): void;
436
+ load(): Promise<void>;
437
+ loadPre(): Promise<void>;
438
+ } & {
439
+ getAdapterMapEntry(adapterConf: {
440
+ [x: string]: unknown;
441
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
442
+ getRefNameMapForAdapter(adapterConf: {
443
+ [x: string]: unknown;
444
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
445
+ [x: string]: string;
446
+ }>;
447
+ getReverseRefNameMapForAdapter(adapterConf: {
448
+ [x: string]: unknown;
449
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
450
+ [x: string]: string;
451
+ }>;
452
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
453
+ readonly assemblyNamesList: any[];
454
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
455
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
456
+ } & {
457
+ waitForAssembly(assemblyName: string): Promise<({
458
+ configuration: any;
459
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
460
+ error: unknown;
461
+ loadingP: Promise<void> | undefined;
462
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
463
+ refNameAliases: {
464
+ [x: string]: string;
465
+ } | undefined;
466
+ lowerCaseRefNameAliases: {
467
+ [x: string]: string;
468
+ } | undefined;
469
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
470
+ } & {
471
+ getConf(arg: string): any;
472
+ } & {
473
+ readonly initialized: boolean;
474
+ readonly name: string;
475
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
476
+ readonly aliases: string[];
477
+ readonly displayName: string | undefined;
478
+ hasName(name: string): boolean;
479
+ readonly allAliases: string[];
480
+ readonly allRefNames: string[] | undefined;
481
+ readonly lowerCaseRefNames: string[] | undefined;
482
+ readonly allRefNamesWithLowerCase: string[] | undefined;
483
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
484
+ readonly refNameColors: string[];
485
+ } & {
486
+ readonly refNames: string[] | undefined;
487
+ } & {
488
+ getCanonicalRefName(refName: string): string | undefined;
489
+ getRefNameColor(refName: string): string | undefined;
490
+ isValidRefName(refName: string): boolean;
491
+ } & {
492
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
493
+ regions: import("@jbrowse/core/util").Region[];
494
+ refNameAliases: {
495
+ [x: string]: string;
496
+ };
497
+ lowerCaseRefNameAliases: {
498
+ [x: string]: string;
499
+ };
500
+ cytobands: import("@jbrowse/core/util").Feature[];
501
+ }): void;
502
+ setError(e: unknown): void;
503
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
504
+ setRefNameAliases(aliases: {
505
+ [x: string]: string;
506
+ }, lowerCaseAliases: {
507
+ [x: string]: string;
508
+ }): void;
509
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
510
+ setLoadingP(p?: Promise<void>): void;
511
+ load(): Promise<void>;
512
+ loadPre(): Promise<void>;
513
+ } & {
514
+ getAdapterMapEntry(adapterConf: {
515
+ [x: string]: unknown;
516
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
517
+ getRefNameMapForAdapter(adapterConf: {
518
+ [x: string]: unknown;
519
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
520
+ [x: string]: string;
521
+ }>;
522
+ getReverseRefNameMapForAdapter(adapterConf: {
523
+ [x: string]: unknown;
524
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
525
+ [x: string]: string;
526
+ }>;
527
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
528
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
529
+ }, {
530
+ error: unknown;
531
+ loadingP: Promise<void> | undefined;
532
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
533
+ refNameAliases: {
534
+ [x: string]: string;
535
+ } | undefined;
536
+ lowerCaseRefNameAliases: {
537
+ [x: string]: string;
538
+ } | undefined;
539
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
540
+ } & {
541
+ getConf(arg: string): any;
542
+ } & {
543
+ readonly initialized: boolean;
544
+ readonly name: string;
545
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
546
+ readonly aliases: string[];
547
+ readonly displayName: string | undefined;
548
+ hasName(name: string): boolean;
549
+ readonly allAliases: string[];
550
+ readonly allRefNames: string[] | undefined;
551
+ readonly lowerCaseRefNames: string[] | undefined;
552
+ readonly allRefNamesWithLowerCase: string[] | undefined;
553
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
554
+ readonly refNameColors: string[];
555
+ } & {
556
+ readonly refNames: string[] | undefined;
557
+ } & {
558
+ getCanonicalRefName(refName: string): string | undefined;
559
+ getRefNameColor(refName: string): string | undefined;
560
+ isValidRefName(refName: string): boolean;
561
+ } & {
562
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
563
+ regions: import("@jbrowse/core/util").Region[];
564
+ refNameAliases: {
565
+ [x: string]: string;
566
+ };
567
+ lowerCaseRefNameAliases: {
568
+ [x: string]: string;
569
+ };
570
+ cytobands: import("@jbrowse/core/util").Feature[];
571
+ }): void;
572
+ setError(e: unknown): void;
573
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
574
+ setRefNameAliases(aliases: {
575
+ [x: string]: string;
576
+ }, lowerCaseAliases: {
577
+ [x: string]: string;
578
+ }): void;
579
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
580
+ setLoadingP(p?: Promise<void>): void;
581
+ load(): Promise<void>;
582
+ loadPre(): Promise<void>;
583
+ } & {
584
+ getAdapterMapEntry(adapterConf: {
585
+ [x: string]: unknown;
586
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
587
+ getRefNameMapForAdapter(adapterConf: {
588
+ [x: string]: unknown;
589
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
590
+ [x: string]: string;
591
+ }>;
592
+ getReverseRefNameMapForAdapter(adapterConf: {
593
+ [x: string]: unknown;
594
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
