@jbrowse/product-core 2.18.0 → 3.0.1

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 (27) hide show
  1. package/dist/Session/BaseSession.d.ts +2 -34
  2. package/dist/Session/Connections.d.ts +2 -22
  3. package/dist/Session/MultipleViews.d.ts +2 -1705
  4. package/dist/Session/SessionTracks.d.ts +4 -1727
  5. package/dist/Session/Tracks.d.ts +3 -1716
  6. package/dist/ui/AboutDialog.d.ts +1 -2
  7. package/dist/ui/AboutDialog.js +2 -3
  8. package/dist/ui/AboutDialogContents.d.ts +1 -2
  9. package/dist/ui/AboutDialogContents.js +14 -45
  10. package/dist/ui/FileInfoPanel.d.ts +1 -2
  11. package/dist/ui/FileInfoPanel.js +3 -25
  12. package/dist/ui/RefNameInfoDialog.d.ts +1 -2
  13. package/dist/ui/RefNameInfoDialog.js +15 -40
  14. package/esm/Session/BaseSession.d.ts +2 -34
  15. package/esm/Session/Connections.d.ts +2 -22
  16. package/esm/Session/MultipleViews.d.ts +2 -1705
  17. package/esm/Session/SessionTracks.d.ts +4 -1727
  18. package/esm/Session/Tracks.d.ts +3 -1716
  19. package/esm/ui/AboutDialog.d.ts +1 -2
  20. package/esm/ui/AboutDialog.js +2 -3
  21. package/esm/ui/AboutDialogContents.d.ts +1 -2
  22. package/esm/ui/AboutDialogContents.js +14 -22
  23. package/esm/ui/FileInfoPanel.d.ts +1 -2
  24. package/esm/ui/FileInfoPanel.js +3 -2
  25. package/esm/ui/RefNameInfoDialog.d.ts +1 -2
  26. package/esm/ui/RefNameInfoDialog.js +15 -17
  27. package/package.json +8 -8
package/esm/Session/Tracks.d.ts CHANGED
@@ -9,1677 +9,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
9
9
  selection: unknown;
10
10
  hovered: unknown;
11
11
  } & {
12
- readonly root: {
13
- jbrowse: any;
14
- session: any;
15
- sessionPath: string;
16
- assemblyManager: {
17
- assemblies: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
18
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
19
- }, {
20
- error: unknown;
21
- loadingP: Promise<void> | undefined;
22
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
23
- refNameAliases: {
24
- [x: string]: string;
25
- } | undefined;
26
- lowerCaseRefNameAliases: {
27
- [x: string]: string;
28
- } | undefined;
29
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
30
- } & {
31
- getConf(arg: string): any;
32
- } & {
33
- readonly initialized: boolean;
34
- readonly name: string;
35
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
36
- readonly aliases: string[];
37
- readonly displayName: string | undefined;
38
- hasName(name: string): boolean;
39
- readonly allAliases: string[];
40
- readonly allRefNames: string[] | undefined;
41
- readonly lowerCaseRefNames: string[] | undefined;
42
- readonly allRefNamesWithLowerCase: string[] | undefined;
43
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
44
- readonly refNameColors: string[];
45
- } & {
46
- readonly refNames: string[] | undefined;
47
- } & {
48
- getCanonicalRefName(refName: string): string | undefined;
49
- getRefNameColor(refName: string): string | undefined;
50
- isValidRefName(refName: string): boolean;
51
- } & {
52
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
53
- regions: import("@jbrowse/core/util").Region[];
54
- refNameAliases: {
55
- [x: string]: string;
56
- };
57
- lowerCaseRefNameAliases: {
58
- [x: string]: string;
59
- };
60
- cytobands: import("@jbrowse/core/util").Feature[];
61
- }): void;
62
- setError(e: unknown): void;
63
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
64
- setRefNameAliases(aliases: {
65
- [x: string]: string;
66
- }, lowerCaseAliases: {
67
- [x: string]: string;
68
- }): void;
69
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
70
- setLoadingP(p?: Promise<void>): void;
71
- load(): Promise<void>;
72
- loadPre(): Promise<void>;
73
- } & {
74
- getAdapterMapEntry(adapterConf: {
75
- [x: string]: unknown;
76
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
77
- getRefNameMapForAdapter(adapterConf: {
78
- [x: string]: unknown;
79
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
80
- [x: string]: string;
81
- }>;
82
- getReverseRefNameMapForAdapter(adapterConf: {
83
- [x: string]: unknown;
84
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
85
- [x: string]: string;
86
- }>;
87
- }, 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<{
88
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
89
- }, {
90
- error: unknown;
91
- loadingP: Promise<void> | undefined;
92
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
93
- refNameAliases: {
94
- [x: string]: string;
95
- } | undefined;
96
- lowerCaseRefNameAliases: {
97
- [x: string]: string;
98
- } | undefined;
99
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
100
- } & {
101
- getConf(arg: string): any;
102
- } & {
103
- readonly initialized: boolean;
104
- readonly name: string;
105
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
106
- readonly aliases: string[];
107
- readonly displayName: string | undefined;
108
- hasName(name: string): boolean;
109
- readonly allAliases: string[];
110
- readonly allRefNames: string[] | undefined;
111
- readonly lowerCaseRefNames: string[] | undefined;
112
- readonly allRefNamesWithLowerCase: string[] | undefined;
113
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
114
- readonly refNameColors: string[];
115
- } & {
116
- readonly refNames: string[] | undefined;
117
- } & {
118
- getCanonicalRefName(refName: string): string | undefined;
119
- getRefNameColor(refName: string): string | undefined;
120
- isValidRefName(refName: string): boolean;
121
- } & {
122
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
123
- regions: import("@jbrowse/core/util").Region[];
124
- refNameAliases: {
125
- [x: string]: string;
126
- };
127
- lowerCaseRefNameAliases: {
128
- [x: string]: string;
129
- };
130
- cytobands: import("@jbrowse/core/util").Feature[];
131
- }): void;
132
- setError(e: unknown): void;
133
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
134
- setRefNameAliases(aliases: {
135
- [x: string]: string;
136
- }, lowerCaseAliases: {
137
- [x: string]: string;
138
- }): void;
139
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
140
- setLoadingP(p?: Promise<void>): void;
141
- load(): Promise<void>;
142
- loadPre(): Promise<void>;
143
- } & {
144
- getAdapterMapEntry(adapterConf: {
145
- [x: string]: unknown;
146
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
147
- getRefNameMapForAdapter(adapterConf: {
148
- [x: string]: unknown;
149
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
150
- [x: string]: string;
151
- }>;
152
- getReverseRefNameMapForAdapter(adapterConf: {
153
- [x: string]: unknown;
154
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
155
- [x: string]: string;
156
- }>;
157
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
158
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
159
- readonly assemblyNameMap: Record<string, {
160
- configuration: any;
161
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
162
- error: unknown;
163
- loadingP: Promise<void> | undefined;
164
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
165
- refNameAliases: {
166
- [x: string]: string;
167
- } | undefined;
168
- lowerCaseRefNameAliases: {
169
- [x: string]: string;
170
- } | undefined;
171
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
172
- } & {
173
- getConf(arg: string): any;
174
- } & {
175
- readonly initialized: boolean;
176
- readonly name: string;
177
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
178
- readonly aliases: string[];
179
- readonly displayName: string | undefined;
180
- hasName(name: string): boolean;
181
- readonly allAliases: string[];
182
- readonly allRefNames: string[] | undefined;
183
- readonly lowerCaseRefNames: string[] | undefined;
184
- readonly allRefNamesWithLowerCase: string[] | undefined;
185
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
186
- readonly refNameColors: string[];
187
- } & {
188
- readonly refNames: string[] | undefined;
189
- } & {
190
- getCanonicalRefName(refName: string): string | undefined;
191
- getRefNameColor(refName: string): string | undefined;
192
- isValidRefName(refName: string): boolean;
193
- } & {
194
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