595
+ [x: string]: string;
596
+ }>;
597
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
598
+ getRefNameMapForAdapter(adapterConf: {
599
+ [x: string]: unknown;
600
+ }, assemblyName: string | undefined, opts: {
601
+ stopToken?: string;
602
+ sessionId: string;
603
+ }): Promise<{
604
+ [x: string]: string;
605
+ } | undefined>;
606
+ getReverseRefNameMapForAdapter(adapterConf: {
607
+ [x: string]: unknown;
608
+ }, assemblyName: string | undefined, opts: {
609
+ stopToken?: string;
610
+ sessionId: string;
611
+ }): Promise<{
612
+ [x: string]: string;
613
+ } | undefined>;
614
+ isValidRefName(refName: string, assemblyName: string): boolean;
615
+ } & {
616
+ afterAttach(): void;
617
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
618
+ addAssembly(configuration: any): void;
619
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
620
+ assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
621
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
622
+ }, {
623
+ error: unknown;
624
+ loadingP: Promise<void> | undefined;
625
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
626
+ refNameAliases: {
627
+ [x: string]: string;
628
+ } | undefined;
629
+ lowerCaseRefNameAliases: {
630
+ [x: string]: string;
631
+ } | undefined;
632
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
633
+ } & {
634
+ getConf(arg: string): any;
635
+ } & {
636
+ readonly initialized: boolean;
637
+ readonly name: string;
638
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
639
+ readonly aliases: string[];
640
+ readonly displayName: string | undefined;
641
+ hasName(name: string): boolean;
642
+ readonly allAliases: string[];
643
+ readonly allRefNames: string[] | undefined;
644
+ readonly lowerCaseRefNames: string[] | undefined;
645
+ readonly allRefNamesWithLowerCase: string[] | undefined;
646
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
647
+ readonly refNameColors: string[];
648
+ } & {
649
+ readonly refNames: string[] | undefined;
650
+ } & {
651
+ getCanonicalRefName(refName: string): string | undefined;
652
+ getRefNameColor(refName: string): string | undefined;
653
+ isValidRefName(refName: string): boolean;
654
+ } & {
655
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
656
+ regions: import("@jbrowse/core/util").Region[];
657
+ refNameAliases: {
658
+ [x: string]: string;
659
+ };
660
+ lowerCaseRefNameAliases: {
661
+ [x: string]: string;
662
+ };
663
+ cytobands: import("@jbrowse/core/util").Feature[];
664
+ }): void;
665
+ setError(e: unknown): void;
666
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
667
+ setRefNameAliases(aliases: {
668
+ [x: string]: string;
669
+ }, lowerCaseAliases: {
670
+ [x: string]: string;
671
+ }): void;
672
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
673
+ setLoadingP(p?: Promise<void>): void;
674
+ load(): Promise<void>;
675
+ loadPre(): Promise<void>;
676
+ } & {
677
+ getAdapterMapEntry(adapterConf: {
678
+ [x: string]: unknown;
679
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
680
+ getRefNameMapForAdapter(adapterConf: {
681
+ [x: string]: unknown;
682
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
683
+ [x: string]: string;
684
+ }>;
685
+ getReverseRefNameMapForAdapter(adapterConf: {
686
+ [x: string]: unknown;
687
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
688
+ [x: string]: string;
689
+ }>;
690
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
691
+ }, {
692
+ readonly assemblyNameMap: Record<string, {
693
+ configuration: any;
694
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
695
+ error: unknown;
696
+ loadingP: Promise<void> | undefined;
697
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
698
+ refNameAliases: {
699
+ [x: string]: string;
700
+ } | undefined;
701
+ lowerCaseRefNameAliases: {
702
+ [x: string]: string;
703
+ } | undefined;
704
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
705
+ } & {
706
+ getConf(arg: string): any;
707
+ } & {
708
+ readonly initialized: boolean;
709
+ readonly name: string;
710
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
711
+ readonly aliases: string[];
712
+ readonly displayName: string | undefined;
713
+ hasName(name: string): boolean;
714
+ readonly allAliases: string[];
715
+ readonly allRefNames: string[] | undefined;
716
+ readonly lowerCaseRefNames: string[] | undefined;
717
+ readonly allRefNamesWithLowerCase: string[] | undefined;
718
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
719
+ readonly refNameColors: string[];
720
+ } & {
721
+ readonly refNames: string[] | undefined;
722
+ } & {
723
+ getCanonicalRefName(refName: string): string | undefined;
724
+ getRefNameColor(refName: string): string | undefined;
725
+ isValidRefName(refName: string): boolean;
726
+ } & {
727
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
728
+ regions: import("@jbrowse/core/util").Region[];
729
+ refNameAliases: {
730
+ [x: string]: string;
731
+ };
732
+ lowerCaseRefNameAliases: {
733
+ [x: string]: string;
734
+ };
735
+ cytobands: import("@jbrowse/core/util").Feature[];
736
+ }): void;
737
+ setError(e: unknown): void;
738
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
739
+ setRefNameAliases(aliases: {
740
+ [x: string]: string;
741
+ }, lowerCaseAliases: {
742
+ [x: string]: string;
743
+ }): void;
744
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
745
+ setLoadingP(p?: Promise<void>): void;
746
+ load(): Promise<void>;
747
+ loadPre(): Promise<void>;
748
+ } & {
749
+ getAdapterMapEntry(adapterConf: {
750
+ [x: string]: unknown;
751
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
752
+ getRefNameMapForAdapter(adapterConf: {
753
+ [x: string]: unknown;
754
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
755
+ [x: string]: string;
756
+ }>;
757
+ getReverseRefNameMapForAdapter(adapterConf: {
758
+ [x: string]: unknown;
759
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
760
+ [x: string]: string;
761
+ }>;
762
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
763
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
764
+ }, {
765
+ error: unknown;
766
+ loadingP: Promise<void> | undefined;
767
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
768
+ refNameAliases: {
769
+ [x: string]: string;
770
+ } | undefined;
771
+ lowerCaseRefNameAliases: {
772
+ [x: string]: string;
773
+ } | undefined;
774
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
775
+ } & {
776
+ getConf(arg: string): any;
777
+ } & {
778
+ readonly initialized: boolean;
779
+ readonly name: string;
780
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
781
+ readonly aliases: string[];
782
+ readonly displayName: string | undefined;
783
+ hasName(name: string): boolean;
784
+ readonly allAliases: string[];
785
+ readonly allRefNames: string[] | undefined;
786
+ readonly lowerCaseRefNames: string[] | undefined;
787
+ readonly allRefNamesWithLowerCase: string[] | undefined;
788
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
789
+ readonly refNameColors: string[];
790
+ } & {
791
+ readonly refNames: string[] | undefined;
792
+ } & {
793
+ getCanonicalRefName(refName: string): string | undefined;
794
+ getRefNameColor(refName: string): string | undefined;
795
+ isValidRefName(refName: string): boolean;
796
+ } & {
797
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
798
+ regions: import("@jbrowse/core/util").Region[];
799
+ refNameAliases: {
800
+ [x: string]: string;
801
+ };
802
+ lowerCaseRefNameAliases: {
803
+ [x: string]: string;
804
+ };
805
+ cytobands: import("@jbrowse/core/util").Feature[];
806
+ }): void;
807
+ setError(e: unknown): void;
808
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
809
+ setRefNameAliases(aliases: {
810
+ [x: string]: string;
811
+ }, lowerCaseAliases: {
812
+ [x: string]: string;
813
+ }): void;
814
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
815
+ setLoadingP(p?: Promise<void>): void;
816
+ load(): Promise<void>;
817
+ loadPre(): Promise<void>;
818
+ } & {
819
+ getAdapterMapEntry(adapterConf: {
820
+ [x: string]: unknown;
821
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
822
+ getRefNameMapForAdapter(adapterConf: {
823
+ [x: string]: unknown;
824
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
825
+ [x: string]: string;
826
+ }>;
827
+ getReverseRefNameMapForAdapter(adapterConf: {
828
+ [x: string]: unknown;
829
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
830
+ [x: string]: string;
831
+ }>;
832
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
833
+ } & {
834
+ get(asmName: string): ({
835
+ configuration: any;
836
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
837
+ error: unknown;
838
+ loadingP: Promise<void> | undefined;
839
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
840
+ refNameAliases: {
841
+ [x: string]: string;
842
+ } | undefined;
843
+ lowerCaseRefNameAliases: {
844
+ [x: string]: string;
845
+ } | undefined;
846
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
847
+ } & {
848
+ getConf(arg: string): any;
849
+ } & {
850
+ readonly initialized: boolean;
851
+ readonly name: string;
852
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
853
+ readonly aliases: string[];
854
+ readonly displayName: string | undefined;
855
+ hasName(name: string): boolean;
856
+ readonly allAliases: string[];
857
+ readonly allRefNames: string[] | undefined;
858
+ readonly lowerCaseRefNames: string[] | undefined;
859
+ readonly allRefNamesWithLowerCase: string[] | undefined;
860
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
861
+ readonly refNameColors: string[];
862
+ } & {
863
+ readonly refNames: string[] | undefined;
864
+ } & {
865
+ getCanonicalRefName(refName: string): string | undefined;
866
+ getRefNameColor(refName: string): string | undefined;
867
+ isValidRefName(refName: string): boolean;
868
+ } & {
869
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
870
+ regions: import("@jbrowse/core/util").Region[];
871
+ refNameAliases: {
872
+ [x: string]: string;
873
+ };
874
+ lowerCaseRefNameAliases: {
875
+ [x: string]: string;
876
+ };
877
+ cytobands: import("@jbrowse/core/util").Feature[];
878
+ }): void;
879
+ setError(e: unknown): void;
880
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
881
+ setRefNameAliases(aliases: {
882
+ [x: string]: string;
883
+ }, lowerCaseAliases: {
884
+ [x: string]: string;
885
+ }): void;
886
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
887
+ setLoadingP(p?: Promise<void>): void;
888
+ load(): Promise<void>;
889
+ loadPre(): Promise<void>;
890
+ } & {
891
+ getAdapterMapEntry(adapterConf: {
892
+ [x: string]: unknown;
893
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
894
+ getRefNameMapForAdapter(adapterConf: {
895
+ [x: string]: unknown;
896
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
897
+ [x: string]: string;
898
+ }>;
899
+ getReverseRefNameMapForAdapter(adapterConf: {
900
+ [x: string]: unknown;
901
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
902
+ [x: string]: string;
903
+ }>;
904
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
905
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
906
+ }, {
907
+ error: unknown;
908
+ loadingP: Promise<void> | undefined;
909
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
910
+ refNameAliases: {
911
+ [x: string]: string;
912
+ } | undefined;
913
+ lowerCaseRefNameAliases: {
914
+ [x: string]: string;
915
+ } | undefined;
916
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
917
+ } & {
918