195
- regions: import("@jbrowse/core/util").Region[];
196
- refNameAliases: {
197
- [x: string]: string;
198
- };
199
- lowerCaseRefNameAliases: {
200
- [x: string]: string;
201
- };
202
- cytobands: import("@jbrowse/core/util").Feature[];
203
- }): void;
204
- setError(e: unknown): void;
205
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
206
- setRefNameAliases(aliases: {
207
- [x: string]: string;
208
- }, lowerCaseAliases: {
209
- [x: string]: string;
210
- }): void;
211
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
212
- setLoadingP(p?: Promise<void>): void;
213
- load(): Promise<void>;
214
- loadPre(): Promise<void>;
215
- } & {
216
- getAdapterMapEntry(adapterConf: {
217
- [x: string]: unknown;
218
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
219
- getRefNameMapForAdapter(adapterConf: {
220
- [x: string]: unknown;
221
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
222
- [x: string]: string;
223
- }>;
224
- getReverseRefNameMapForAdapter(adapterConf: {
225
- [x: string]: unknown;
226
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
227
- [x: string]: string;
228
- }>;
229
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
230
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
231
- }, {
232
- error: unknown;
233
- loadingP: Promise<void> | undefined;
234
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
235
- refNameAliases: {
236
- [x: string]: string;
237
- } | undefined;
238
- lowerCaseRefNameAliases: {
239
- [x: string]: string;
240
- } | undefined;
241
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
242
- } & {
243
- getConf(arg: string): any;
244
- } & {
245
- readonly initialized: boolean;
246
- readonly name: string;
247
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
248
- readonly aliases: string[];
249
- readonly displayName: string | undefined;
250
- hasName(name: string): boolean;
251
- readonly allAliases: string[];
252
- readonly allRefNames: string[] | undefined;
253
- readonly lowerCaseRefNames: string[] | undefined;
254
- readonly allRefNamesWithLowerCase: string[] | undefined;
255
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
256
- readonly refNameColors: string[];
257
- } & {
258
- readonly refNames: string[] | undefined;
259
- } & {
260
- getCanonicalRefName(refName: string): string | undefined;
261
- getRefNameColor(refName: string): string | undefined;
262
- isValidRefName(refName: string): boolean;
263
- } & {
264
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
265
- regions: import("@jbrowse/core/util").Region[];
266
- refNameAliases: {
267
- [x: string]: string;
268
- };
269
- lowerCaseRefNameAliases: {
270
- [x: string]: string;
271
- };
272
- cytobands: import("@jbrowse/core/util").Feature[];
273
- }): void;
274
- setError(e: unknown): void;
275
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
276
- setRefNameAliases(aliases: {
277
- [x: string]: string;
278
- }, lowerCaseAliases: {
279
- [x: string]: string;
280
- }): void;
281
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
282
- setLoadingP(p?: Promise<void>): void;
283
- load(): Promise<void>;
284
- loadPre(): Promise<void>;
285
- } & {
286
- getAdapterMapEntry(adapterConf: {
287
- [x: string]: unknown;
288
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
289
- getRefNameMapForAdapter(adapterConf: {
290
- [x: string]: unknown;
291
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
292
- [x: string]: string;
293
- }>;
294
- getReverseRefNameMapForAdapter(adapterConf: {
295
- [x: string]: unknown;
296
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
297
- [x: string]: string;
298
- }>;
299
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
300
- } & {
301
- get(asmName: string): ({
302
- configuration: any;
303
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
304
- error: unknown;
305
- loadingP: Promise<void> | undefined;
306
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
307
- refNameAliases: {
308
- [x: string]: string;
309
- } | undefined;
310
- lowerCaseRefNameAliases: {
311
- [x: string]: string;
312
- } | undefined;
313
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
314
- } & {
315
- getConf(arg: string): any;
316
- } & {
317
- readonly initialized: boolean;
318
- readonly name: string;
319
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
320
- readonly aliases: string[];
321
- readonly displayName: string | undefined;
322
- hasName(name: string): boolean;
323
- readonly allAliases: string[];
324
- readonly allRefNames: string[] | undefined;
325
- readonly lowerCaseRefNames: string[] | undefined;
326
- readonly allRefNamesWithLowerCase: string[] | undefined;
327
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
328
- readonly refNameColors: string[];
329
- } & {
330
- readonly refNames: string[] | undefined;
331
- } & {
332
- getCanonicalRefName(refName: string): string | undefined;
333
- getRefNameColor(refName: string): string | undefined;
334
- isValidRefName(refName: string): boolean;
335
- } & {
336
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
337
- regions: import("@jbrowse/core/util").Region[];
338
- refNameAliases: {
339
- [x: string]: string;
340
- };
341
- lowerCaseRefNameAliases: {
342
- [x: string]: string;
343
- };
344
- cytobands: import("@jbrowse/core/util").Feature[];
345
- }): void;
346
- setError(e: unknown): void;
347
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
348
- setRefNameAliases(aliases: {
349
- [x: string]: string;
350
- }, lowerCaseAliases: {
351
- [x: string]: string;
352
- }): void;
353
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
354
- setLoadingP(p?: Promise<void>): void;
355
- load(): Promise<void>;
356
- loadPre(): Promise<void>;
357
- } & {
358
- getAdapterMapEntry(adapterConf: {
359
- [x: string]: unknown;
360
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
361
- getRefNameMapForAdapter(adapterConf: {
362
- [x: string]: unknown;
363
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
364
- [x: string]: string;
365
- }>;
366
- getReverseRefNameMapForAdapter(adapterConf: {
367
- [x: string]: unknown;
368
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
369
- [x: string]: string;
370
- }>;
371
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
372
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
373
- }, {
374
- error: unknown;
375
- loadingP: Promise<void> | undefined;
376
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
377
- refNameAliases: {
378
- [x: string]: string;
379
- } | undefined;
380
- lowerCaseRefNameAliases: {
381
- [x: string]: string;
382
- } | undefined;
383
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
384
- } & {
385
- getConf(arg: string): any;
386
- } & {
387
- readonly initialized: boolean;
388
- readonly name: string;
389
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
390
- readonly aliases: string[];
391
- readonly displayName: string | undefined;
392
- hasName(name: string): boolean;
393
- readonly allAliases: string[];
394
- readonly allRefNames: string[] | undefined;
395
- readonly lowerCaseRefNames: string[] | undefined;
396
- readonly allRefNamesWithLowerCase: string[] | undefined;
397
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
398
- readonly refNameColors: string[];
399
- } & {
400
- readonly refNames: string[] | undefined;
401
- } & {
402
- getCanonicalRefName(refName: string): string | undefined;
403
- getRefNameColor(refName: string): string | undefined;
404
- isValidRefName(refName: string): boolean;
405
- } & {
406
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
407
- regions: import("@jbrowse/core/util").Region[];
408
- refNameAliases: {
409
- [x: string]: string;
410
- };
411
- lowerCaseRefNameAliases: {
412
- [x: string]: string;
413
- };
414
- cytobands: import("@jbrowse/core/util").Feature[];
415
- }): void;
416
- setError(e: unknown): void;
417
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
418
- setRefNameAliases(aliases: {
419
- [x: string]: string;
420
- }, lowerCaseAliases: {
421
- [x: string]: string;
422
- }): void;
423
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
424
- setLoadingP(p?: Promise<void>): void;
425
- load(): Promise<void>;
426
- loadPre(): Promise<void>;
427
- } & {
428
- getAdapterMapEntry(adapterConf: {
429
- [x: string]: unknown;
430
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
431
- getRefNameMapForAdapter(adapterConf: {
432
- [x: string]: unknown;
433
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
434
- [x: string]: string;
435
- }>;
436
- getReverseRefNameMapForAdapter(adapterConf: {
437
- [x: string]: unknown;
438
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
439
- [x: string]: string;
440
- }>;
441
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
442
- readonly assemblyNamesList: any[];
443
- readonly assemblyList: AnyConfigurationModel[];
444
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
445
- } & {
446
- waitForAssembly(assemblyName: string): Promise<({
447
- configuration: any;
448
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
449
- error: unknown;
450
- loadingP: Promise<void> | undefined;
451
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
452
- refNameAliases: {
453
- [x: string]: string;
454
- } | undefined;
455
- lowerCaseRefNameAliases: {
456
- [x: string]: string;
457
- } | undefined;
458
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
459
- } & {
460
- getConf(arg: string): any;
461
- } & {
462
- readonly initialized: boolean;
463
- readonly name: string;
464
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
465
- readonly aliases: string[];
466
- readonly displayName: string | undefined;
467
- hasName(name: string): boolean;
468
- readonly allAliases: string[];
469
- readonly allRefNames: string[] | undefined;
470
- readonly lowerCaseRefNames: string[] | undefined;
471
- readonly allRefNamesWithLowerCase: string[] | undefined;
472
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
473
- readonly refNameColors: string[];
474
- } & {
475
- readonly refNames: string[] | undefined;
476
- } & {
477
- getCanonicalRefName(refName: string): string | undefined;
478
- getRefNameColor(refName: string): string | undefined;
479
- isValidRefName(refName: string): boolean;
480
- } & {
481
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
482
- regions: import("@jbrowse/core/util").Region[];
483
- refNameAliases: {
484
- [x: string]: string;
485
- };
486
- lowerCaseRefNameAliases: {
487
- [x: string]: string;
488
- };
489
- cytobands: import("@jbrowse/core/util").Feature[];
490
- }): void;
491
- setError(e: unknown): void;
492
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
493
- setRefNameAliases(aliases: {
494
- [x: string]: string;
495
- }, lowerCaseAliases: {
496
- [x: string]: string;
497
- }): void;
498
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
499
- setLoadingP(p?: Promise<void>): void;
500
- load(): Promise<void>;
501
- loadPre(): Promise<void>;
502
- } & {
503
- getAdapterMapEntry(adapterConf: {
504
- [x: string]: unknown;
505
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
506
- getRefNameMapForAdapter(adapterConf: {
507
- [x: string]: unknown;
508
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
509
- [x: string]: string;
510
- }>;
511
- getReverseRefNameMapForAdapter(adapterConf: {
512
- [x: string]: unknown;
513
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
514
- [x: string]: string;
515
- }>;
516
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
517
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
518
- }, {
519
- error: unknown;
520
- loadingP: Promise<void> | undefined;
521
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
522
- refNameAliases: {
523
- [x: string]: string;
524
- } | undefined;
525
- lowerCaseRefNameAliases: {
526
- [x: string]: string;
527
- } | undefined;
528
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
529
- } & {
530
- getConf(arg: string): any;
531
- } & {
532
- readonly initialized: boolean;
533
- readonly name: string;
534
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
535
- readonly aliases: string[];
536
- readonly displayName: string | undefined;
537
- hasName(name: string): boolean;
538
- readonly allAliases: string[];
539
- readonly allRefNames: string[] | undefined;
540
- readonly lowerCaseRefNames: string[] | undefined;
541
- readonly allRefNamesWithLowerCase: string[] | undefined;
542
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
543
- readonly refNameColors: string[];
544
- } & {
545
- readonly refNames: string[] | undefined;
546
- } & {
547
- getCanonicalRefName(refName: string): string | undefined;
548
- getRefNameColor(refName: string): string | undefined;
549
- isValidRefName(refName: string): boolean;
550
- } & {
551
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
552
- regions: import("@jbrowse/core/util").Region[];
553
- refNameAliases: {
554
- [x: string]: string;
555
- };
556
- lowerCaseRefNameAliases: {
557
- [x: string]: string;
558
- };
559
- cytobands: import("@jbrowse/core/util").Feature[];
560
- }): void;
561
- setError(e: unknown): void;
562
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
563
- setRefNameAliases(aliases: {
564
- [x: string]: string;
565
- }, lowerCaseAliases: {
566
- [x: string]: string;
567
- }): void;
568
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
569
- setLoadingP(p?: Promise<void>): void;
570
- load(): Promise<void>;
571
- loadPre(): Promise<void>;
572
- } & {
573
- getAdapterMapEntry(adapterConf: {
574
- [x: string]: unknown;
575
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
576
- getRefNameMapForAdapter(adapterConf: {
577
- [x: string]: unknown;
578
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
579
- [x: string]: string;
580
- }>;
581
- getReverseRefNameMapForAdapter(adapterConf: {
582
- [x: string]: unknown;
583
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
584
- [x: string]: string;
585
- }>;
586
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
587
- getRefNameMapForAdapter(adapterConf: {
588
- [x: string]: unknown;
589
- }, assemblyName: string | undefined, opts: {
590
- stopToken?: string;
591
- sessionId: string;
592
- }): Promise<{
593
- [x: string]: string;
594
- } | undefined>;
595
- getReverseRefNameMapForAdapter(adapterConf: {
596
- [x: string]: unknown;
597
- }, assemblyName: string | undefined, opts: {
598
- stopToken?: string;
599
- sessionId: string;
600
- }): Promise<{
601
- [x: string]: string;
602
- } | undefined>;
603
- isValidRefName(refName: string, assemblyName: string): boolean;
604
- } & {
605
- afterAttach(): void;
606
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
607
- addAssembly(configuration: any): void;
608
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
609
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
610
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
611
- }, {
612
- error: unknown;
613
- loadingP: Promise<void> | undefined;
614
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
615
- refNameAliases: {
616
- [x: string]: string;
617
- } | undefined;
618
- lowerCaseRefNameAliases: {
619
- [x: string]: string;
620
- } | undefined;
621
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
622
- } & {
623
- getConf(arg: string): any;
624
- } & {
625
- readonly initialized: boolean;
626
- readonly name: string;
627
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
628
- readonly aliases: string[];
629
- readonly displayName: string | undefined;
630
- hasName(name: string): boolean;
631
- readonly allAliases: string[];
632
- readonly allRefNames: string[] | undefined;
633
- readonly lowerCaseRefNames: string[] | undefined;
634
- readonly allRefNamesWithLowerCase: string[] | undefined;
635
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
636
- readonly refNameColors: string[];
637
- } & {
638
- readonly refNames: string[] | undefined;
639
- } & {
640
- getCanonicalRefName(refName: string): string | undefined;
641
- getRefNameColor(refName: string): string | undefined;
642
- isValidRefName(refName: string): boolean;
643
- } & {
644
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
645
- regions: import("@jbrowse/core/util").Region[];
646
- refNameAliases: {
647
- [x: string]: string;