+ getConf(arg: string): any;
919
+ } & {
920
+ readonly initialized: boolean;
921
+ readonly name: string;
922
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
923
+ readonly aliases: string[];
924
+ readonly displayName: string | undefined;
925
+ hasName(name: string): boolean;
926
+ readonly allAliases: string[];
927
+ readonly allRefNames: string[] | undefined;
928
+ readonly lowerCaseRefNames: string[] | undefined;
929
+ readonly allRefNamesWithLowerCase: string[] | undefined;
930
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
931
+ readonly refNameColors: string[];
932
+ } & {
933
+ readonly refNames: string[] | undefined;
934
+ } & {
935
+ getCanonicalRefName(refName: string): string | undefined;
936
+ getRefNameColor(refName: string): string | undefined;
937
+ isValidRefName(refName: string): boolean;
938
+ } & {
939
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
940
+ regions: import("@jbrowse/core/util").Region[];
941
+ refNameAliases: {
942
+ [x: string]: string;
943
+ };
944
+ lowerCaseRefNameAliases: {
945
+ [x: string]: string;
946
+ };
947
+ cytobands: import("@jbrowse/core/util").Feature[];
948
+ }): void;
949
+ setError(e: unknown): void;
950
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
951
+ setRefNameAliases(aliases: {
952
+ [x: string]: string;
953
+ }, lowerCaseAliases: {
954
+ [x: string]: string;
955
+ }): void;
956
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
957
+ setLoadingP(p?: Promise<void>): void;
958
+ load(): Promise<void>;
959
+ loadPre(): Promise<void>;
960
+ } & {
961
+ getAdapterMapEntry(adapterConf: {
962
+ [x: string]: unknown;
963
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
964
+ getRefNameMapForAdapter(adapterConf: {
965
+ [x: string]: unknown;
966
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
967
+ [x: string]: string;
968
+ }>;
969
+ getReverseRefNameMapForAdapter(adapterConf: {
970
+ [x: string]: unknown;
971
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
972
+ [x: string]: string;
973
+ }>;
974
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
975
+ readonly assemblyNamesList: any[];
976
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
977
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
978
+ } & {
979
+ waitForAssembly(assemblyName: string): Promise<({
980
+ configuration: any;
981
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
982
+ error: unknown;
983
+ loadingP: Promise<void> | undefined;
984
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
985
+ refNameAliases: {
986
+ [x: string]: string;
987
+ } | undefined;
988
+ lowerCaseRefNameAliases: {
989
+ [x: string]: string;
990
+ } | undefined;
991
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
992
+ } & {
993
+ getConf(arg: string): any;
994
+ } & {
995
+ readonly initialized: boolean;
996
+ readonly name: string;
997
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
998
+ readonly aliases: string[];
999
+ readonly displayName: string | undefined;
1000
+ hasName(name: string): boolean;
1001
+ readonly allAliases: string[];
1002
+ readonly allRefNames: string[] | undefined;
1003
+ readonly lowerCaseRefNames: string[] | undefined;
1004
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1005
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1006
+ readonly refNameColors: string[];
1007
+ } & {
1008
+ readonly refNames: string[] | undefined;
1009
+ } & {
1010
+ getCanonicalRefName(refName: string): string | undefined;
1011
+ getRefNameColor(refName: string): string | undefined;
1012
+ isValidRefName(refName: string): boolean;
1013
+ } & {
1014
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1015
+ regions: import("@jbrowse/core/util").Region[];
1016
+ refNameAliases: {
1017
+ [x: string]: string;
1018
+ };
1019
+ lowerCaseRefNameAliases: {
1020
+ [x: string]: string;
1021
+ };
1022
+ cytobands: import("@jbrowse/core/util").Feature[];
1023
+ }): void;
1024
+ setError(e: unknown): void;
1025
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1026
+ setRefNameAliases(aliases: {
1027
+ [x: string]: string;
1028
+ }, lowerCaseAliases: {
1029
+ [x: string]: string;
1030
+ }): void;
1031
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1032
+ setLoadingP(p?: Promise<void>): void;
1033
+ load(): Promise<void>;
1034
+ loadPre(): Promise<void>;
1035
+ } & {
1036
+ getAdapterMapEntry(adapterConf: {
1037
+ [x: string]: unknown;
1038
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1039
+ getRefNameMapForAdapter(adapterConf: {
1040
+ [x: string]: unknown;
1041
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1042
+ [x: string]: string;
1043
+ }>;
1044
+ getReverseRefNameMapForAdapter(adapterConf: {
1045
+ [x: string]: unknown;
1046
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1047
+ [x: string]: string;
1048
+ }>;
1049
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1050
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1051
+ }, {
1052
+ error: unknown;
1053
+ loadingP: Promise<void> | undefined;
1054
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1055
+ refNameAliases: {
1056
+ [x: string]: string;
1057
+ } | undefined;
1058
+ lowerCaseRefNameAliases: {
1059
+ [x: string]: string;
1060
+ } | undefined;
1061
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1062
+ } & {
1063
+ getConf(arg: string): any;
1064
+ } & {
1065
+ readonly initialized: boolean;
1066
+ readonly name: string;
1067
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1068
+ readonly aliases: string[];
1069
+ readonly displayName: string | undefined;
1070
+ hasName(name: string): boolean;
1071
+ readonly allAliases: string[];
1072
+ readonly allRefNames: string[] | undefined;
1073
+ readonly lowerCaseRefNames: string[] | undefined;
1074