648
- };
649
- lowerCaseRefNameAliases: {
650
- [x: string]: string;
651
- };
652
- cytobands: import("@jbrowse/core/util").Feature[];
653
- }): void;
654
- setError(e: unknown): void;
655
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
656
- setRefNameAliases(aliases: {
657
- [x: string]: string;
658
- }, lowerCaseAliases: {
659
- [x: string]: string;
660
- }): void;
661
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
662
- setLoadingP(p?: Promise<void>): void;
663
- load(): Promise<void>;
664
- loadPre(): Promise<void>;
665
- } & {
666
- getAdapterMapEntry(adapterConf: {
667
- [x: string]: unknown;
668
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
669
- getRefNameMapForAdapter(adapterConf: {
670
- [x: string]: unknown;
671
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
672
- [x: string]: string;
673
- }>;
674
- getReverseRefNameMapForAdapter(adapterConf: {
675
- [x: string]: unknown;
676
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
677
- [x: string]: string;
678
- }>;
679
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
680
- }, {
681
- readonly assemblyNameMap: Record<string, {
682
- configuration: any;
683
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
684
- error: unknown;
685
- loadingP: Promise<void> | undefined;
686
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
687
- refNameAliases: {
688
- [x: string]: string;
689
- } | undefined;
690
- lowerCaseRefNameAliases: {
691
- [x: string]: string;
692
- } | undefined;
693
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
694
- } & {
695
- getConf(arg: string): any;
696
- } & {
697
- readonly initialized: boolean;
698
- readonly name: string;
699
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
700
- readonly aliases: string[];
701
- readonly displayName: string | undefined;
702
- hasName(name: string): boolean;
703
- readonly allAliases: string[];
704
- readonly allRefNames: string[] | undefined;
705
- readonly lowerCaseRefNames: string[] | undefined;
706
- readonly allRefNamesWithLowerCase: string[] | undefined;
707
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
708
- readonly refNameColors: string[];
709
- } & {
710
- readonly refNames: string[] | undefined;
711
- } & {
712
- getCanonicalRefName(refName: string): string | undefined;
713
- getRefNameColor(refName: string): string | undefined;
714
- isValidRefName(refName: string): boolean;
715
- } & {
716
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
717
- regions: import("@jbrowse/core/util").Region[];
718
- refNameAliases: {
719
- [x: string]: string;
720
- };
721
- lowerCaseRefNameAliases: {
722
- [x: string]: string;
723
- };
724
- cytobands: import("@jbrowse/core/util").Feature[];
725
- }): void;
726
- setError(e: unknown): void;
727
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
728
- setRefNameAliases(aliases: {
729
- [x: string]: string;
730
- }, lowerCaseAliases: {
731
- [x: string]: string;
732
- }): void;
733
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
734
- setLoadingP(p?: Promise<void>): void;
735
- load(): Promise<void>;
736
- loadPre(): Promise<void>;
737
- } & {
738
- getAdapterMapEntry(adapterConf: {
739
- [x: string]: unknown;
740
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
741
- getRefNameMapForAdapter(adapterConf: {
742
- [x: string]: unknown;
743
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
744
- [x: string]: string;
745
- }>;
746
- getReverseRefNameMapForAdapter(adapterConf: {
747
- [x: string]: unknown;
748
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
749
- [x: string]: string;
750
- }>;
751
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
752
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
753
- }, {
754
- error: unknown;
755
- loadingP: Promise<void> | undefined;
756
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
757
- refNameAliases: {
758
- [x: string]: string;
759
- } | undefined;
760
- lowerCaseRefNameAliases: {
761
- [x: string]: string;
762
- } | undefined;
763
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
764
- } & {
765
- getConf(arg: string): any;
766
- } & {
767
- readonly initialized: boolean;
768
- readonly name: string;
769
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
770
- readonly aliases: string[];
771
- readonly displayName: string | undefined;
772
- hasName(name: string): boolean;
773
- readonly allAliases: string[];
774
- readonly allRefNames: string[] | undefined;
775
- readonly lowerCaseRefNames: string[] | undefined;
776
- readonly allRefNamesWithLowerCase: string[] | undefined;
777
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
778
- readonly refNameColors: string[];
779
- } & {
780
- readonly refNames: string[] | undefined;
781
- } & {
782
- getCanonicalRefName(refName: string): string | undefined;
783
- getRefNameColor(refName: string): string | undefined;
784
- isValidRefName(refName: string): boolean;
785
- } & {
786
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
787
- regions: import("@jbrowse/core/util").Region[];
788
- refNameAliases: {
789
- [x: string]: string;
790
- };
791
- lowerCaseRefNameAliases: {
792
- [x: string]: string;
793
- };
794
- cytobands: import("@jbrowse/core/util").Feature[];
795
- }): void;
796
- setError(e: unknown): void;
797
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
798
- setRefNameAliases(aliases: {
799
- [x: string]: string;
800
- }, lowerCaseAliases: {
801
- [x: string]: string;
802
- }): void;
803
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
804
- setLoadingP(p?: Promise<void>): void;
805
- load(): Promise<void>;
806
- loadPre(): Promise<void>;
807
- } & {
808
- getAdapterMapEntry(adapterConf: {
809
- [x: string]: unknown;
810
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
811
- getRefNameMapForAdapter(adapterConf: {
812
- [x: string]: unknown;
813
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
814
- [x: string]: string;
815
- }>;
816
- getReverseRefNameMapForAdapter(adapterConf: {
817
- [x: string]: unknown;
818
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
819
- [x: string]: string;
820
- }>;
821
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
822
- } & {
823
- get(asmName: string): ({
824
- configuration: any;
825
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
826
- error: unknown;
827
- loadingP: Promise<void> | undefined;
828
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
829
- refNameAliases: {
830
- [x: string]: string;
831
- } | undefined;
832
- lowerCaseRefNameAliases: {
833
- [x: string]: string;
834
- } | undefined;
835
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
836
- } & {
837
- getConf(arg: string): any;
838
- } & {
839
- readonly initialized: boolean;
840
- readonly name: string;
841
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
842
- readonly aliases: string[];
843
- readonly displayName: string | undefined;
844
- hasName(name: string): boolean;
845
- readonly allAliases: string[];
846
- readonly allRefNames: string[] | undefined;
847
- readonly lowerCaseRefNames: string[] | undefined;
848
- readonly allRefNamesWithLowerCase: string[] | undefined;
849
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
850
- readonly refNameColors: string[];
851
- } & {
852
- readonly refNames: string[] | undefined;
853
- } & {
854
- getCanonicalRefName(refName: string): string | undefined;
855
- getRefNameColor(refName: string): string | undefined;
856
- isValidRefName(refName: string): boolean;
857
- } & {
858
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
859
- regions: import("@jbrowse/core/util").Region[];
860
- refNameAliases: {
861
- [x: string]: string;
862
- };
863
- lowerCaseRefNameAliases: {
864
- [x: string]: string;
865
- };
866
- cytobands: import("@jbrowse/core/util").Feature[];
867
- }): void;
868
- setError(e: unknown): void;
869
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
870
- setRefNameAliases(aliases: {
871
- [x: string]: string;
872
- }, lowerCaseAliases: {
873
- [x: string]: string;
874
- }): void;
875
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
876
- setLoadingP(p?: Promise<void>): void;
877
- load(): Promise<void>;
878
- loadPre(): Promise<void>;
879
- } & {
880
- getAdapterMapEntry(adapterConf: {
881
- [x: string]: unknown;
882
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
883
- getRefNameMapForAdapter(adapterConf: {
884
- [x: string]: unknown;
885
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
886
- [x: string]: string;
887
- }>;
888
- getReverseRefNameMapForAdapter(adapterConf: {
889
- [x: string]: unknown;
890
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
891
- [x: string]: string;
892
- }>;
893
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
894
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
895
- }, {
896
- error: unknown;
897
- loadingP: Promise<void> | undefined;
898
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
899
- refNameAliases: {
900
- [x: string]: string;
901
- } | undefined;
902
- lowerCaseRefNameAliases: {
903
- [x: string]: string;
904
- } | undefined;
905
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
906
- } & {
907
- getConf(arg: string): any;
908
- } & {
909
- readonly initialized: boolean;
910
- readonly name: string;
911
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
912
- readonly aliases: string[];
913
- readonly displayName: string | undefined;
914
- hasName(name: string): boolean;
915
- readonly allAliases: string[];
916
- readonly allRefNames: string[] | undefined;
917
- readonly lowerCaseRefNames: string[] | undefined;
918
- readonly allRefNamesWithLowerCase: string[] | undefined;
919
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
920
- readonly refNameColors: string[];
921
- } & {
922
- readonly refNames: string[] | undefined;
923
- } & {
924
- getCanonicalRefName(refName: string): string | undefined;
925
- getRefNameColor(refName: string): string | undefined;
926
- isValidRefName(refName: string): boolean;
927
- } & {
928
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
929
- regions: import("@jbrowse/core/util").Region[];
930
- refNameAliases: {
931
- [x: string]: string;
932
- };
933
- lowerCaseRefNameAliases: {
934
- [x: string]: string;
935
- };
936
- cytobands: import("@jbrowse/core/util").Feature[];
937
- }): void;
938
- setError(e: unknown): void;
939
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
940
- setRefNameAliases(aliases: {
941
- [x: string]: string;
942
- }, lowerCaseAliases: {
943
- [x: string]: string;
944
- }): void;
945
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
946
- setLoadingP(p?: Promise<void>): void;
947
- load(): Promise<void>;
948
- loadPre(): Promise<void>;
949
- } & {
950
- getAdapterMapEntry(adapterConf: {
951
- [x: string]: unknown;
952
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
953
- getRefNameMapForAdapter(adapterConf: {
954
- [x: string]: unknown;
955
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
956
- [x: string]: string;
957
- }>;
958
- getReverseRefNameMapForAdapter(adapterConf: {
959
- [x: string]: unknown;
960
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
961
- [x: string]: string;
962
- }>;
963
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
964
- readonly assemblyNamesList: any[];
965
- readonly assemblyList: AnyConfigurationModel[];
966
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
967
- } & {
968
- waitForAssembly(assemblyName: string): Promise<({
969
- configuration: any;
970
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
971
- error: unknown;
972
- loadingP: Promise<void> | undefined;
973
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
974
- refNameAliases: {
975
- [x: string]: string;
976
- } | undefined;
977
- lowerCaseRefNameAliases: {
978
- [x: string]: string;
979
- } | undefined;
980
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
981
- } & {
982
- getConf(arg: string): any;
983
- } & {
984
- readonly initialized: boolean;
985
- readonly name: string;
986
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
987
- readonly aliases: string[];
988
- readonly displayName: string | undefined;
989
- hasName(name: string): boolean;
990
- readonly allAliases: string[];
991
- readonly allRefNames: string[] | undefined;
992
- readonly lowerCaseRefNames: string[] | undefined;
993
- readonly allRefNamesWithLowerCase: string[] | undefined;
994
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
995
- readonly refNameColors: string[];
996
- } & {
997
- readonly refNames: string[] | undefined;
998
- } & {
999
- getCanonicalRefName(refName: string): string | undefined;
1000
- getRefNameColor(refName: string): string | undefined;
1001
- isValidRefName(refName: string): boolean;
1002
- } & {
1003
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1004
- regions: import("@jbrowse/core/util").Region[];
1005
- refNameAliases: {
1006
- [x: string]: string;
1007
- };
1008
- lowerCaseRefNameAliases: {
1009
- [x: string]: string;
1010
- };
1011
- cytobands: import("@jbrowse/core/util").Feature[];
1012
- }): void;
1013
- setError(e: unknown): void;
1014
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1015
- setRefNameAliases(aliases: {
1016
- [x: string]: string;
1017
- }, lowerCaseAliases: {
1018
- [x: string]: string;
1019
- }): void;
1020
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1021
- setLoadingP(p?: Promise<void>): void;
1022
- load(): Promise<void>;
1023
- loadPre(): Promise<void>;
1024
- } & {
1025
- getAdapterMapEntry(adapterConf: {
1026
- [x: string]: unknown;
1027
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1028
- getRefNameMapForAdapter(adapterConf: {
1029
- [x: string]: unknown;
1030
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1031
- [x: string]: string;
1032
- }>;
1033
- getReverseRefNameMapForAdapter(adapterConf: {
1034
- [x: string]: unknown;
1035
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1036
- [x: string]: string;
1037
- }>;
1038
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1039
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1040
- }, {
1041
- error: unknown;
1042
- loadingP: Promise<void> | undefined;
1043
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1044
- refNameAliases: {
1045
- [x: string]: string;
1046
- } | undefined;
1047
- lowerCaseRefNameAliases: {
1048
- [x: string]: string;
1049
- } | undefined;
1050
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1051
- } & {
1052
- getConf(arg: string): any;
1053
- } & {
1054
- readonly initialized: boolean;
1055
- readonly name: string;
1056
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1057
- readonly aliases: string[];
1058
- readonly displayName: string | undefined;
1059
- hasName(name: string): boolean;
1060
- readonly allAliases: string[];
1061
- readonly allRefNames: string[] | undefined;
1062
- readonly lowerCaseRefNames: string[] | undefined;
1063
- readonly allRefNamesWithLowerCase: string[] | undefined;
1064
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1065
- readonly refNameColors: string[];
1066
- } & {
1067
- readonly refNames: string[] | undefined;
1068
- } & {
1069
- getCanonicalRefName(refName: string): string | undefined;
1070
- getRefNameColor(refName: string): string | undefined;
1071
- isValidRefName(refName: string): boolean;
1072
- } & {
1073
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1074
- regions: import("@jbrowse/core/util").Region[];
1075
- refNameAliases: {
1076
- [x: string]: string;
1077
- };
1078
- lowerCaseRefNameAliases: {
1079
- [x: string]: string;
1080
- };
1081
- cytobands: import("@jbrowse/core/util").Feature[];
1082
- }): void;
1083
- setError(e: unknown): void;
1084
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1085
- setRefNameAliases(aliases: {
1086
- [x: string]: string;
1087
- }, lowerCaseAliases: {
1088
- [x: string]: string;
1089
- }): void;
1090
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1091
- setLoadingP(p?: Promise<void>): void;
1092
- load(): Promise<void>;
1093
- loadPre(): Promise<void>;
1094
- } & {
1095
- getAdapterMapEntry(adapterConf: {
1096
- [x: string]: unknown;
1097
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1098
- getRefNameMapForAdapter(adapterConf: {
1099
- [x: string]: unknown;
1100