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1075
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1076
+ readonly refNameColors: string[];
1077
+ } & {
1078
+ readonly refNames: string[] | undefined;
1079
+ } & {
1080
+ getCanonicalRefName(refName: string): string | undefined;
1081
+ getRefNameColor(refName: string): string | undefined;
1082
+ isValidRefName(refName: string): boolean;
1083
+ } & {
1084
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1085
+ regions: import("@jbrowse/core/util").Region[];
1086
+ refNameAliases: {
1087
+ [x: string]: string;
1088
+ };
1089
+ lowerCaseRefNameAliases: {
1090
+ [x: string]: string;
1091
+ };
1092
+ cytobands: import("@jbrowse/core/util").Feature[];
1093
+ }): void;
1094
+ setError(e: unknown): void;
1095
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1096
+ setRefNameAliases(aliases: {
1097
+ [x: string]: string;
1098
+ }, lowerCaseAliases: {
1099
+ [x: string]: string;
1100
+ }): void;
1101
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1102
+ setLoadingP(p?: Promise<void>): void;
1103
+ load(): Promise<void>;
1104
+ loadPre(): Promise<void>;
1105
+ } & {
1106
+ getAdapterMapEntry(adapterConf: {
1107
+ [x: string]: unknown;
1108
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1109
+ getRefNameMapForAdapter(adapterConf: {
1110
+ [x: string]: unknown;
1111
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1112
+ [x: string]: string;
1113
+ }>;
1114
+ getReverseRefNameMapForAdapter(adapterConf: {
1115
+ [x: string]: unknown;
1116
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1117
+ [x: string]: string;
1118
+ }>;
1119
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1120
+ getRefNameMapForAdapter(adapterConf: {
1121
+ [x: string]: unknown;
1122
+ }, assemblyName: string | undefined, opts: {
1123
+ stopToken?: string;
1124
+ sessionId: string;
1125
+ }): Promise<{
1126
+ [x: string]: string;
1127
+ } | undefined>;
1128
+ getReverseRefNameMapForAdapter(adapterConf: {
1129
+ [x: string]: unknown;
1130
+ }, assemblyName: string | undefined, opts: {
1131
+ stopToken?: string;
1132
+ sessionId: string;
1133
+ }): Promise<{
1134
+ [x: string]: string;
1135
+ } | undefined>;
1136
+ isValidRefName(refName: string, assemblyName: string): boolean;
1137
+ } & {
1138
+ afterAttach(): void;
1139
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1140
+ addAssembly(configuration: any): void;
1141
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
1142
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1143
+ rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1144
+ adminMode: boolean;
1145
+ error: unknown;
1146
+ textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1147
+ pluginManager: PluginManager;
1148
+ } & {
1149
+ setError(error: unknown): void;
1150
+ setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1151
+ setDefaultSession(): void;
1152
+ setSessionPath(path: string): void;
1153
+ renameCurrentSession(newName: string): void;
1154
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1155
+ jbrowse: import("mobx-state-tree").IAnyType;
1156
+ session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
1157
+ sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1158
+ assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1159
+ assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1160
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1161
+ }, {
1162
+ error: unknown;
1163
+ loadingP: Promise<void> | undefined;
1164
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1165
+ refNameAliases: {
1166
+ [x: string]: string;
1167
+ } | undefined;
1168
+ lowerCaseRefNameAliases: {
1169
+ [x: string]: string;
1170
+ } | undefined;
1171
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1172
+ } & {
1173
+ getConf(arg: string): any;
1174
+ } & {
1175
+ readonly initialized: boolean;
1176
+ readonly name: string;
1177
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1178
+ readonly aliases: string[];
1179
+ readonly displayName: string | undefined;
1180
+ hasName(name: string): boolean;
1181
+ readonly allAliases: string[];
1182
+ readonly allRefNames: string[] | undefined;
1183
+ readonly lowerCaseRefNames: string[] | undefined;
1184
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1185
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1186
+ readonly refNameColors: string[];
1187
+ } & {
1188
+ readonly refNames: string[] | undefined;
1189
+ } & {
1190
+ getCanonicalRefName(refName: string): string | undefined;
1191
+ getRefNameColor(refName: string): string | undefined;
1192
+ isValidRefName(refName: string): boolean;
1193
+ } & {
1194
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1195
+ regions: import("@jbrowse/core/util").Region[];
1196
+ refNameAliases: {
1197
+ [x: string]: string;
1198
+ };
1199
+ lowerCaseRefNameAliases: {
1200
+ [x: string]: string;
1201
+ };
1202
+ cytobands: import("@jbrowse/core/util").Feature[];
1203
+ }): void;
1204
+ setError(e: unknown): void;
1205
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1206
+ setRefNameAliases(aliases: {
1207
+ [x: string]: string;
1208
+ }, lowerCaseAliases: {
1209
+ [x: string]: string;
1210
+ }): void;
1211
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1212
+ setLoadingP(p?: Promise<void>): void;
1213
+ load(): Promise<void>;
1214
+ loadPre(): Promise<void>;
1215
+ } & {
1216
+ getAdapterMapEntry(adapterConf: {
1217
+ [x: string]: unknown;
1218
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1219
+ getRefNameMapForAdapter(adapterConf: {
1220
+ [x: string]: unknown;
1221
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1222
+ [x: string]: string;
1223
+ }>;
1224
+ getReverseRefNameMapForAdapter(adapterConf: {
1225
+ [x: string]: unknown;
1226