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1101
- [x: string]: string;
1102
- }>;
1103
- getReverseRefNameMapForAdapter(adapterConf: {
1104
- [x: string]: unknown;
1105
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1106
- [x: string]: string;
1107
- }>;
1108
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1109
- getRefNameMapForAdapter(adapterConf: {
1110
- [x: string]: unknown;
1111
- }, assemblyName: string | undefined, opts: {
1112
- stopToken?: string;
1113
- sessionId: string;
1114
- }): Promise<{
1115
- [x: string]: string;
1116
- } | undefined>;
1117
- getReverseRefNameMapForAdapter(adapterConf: {
1118
- [x: string]: unknown;
1119
- }, assemblyName: string | undefined, opts: {
1120
- stopToken?: string;
1121
- sessionId: string;
1122
- }): Promise<{
1123
- [x: string]: string;
1124
- } | undefined>;
1125
- isValidRefName(refName: string, assemblyName: string): boolean;
1126
- } & {
1127
- afterAttach(): void;
1128
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1129
- addAssembly(configuration: any): void;
1130
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
1131
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1132
- rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1133
- adminMode: boolean;
1134
- error: unknown;
1135
- textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1136
- pluginManager: PluginManager;
1137
- } & {
1138
- setError(error: unknown): void;
1139
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1140
- setDefaultSession(): void;
1141
- setSessionPath(path: string): void;
1142
- renameCurrentSession(newName: string): void;
1143
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1144
- jbrowse: import("mobx-state-tree").IAnyType;
1145
- session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
1146
- sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1147
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1148
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1149
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1150
- }, {
1151
- error: unknown;
1152
- loadingP: Promise<void> | undefined;
1153
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1154
- refNameAliases: {
1155
- [x: string]: string;
1156
- } | undefined;
1157
- lowerCaseRefNameAliases: {
1158
- [x: string]: string;
1159
- } | undefined;
1160
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1161
- } & {
1162
- getConf(arg: string): any;
1163
- } & {
1164
- readonly initialized: boolean;
1165
- readonly name: string;
1166
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1167
- readonly aliases: string[];
1168
- readonly displayName: string | undefined;
1169
- hasName(name: string): boolean;
1170
- readonly allAliases: string[];
1171
- readonly allRefNames: string[] | undefined;
1172
- readonly lowerCaseRefNames: string[] | undefined;
1173
- readonly allRefNamesWithLowerCase: string[] | undefined;
1174
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1175
- readonly refNameColors: string[];
1176
- } & {
1177
- readonly refNames: string[] | undefined;
1178
- } & {
1179
- getCanonicalRefName(refName: string): string | undefined;
1180
- getRefNameColor(refName: string): string | undefined;
1181
- isValidRefName(refName: string): boolean;
1182
- } & {
1183
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1184
- regions: import("@jbrowse/core/util").Region[];
1185
- refNameAliases: {
1186
- [x: string]: string;
1187
- };
1188
- lowerCaseRefNameAliases: {
1189
- [x: string]: string;
1190
- };
1191
- cytobands: import("@jbrowse/core/util").Feature[];
1192
- }): void;
1193
- setError(e: unknown): void;
1194
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1195
- setRefNameAliases(aliases: {
1196
- [x: string]: string;
1197
- }, lowerCaseAliases: {
1198
- [x: string]: string;
1199
- }): void;
1200
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1201
- setLoadingP(p?: Promise<void>): void;
1202
- load(): Promise<void>;
1203
- loadPre(): Promise<void>;
1204
- } & {
1205
- getAdapterMapEntry(adapterConf: {
1206
- [x: string]: unknown;
1207
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1208
- getRefNameMapForAdapter(adapterConf: {
1209
- [x: string]: unknown;
1210
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1211
- [x: string]: string;
1212
- }>;
1213
- getReverseRefNameMapForAdapter(adapterConf: {
1214
- [x: string]: unknown;
1215
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1216
- [x: string]: string;
1217
- }>;
1218
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1219
- }, {
1220
- readonly assemblyNameMap: Record<string, {
1221
- configuration: any;
1222
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1223
- error: unknown;
1224
- loadingP: Promise<void> | undefined;
1225
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1226
- refNameAliases: {
1227
- [x: string]: string;
1228
- } | undefined;
1229
- lowerCaseRefNameAliases: {
1230
- [x: string]: string;
1231
- } | undefined;
1232
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1233
- } & {
1234
- getConf(arg: string): any;
1235
- } & {
1236
- readonly initialized: boolean;
1237
- readonly name: string;
1238
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1239
- readonly aliases: string[];
1240
- readonly displayName: string | undefined;
1241
- hasName(name: string): boolean;
1242
- readonly allAliases: string[];
1243
- readonly allRefNames: string[] | undefined;
1244
- readonly lowerCaseRefNames: string[] | undefined;
1245
- readonly allRefNamesWithLowerCase: string[] | undefined;
1246
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1247
- readonly refNameColors: string[];
1248
- } & {
1249
- readonly refNames: string[] | undefined;
1250
- } & {
1251
- getCanonicalRefName(refName: string): string | undefined;
1252
- getRefNameColor(refName: string): string | undefined;
1253
- isValidRefName(refName: string): boolean;
1254
- } & {
1255
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1256
- regions: import("@jbrowse/core/util").Region[];
1257
- refNameAliases: {
1258
- [x: string]: string;
1259
- };
1260
- lowerCaseRefNameAliases: {
1261
- [x: string]: string;
1262
- };
1263
- cytobands: import("@jbrowse/core/util").Feature[];
1264
- }): void;
1265
- setError(e: unknown): void;
1266
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1267
- setRefNameAliases(aliases: {
1268
- [x: string]: string;
1269
- }, lowerCaseAliases: {
1270
- [x: string]: string;
1271
- }): void;
1272
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1273
- setLoadingP(p?: Promise<void>): void;
1274
- load(): Promise<void>;
1275
- loadPre(): Promise<void>;
1276
- } & {
1277
- getAdapterMapEntry(adapterConf: {
1278
- [x: string]: unknown;
1279
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1280
- getRefNameMapForAdapter(adapterConf: {
1281
- [x: string]: unknown;
1282
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1283
- [x: string]: string;
1284
- }>;
1285
- getReverseRefNameMapForAdapter(adapterConf: {
1286
- [x: string]: unknown;
1287
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1288
- [x: string]: string;
1289
- }>;
1290
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1291
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1292
- }, {
1293
- error: unknown;
1294
- loadingP: Promise<void> | undefined;
1295
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1296
- refNameAliases: {
1297
- [x: string]: string;
1298
- } | undefined;
1299
- lowerCaseRefNameAliases: {
1300
- [x: string]: string;
1301
- } | undefined;
1302
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1303
- } & {
1304
- getConf(arg: string): any;
1305
- } & {
1306
- readonly initialized: boolean;
1307
- readonly name: string;
1308
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1309
- readonly aliases: string[];
1310
- readonly displayName: string | undefined;
1311
- hasName(name: string): boolean;
1312
- readonly allAliases: string[];
1313
- readonly allRefNames: string[] | undefined;
1314
- readonly lowerCaseRefNames: string[] | undefined;
1315
- readonly allRefNamesWithLowerCase: string[] | undefined;
1316
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1317