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1227
+ [x: string]: string;
1228
+ }>;
1229
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1230
+ }, {
1231
+ readonly assemblyNameMap: Record<string, {
1232
+ configuration: any;
1233
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1234
+ error: unknown;
1235
+ loadingP: Promise<void> | undefined;
1236
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1237
+ refNameAliases: {
1238
+ [x: string]: string;
1239
+ } | undefined;
1240
+ lowerCaseRefNameAliases: {
1241
+ [x: string]: string;
1242
+ } | undefined;
1243
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1244
+ } & {
1245
+ getConf(arg: string): any;
1246
+ } & {
1247
+ readonly initialized: boolean;
1248
+ readonly name: string;
1249
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1250
+ readonly aliases: string[];
1251
+ readonly displayName: string | undefined;
1252
+ hasName(name: string): boolean;
1253
+ readonly allAliases: string[];
1254
+ readonly allRefNames: string[] | undefined;
1255
+ readonly lowerCaseRefNames: string[] | undefined;
1256
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1257
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1258
+ readonly refNameColors: string[];
1259
+ } & {
1260
+ readonly refNames: string[] | undefined;
1261
+ } & {
1262
+ getCanonicalRefName(refName: string): string | undefined;
1263
+ getRefNameColor(refName: string): string | undefined;
1264
+ isValidRefName(refName: string): boolean;
1265
+ } & {
1266
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1267
+ regions: import("@jbrowse/core/util").Region[];
1268
+ refNameAliases: {
1269
+ [x: string]: string;
1270
+ };
1271
+ lowerCaseRefNameAliases: {
1272
+ [x: string]: string;
1273
+ };
1274
+ cytobands: import("@jbrowse/core/util").Feature[];
1275
+ }): void;
1276
+ setError(e: unknown): void;
1277
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1278
+ setRefNameAliases(aliases: {
1279
+ [x: string]: string;
1280
+ }, lowerCaseAliases: {
1281
+ [x: string]: string;
1282
+ }): void;
1283
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1284
+ setLoadingP(p?: Promise<void>): void;
1285
+ load(): Promise<void>;
1286
+ loadPre(): Promise<void>;
1287
+ } & {
1288
+ getAdapterMapEntry(adapterConf: {
1289
+ [x: string]: unknown;
1290
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1291
+ getRefNameMapForAdapter(adapterConf: {
1292
+ [x: string]: unknown;
1293
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1294
+ [x: string]: string;
1295
+ }>;
1296
+ getReverseRefNameMapForAdapter(adapterConf: {
1297
+ [x: string]: unknown;
1298
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1299
+ [x: string]: string;
1300
+ }>;
1301
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1302
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1303
+ }, {
1304
+ error: unknown;
1305
+ loadingP: Promise<void> | undefined;
1306
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1307
+ refNameAliases: {
1308
+ [x: string]: string;
1309
+ } | undefined;
1310
+ lowerCaseRefNameAliases: {
1311
+ [x: string]: string;
1312
+ } | undefined;
1313
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1314
+ } & {
1315
+ getConf(arg: string): any;
1316
+ } & {
1317
+ readonly initialized: boolean;
1318
+ readonly name: string;
1319
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1320
+ readonly aliases: string[];
1321
+ readonly displayName: string | undefined;
1322
+ hasName(name: string): boolean;
1323
+ readonly allAliases: string[];
1324
+ readonly allRefNames: string[] | undefined;
1325
+ readonly lowerCaseRefNames: string[] | undefined;
1326
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1327
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1328
+ readonly refNameColors: string[];
1329
+ } & {
1330
+ readonly refNames: string[] | undefined;
1331
+ } & {
1332
+ getCanonicalRefName(refName: string): string | undefined;
1333
+ getRefNameColor(refName: string): string | undefined;
1334
+ isValidRefName(refName: string): boolean;
1335
+ } & {
1336
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1337
+ regions: import("@jbrowse/core/util").Region[];
1338
+ refNameAliases: {
1339
+ [x: string]: string;
1340
+ };
1341
+ lowerCaseRefNameAliases: {
1342
+ [x: string]: string;
1343
+ };
1344
+ cytobands: import("@jbrowse/core/util").Feature[];
1345
+ }): void;
1346
+ setError(e: unknown): void;
1347
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1348
+ setRefNameAliases(aliases: {
1349
+ [x: string]: string;
1350
+ }, lowerCaseAliases: {
1351
+ [x: string]: string;
1352
+ }): void;
1353
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1354
+ setLoadingP(p?: Promise<void>): void;
1355
+ load(): Promise<void>;
1356
+ loadPre(): Promise<void>;
1357
+ } & {
1358
+ getAdapterMapEntry(adapterConf: {
1359
+ [x: string]: unknown;
1360
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1361
+ getRefNameMapForAdapter(adapterConf: {
1362
+ [x: string]: unknown;
1363
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1364
+ [x: string]: string;
1365
+ }>;
1366
+ getReverseRefNameMapForAdapter(adapterConf: {
1367
+ [x: string]: unknown;
1368
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1369
+ [x: string]: string;
1370
+ }>;
1371
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
1372
+ } & {
1373
+ get(asmName: string): ({
1374
+ configuration: any;
1375
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1376
+ error: unknown;
1377
+ loadingP: Promise<void> | undefined;
1378
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1379
+ refNameAliases: {
1380
+ [x: string]: string;
1381
+ } | undefined;
1382
+ lowerCaseRefNameAliases: {
1383
+ [x: string]: string;
1384
+ } | undefined;
1385
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1386
+ } & {
1387
+ getConf(arg: string): any;
1388
+ } & {
1389
+ readonly initialized: boolean;
1390
+ readonly name: string;
1391
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1392
+ readonly aliases: string[];
1393
+ readonly displayName: string | undefined;
1394
+ hasName(name: string): boolean;
1395
+ readonly allAliases: string[];
1396
+ readonly allRefNames: string[] | undefined;
1397
+ readonly lowerCaseRefNames: string[] | undefined;
1398
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1399
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1400
+ readonly refNameColors: string[];
1401
+ } & {
1402
+ readonly refNames: string[] | undefined;
1403
+ } & {
1404
+ getCanonicalRefName(refName: string): string | undefined;
1405
+ getRefNameColor(refName: string): string | undefined;
1406
+ isValidRefName(refName: string): boolean;
1407
+ } & {
1408
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1409
+ regions: import("@jbrowse/core/util").Region[];
1410
+ refNameAliases: {
1411
+ [x: string]: string;
1412
+ };
1413
+ lowerCaseRefNameAliases: {
1414
+ [x: string]: string;
1415
+ };
1416
+ cytobands: import("@jbrowse/core/util").Feature[];
1417
+ }): void;
1418
+ setError(e: unknown): void;
1419
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1420
+ setRefNameAliases(aliases: {
1421
+ [x: string]: string;
1422
+ }, lowerCaseAliases: {
1423
+ [x: string]: string;
1424
+ }): void;
1425
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1426
+ setLoadingP(p?: Promise<void>): void;
1427
+ load(): Promise<void>;
1428
+ loadPre(): Promise<void>;
1429
+ } & {
1430
+ getAdapterMapEntry(adapterConf: {
1431
+ [x: string]: unknown;
1432
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1433
+ getRefNameMapForAdapter(adapterConf: {
1434
+ [x: string]: unknown;
1435
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1436
+ [x: string]: string;
1437
+ }>;
1438
+ getReverseRefNameMapForAdapter(adapterConf: {
1439
+ [x: string]: unknown;
1440
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1441
+ [x: string]: string;
1442
+ }>;
1443
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1444
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1445
+ }, {
1446
+ error: unknown;
1447
+ loadingP: Promise<void> | undefined;
1448
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1449
+ refNameAliases: {
1450
+ [x: string]: string;
1451
+ } | undefined;
1452
+ lowerCaseRefNameAliases: {
1453
+ [x: string]: string;
1454
+ } | undefined;
1455
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1456
+ } & {
1457
+ getConf(arg: string): any;
1458
+ } & {
1459
+ readonly initialized: boolean;
1460
+ readonly name: string;
1461
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1462
+ readonly aliases: string[];
1463
+ readonly displayName: string | undefined;
1464
+ hasName(name: string): boolean;
1465
+ readonly allAliases: string[];
1466
+ readonly allRefNames: string[] | undefined;
1467
+ readonly lowerCaseRefNames: string[] | undefined;
1468
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1469
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1470
+ readonly refNameColors: string[];
1471
+ } & {
1472
+ readonly refNames: string[] | undefined;
1473
+ } & {
1474
+ getCanonicalRefName(refName: string): string | undefined;
1475
+ getRefNameColor(refName: string): string | undefined;
1476
+ isValidRefName(refName: string): boolean;
1477
+ } & {
1478
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1479
+ regions: import("@jbrowse/core/util").Region[];
1480
+ refNameAliases: {
1481
+ [x: string]: string;
1482
+ };
1483
+ lowerCaseRefNameAliases: {
1484
+ [x: string]: string;
1485
+ };
1486
+ cytobands: import("@jbrowse/core/util").Feature[];
1487
+ }): void;
1488
+ setError(e: unknown): void;
1489
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1490
+ setRefNameAliases(aliases: {
1491
+ [x: string]: string;
1492
+ }, lowerCaseAliases: {
1493
+ [x: string]: string;
1494
+ }): void;
1495
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1496
+ setLoadingP(p?: Promise<void>): void;
1497
+ load(): Promise<void>;
1498
+ loadPre(): Promise<void>;
1499
+ } & {
1500
+ getAdapterMapEntry(adapterConf: {
1501
+ [x: string]: unknown;
1502
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1503
+ getRefNameMapForAdapter(adapterConf: {
1504
+ [x: string]: unknown;
1505
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1506
+ [x: string]: string;
1507
+ }>;
1508
+ getReverseRefNameMapForAdapter(adapterConf: {
1509
+ [x: string]: unknown;
1510
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1511
+ [x: string]: string;
1512
+ }>;
1513
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1514
+ readonly assemblyNamesList: any[];
1515
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1516
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1517
+ } & {
1518
+ waitForAssembly(assemblyName: string): Promise<({
1519
+ configuration: any;
1520
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1521
+ error: unknown;
1522
+ loadingP: Promise<void> | undefined;
1523
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1524
+ refNameAliases: {
1525
+ [x: string]: string;
1526
+ } | undefined;
1527
+ lowerCaseRefNameAliases: {
1528
+ [x: string]: string;
1529
+ } | undefined;
1530
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1531
+ } & {
1532
+ getConf(arg: string): any;
1533
+ } & {
1534
+ readonly initialized: boolean;
1535
+ readonly name: string;
1536
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1537
+ readonly aliases: string[];
1538
+ readonly displayName: string | undefined;
1539
+ hasName(name: string): boolean;
1540
+ readonly allAliases: string[];
1541