- readonly refNameColors: string[];
1318
- } & {
1319
- readonly refNames: string[] | undefined;
1320
- } & {
1321
- getCanonicalRefName(refName: string): string | undefined;
1322
- getRefNameColor(refName: string): string | undefined;
1323
- isValidRefName(refName: string): boolean;
1324
- } & {
1325
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1326
- regions: import("@jbrowse/core/util").Region[];
1327
- refNameAliases: {
1328
- [x: string]: string;
1329
- };
1330
- lowerCaseRefNameAliases: {
1331
- [x: string]: string;
1332
- };
1333
- cytobands: import("@jbrowse/core/util").Feature[];
1334
- }): void;
1335
- setError(e: unknown): void;
1336
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1337
- setRefNameAliases(aliases: {
1338
- [x: string]: string;
1339
- }, lowerCaseAliases: {
1340
- [x: string]: string;
1341
- }): void;
1342
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1343
- setLoadingP(p?: Promise<void>): void;
1344
- load(): Promise<void>;
1345
- loadPre(): Promise<void>;
1346
- } & {
1347
- getAdapterMapEntry(adapterConf: {
1348
- [x: string]: unknown;
1349
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1350
- getRefNameMapForAdapter(adapterConf: {
1351
- [x: string]: unknown;
1352
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1353
- [x: string]: string;
1354
- }>;
1355
- getReverseRefNameMapForAdapter(adapterConf: {
1356
- [x: string]: unknown;
1357
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1358
- [x: string]: string;
1359
- }>;
1360
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
1361
- } & {
1362
- get(asmName: string): ({
1363
- configuration: any;
1364
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1365
- error: unknown;
1366
- loadingP: Promise<void> | undefined;
1367
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1368
- refNameAliases: {
1369
- [x: string]: string;
1370
- } | undefined;
1371
- lowerCaseRefNameAliases: {
1372
- [x: string]: string;
1373
- } | undefined;
1374
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1375
- } & {
1376
- getConf(arg: string): any;
1377
- } & {
1378
- readonly initialized: boolean;
1379
- readonly name: string;
1380
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1381
- readonly aliases: string[];
1382
- readonly displayName: string | undefined;
1383
- hasName(name: string): boolean;
1384
- readonly allAliases: string[];
1385
- readonly allRefNames: string[] | undefined;
1386
- readonly lowerCaseRefNames: string[] | undefined;
1387
- readonly allRefNamesWithLowerCase: string[] | undefined;
1388
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1389
- readonly refNameColors: string[];
1390
- } & {
1391
- readonly refNames: string[] | undefined;
1392
- } & {
1393
- getCanonicalRefName(refName: string): string | undefined;
1394
- getRefNameColor(refName: string): string | undefined;
1395
- isValidRefName(refName: string): boolean;
1396
- } & {
1397
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1398
- regions: import("@jbrowse/core/util").Region[];
1399
- refNameAliases: {
1400
- [x: string]: string;
1401
- };
1402
- lowerCaseRefNameAliases: {
1403
- [x: string]: string;
1404
- };
1405
- cytobands: import("@jbrowse/core/util").Feature[];
1406
- }): void;
1407
- setError(e: unknown): void;
1408
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1409
- setRefNameAliases(aliases: {
1410
- [x: string]: string;
1411
- }, lowerCaseAliases: {
1412
- [x: string]: string;
1413
- }): void;
1414
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1415
- setLoadingP(p?: Promise<void>): void;
1416
- load(): Promise<void>;
1417
- loadPre(): Promise<void>;
1418
- } & {
1419
- getAdapterMapEntry(adapterConf: {
1420
- [x: string]: unknown;
1421
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1422
- getRefNameMapForAdapter(adapterConf: {
1423
- [x: string]: unknown;
1424
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1425
- [x: string]: string;
1426
- }>;
1427
- getReverseRefNameMapForAdapter(adapterConf: {
1428
- [x: string]: unknown;
1429
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1430
- [x: string]: string;
1431
- }>;
1432
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1433
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1434
- }, {
1435
- error: unknown;
1436
- loadingP: Promise<void> | undefined;
1437
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1438
- refNameAliases: {
1439
- [x: string]: string;
1440
- } | undefined;
1441
- lowerCaseRefNameAliases: {
1442
- [x: string]: string;
1443
- } | undefined;
1444
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1445
- } & {
1446
- getConf(arg: string): any;
1447
- } & {
1448
- readonly initialized: boolean;
1449
- readonly name: string;
1450
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1451
- readonly aliases: string[];
1452
- readonly displayName: string | undefined;
1453
- hasName(name: string): boolean;
1454
- readonly allAliases: string[];
1455
- readonly allRefNames: string[] | undefined;
1456
- readonly lowerCaseRefNames: string[] | undefined;
1457
- readonly allRefNamesWithLowerCase: string[] | undefined;
1458
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1459
- readonly refNameColors: string[];
1460
- } & {
1461
- readonly refNames: string[] | undefined;
1462
- } & {
1463
- getCanonicalRefName(refName: string): string | undefined;
1464
- getRefNameColor(refName: string): string | undefined;
1465
- isValidRefName(refName: string): boolean;
1466
- } & {
1467
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1468
- regions: import("@jbrowse/core/util").Region[];
1469
- refNameAliases: {
1470
- [x: string]: string;
1471
- };
1472
- lowerCaseRefNameAliases: {
1473
- [x: string]: string;
1474
- };
1475
- cytobands: import("@jbrowse/core/util").Feature[];
1476
- }): void;
1477
- setError(e: unknown): void;
1478
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1479
- setRefNameAliases(aliases: {
1480
- [x: string]: string;
1481
- }, lowerCaseAliases: {
1482
- [x: string]: string;
1483
- }): void;
1484
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1485
- setLoadingP(p?: Promise<void>): void;
1486
- load(): Promise<void>;
1487
- loadPre(): Promise<void>;
1488
- } & {
1489
- getAdapterMapEntry(adapterConf: {
1490
- [x: string]: unknown;
1491
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1492
- getRefNameMapForAdapter(adapterConf: {
1493
- [x: string]: unknown;
1494
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1495
- [x: string]: string;
1496
- }>;
1497
- getReverseRefNameMapForAdapter(adapterConf: {
1498
- [x: string]: unknown;
1499
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1500
- [x: string]: string;
1501
- }>;
1502
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1503
- readonly assemblyNamesList: any[];
1504
- readonly assemblyList: AnyConfigurationModel[];
1505
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1506
- } & {
1507
- waitForAssembly(assemblyName: string): Promise<({
1508
- configuration: any;
1509
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1510
- error: unknown;
1511
- loadingP: Promise<void> | undefined;
1512
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1513
- refNameAliases: {
1514
- [x: string]: string;
1515
- } | undefined;
1516
- lowerCaseRefNameAliases: {
1517
- [x: string]: string;
1518
- } | undefined;
1519
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1520
- } & {
1521
- getConf(arg: string): any;
1522
- } & {
1523
- readonly initialized: boolean;
1524
- readonly name: string;
1525
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1526
- readonly aliases: string[];
1527
- readonly displayName: string | undefined;
1528
- hasName(name: string): boolean;
1529
- readonly allAliases: string[];
1530
- readonly allRefNames: string[] | undefined;
1531
- readonly lowerCaseRefNames: string[] | undefined;
1532
- readonly allRefNamesWithLowerCase: string[] | undefined;
1533
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1534
- readonly refNameColors: string[];
1535
- } & {
1536
- readonly refNames: string[] | undefined;
1537
- } & {
1538