+ readonly allRefNames: string[] | undefined;
1542
+ readonly lowerCaseRefNames: string[] | undefined;
1543
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1544
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1545
+ readonly refNameColors: string[];
1546
+ } & {
1547
+ readonly refNames: string[] | undefined;
1548
+ } & {
1549
+ getCanonicalRefName(refName: string): string | undefined;
1550
+ getRefNameColor(refName: string): string | undefined;
1551
+ isValidRefName(refName: string): boolean;
1552
+ } & {
1553
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1554
+ regions: import("@jbrowse/core/util").Region[];
1555
+ refNameAliases: {
1556
+ [x: string]: string;
1557
+ };
1558
+ lowerCaseRefNameAliases: {
1559
+ [x: string]: string;
1560
+ };
1561
+ cytobands: import("@jbrowse/core/util").Feature[];
1562
+ }): void;
1563
+ setError(e: unknown): void;
1564
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1565
+ setRefNameAliases(aliases: {
1566
+ [x: string]: string;
1567
+ }, lowerCaseAliases: {
1568
+ [x: string]: string;
1569
+ }): void;
1570
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1571
+ setLoadingP(p?: Promise<void>): void;
1572
+ load(): Promise<void>;
1573
+ loadPre(): Promise<void>;
1574
+ } & {
1575
+ getAdapterMapEntry(adapterConf: {
1576
+ [x: string]: unknown;
1577
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1578
+ getRefNameMapForAdapter(adapterConf: {
1579
+ [x: string]: unknown;
1580
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1581
+ [x: string]: string;
1582
+ }>;
1583
+ getReverseRefNameMapForAdapter(adapterConf: {
1584
+ [x: string]: unknown;
1585
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1586
+ [x: string]: string;
1587
+ }>;
1588
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1589
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1590
+ }, {
1591
+ error: unknown;
1592
+ loadingP: Promise<void> | undefined;
1593
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1594
+ refNameAliases: {
1595
+ [x: string]: string;
1596
+ } | undefined;
1597
+ lowerCaseRefNameAliases: {
1598
+ [x: string]: string;
1599
+ } | undefined;
1600
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1601
+ } & {
1602
+ getConf(arg: string): any;
1603
+ } & {
1604
+ readonly initialized: boolean;
1605
+ readonly name: string;
1606
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1607
+ readonly aliases: string[];
1608
+ readonly displayName: string | undefined;
1609
+ hasName(name: string): boolean;
1610
+ readonly allAliases: string[];
1611
+ readonly allRefNames: string[] | undefined;
1612
+ readonly lowerCaseRefNames: string[] | undefined;
1613
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1614
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1615
+ readonly refNameColors: string[];
1616
+ } & {
1617
+ readonly refNames: string[] | undefined;
1618
+ } & {
1619
+ getCanonicalRefName(refName: string): string | undefined;
1620
+ getRefNameColor(refName: string): string | undefined;
1621
+ isValidRefName(refName: string): boolean;
1622
+ } & {
1623
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1624
+ regions: import("@jbrowse/core/util").Region[];
1625
+ refNameAliases: {
1626
+ [x: string]: string;
1627
+ };
1628
+ lowerCaseRefNameAliases: {
1629
+ [x: string]: string;
1630
+ };
1631
+ cytobands: import("@jbrowse/core/util").Feature[];
1632
+ }): void;
1633
+ setError(e: unknown): void;
1634
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1635
+ setRefNameAliases(aliases: {
1636
+ [x: string]: string;
1637
+ }, lowerCaseAliases: {
1638
+ [x: string]: string;
1639
+ }): void;
1640
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1641
+ setLoadingP(p?: Promise<void>): void;
1642
+ load(): Promise<void>;
1643
+ loadPre(): Promise<void>;
1644
+ } & {
1645
+ getAdapterMapEntry(adapterConf: {
1646
+ [x: string]: unknown;
1647
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1648
+ getRefNameMapForAdapter(adapterConf: {
1649
+ [x: string]: unknown;
1650
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1651
+ [x: string]: string;
1652
+ }>;
1653
+ getReverseRefNameMapForAdapter(adapterConf: {
1654
+ [x: string]: unknown;
1655
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1656
+ [x: string]: string;
1657
+ }>;
1658
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1659
+ getRefNameMapForAdapter(adapterConf: {
1660
+ [x: string]: unknown;
1661
+ }, assemblyName: string | undefined, opts: {
1662
+ stopToken?: string;
1663
+ sessionId: string;
1664
+ }): Promise<{
1665
+ [x: string]: string;
1666
+ } | undefined>;
1667
+ getReverseRefNameMapForAdapter(adapterConf: {
1668
+ [x: string]: unknown;
1669
+ }, assemblyName: string | undefined, opts: {
1670
+ stopToken?: string;
1671
+ sessionId: string;
1672
+ }): Promise<{
1673
+ [x: string]: string;
1674
+ } | undefined>;
1675
+ isValidRefName(refName: string, assemblyName: string): boolean;
1676
+ } & {
1677
+ afterAttach(): void;
1678
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1679
+ addAssembly(configuration: any): void;
1680
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
1681
+ }, {
1682
+ rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1683
+ adminMode: boolean;
1684
+ error: unknown;
1685
+ textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1686
+ pluginManager: PluginManager;
1687
+ } & {
1688
+ setError(error: unknown): void;
1689
+ setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1690
+ setDefaultSession(): void;
1691
+ setSessionPath(path: string): void;
1692
+ renameCurrentSession(newName: string): void;
1693
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
24
1694
  } & {
25
1695
  readonly jbrowse: any;
26
1696
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;