- getCanonicalRefName(refName: string): string | undefined;
1539
- getRefNameColor(refName: string): string | undefined;
1540
- isValidRefName(refName: string): boolean;
1541
- } & {
1542
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1543
- regions: import("@jbrowse/core/util").Region[];
1544
- refNameAliases: {
1545
- [x: string]: string;
1546
- };
1547
- lowerCaseRefNameAliases: {
1548
- [x: string]: string;
1549
- };
1550
- cytobands: import("@jbrowse/core/util").Feature[];
1551
- }): void;
1552
- setError(e: unknown): void;
1553
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1554
- setRefNameAliases(aliases: {
1555
- [x: string]: string;
1556
- }, lowerCaseAliases: {
1557
- [x: string]: string;
1558
- }): void;
1559
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1560
- setLoadingP(p?: Promise<void>): void;
1561
- load(): Promise<void>;
1562
- loadPre(): Promise<void>;
1563
- } & {
1564
- getAdapterMapEntry(adapterConf: {
1565
- [x: string]: unknown;
1566
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1567
- getRefNameMapForAdapter(adapterConf: {
1568
- [x: string]: unknown;
1569
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1570
- [x: string]: string;
1571
- }>;
1572
- getReverseRefNameMapForAdapter(adapterConf: {
1573
- [x: string]: unknown;
1574
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1575
- [x: string]: string;
1576
- }>;
1577
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1578
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1579
- }, {
1580
- error: unknown;
1581
- loadingP: Promise<void> | undefined;
1582
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1583
- refNameAliases: {
1584
- [x: string]: string;
1585
- } | undefined;
1586
- lowerCaseRefNameAliases: {
1587
- [x: string]: string;
1588
- } | undefined;
1589
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1590
- } & {
1591
- getConf(arg: string): any;
1592
- } & {
1593
- readonly initialized: boolean;
1594
- readonly name: string;
1595
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1596
- readonly aliases: string[];
1597
- readonly displayName: string | undefined;
1598
- hasName(name: string): boolean;
1599
- readonly allAliases: string[];
1600
- readonly allRefNames: string[] | undefined;
1601
- readonly lowerCaseRefNames: string[] | undefined;
1602
- readonly allRefNamesWithLowerCase: string[] | undefined;
1603
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1604
- readonly refNameColors: string[];
1605
- } & {
1606
- readonly refNames: string[] | undefined;
1607
- } & {
1608
- getCanonicalRefName(refName: string): string | undefined;
1609
- getRefNameColor(refName: string): string | undefined;
1610
- isValidRefName(refName: string): boolean;
1611
- } & {
1612
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1613
- regions: import("@jbrowse/core/util").Region[];
1614
- refNameAliases: {
1615
- [x: string]: string;
1616
- };
1617
- lowerCaseRefNameAliases: {
1618
- [x: string]: string;
1619
- };
1620
- cytobands: import("@jbrowse/core/util").Feature[];
1621
- }): void;
1622
- setError(e: unknown): void;
1623
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1624
- setRefNameAliases(aliases: {
1625
- [x: string]: string;
1626
- }, lowerCaseAliases: {
1627
- [x: string]: string;
1628
- }): void;
1629
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1630
- setLoadingP(p?: Promise<void>): void;
1631
- load(): Promise<void>;
1632
- loadPre(): Promise<void>;
1633
- } & {
1634
- getAdapterMapEntry(adapterConf: {
1635
- [x: string]: unknown;
1636
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1637
- getRefNameMapForAdapter(adapterConf: {
1638
- [x: string]: unknown;
1639
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1640
- [x: string]: string;
1641
- }>;
1642
- getReverseRefNameMapForAdapter(adapterConf: {
1643
- [x: string]: unknown;
1644
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1645
- [x: string]: string;
1646
- }>;
1647
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1648
- getRefNameMapForAdapter(adapterConf: {
1649
- [x: string]: unknown;
1650
- }, assemblyName: string | undefined, opts: {
1651
- stopToken?: string;
1652
- sessionId: string;
1653
- }): Promise<{
1654
- [x: string]: string;
1655
- } | undefined>;
1656
- getReverseRefNameMapForAdapter(adapterConf: {
1657
- [x: string]: unknown;
1658
- }, assemblyName: string | undefined, opts: {
1659
- stopToken?: string;
1660
- sessionId: string;
1661
- }): Promise<{
1662
- [x: string]: string;
1663
- } | undefined>;
1664
- isValidRefName(refName: string, assemblyName: string): boolean;
1665
- } & {
1666
- afterAttach(): void;
1667
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1668
- addAssembly(configuration: any): void;
1669
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
1670
- }, {
1671
- rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1672
- adminMode: boolean;
1673
- error: unknown;
1674
- textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1675
- pluginManager: PluginManager;
1676
- } & {
1677
- setError(error: unknown): void;
1678
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1679
- setDefaultSession(): void;
1680
- setSessionPath(path: string): void;
1681
- renameCurrentSession(newName: string): void;
1682
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
12
+ readonly root: import("mobx-state-tree").TypeOrStateTreeNodeToStateTreeNode<ROOT_MODEL_TYPE>;
1683
13
  } & {
1684
14
  readonly jbrowse: any;
1685
15
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1697,40 +27,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
1697
27
  readonly adminMode: boolean;
1698
28
  readonly textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1699
29
  } & {
1700
- readonly assemblies: ({
1701
- [x: string]: any;
1702
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1703
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1704
- [x: string]: any;
1705
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1706
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1707
- [x: string]: any;
1708
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1709
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1710
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1711
- aliases: {
1712
- type: string;
1713
- defaultValue: never[];
1714
- description: string;
1715
- };
1716
- sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1717
- refNameColors: {
1718
- type: string;
1719
- defaultValue: never[];
1720
- description: string;
1721
- };
1722
- refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1723
- adapter: import("mobx-state-tree").IAnyModelType;
1724
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
1725
- cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1726
- adapter: import("mobx-state-tree").IAnyModelType;
1727
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
1728
- displayName: {
1729
- type: string;
1730
- defaultValue: string;
1731
- description: string;
1732
- };
1733
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name">>>)[];
30
+ readonly assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
1734
31
  } & {
1735
32
  setSelection(thing: unknown): void;
1736
33
  clearSelection(): void;
@@ -1740,17 +37,7 @@ export declare function TracksManagerSessionMixin(pluginManager: PluginManager):
1740
37
  } & {
1741
38
  removeReferring(referring: import("./ReferenceManagement").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
1742
39
  } & {
1743
- readonly tracks: ({
1744
- [x: string]: any;
1745
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1746
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1747
- [x: string]: any;
1748
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1749
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1750
- [x: string]: any;
1751
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1752
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1753
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
40
+ readonly tracks: AnyConfigurationModel[];
1754
41
  } & {
1755
42
  addTrackConf(trackConf: AnyConfiguration): any;
1756
43
  deleteTrackConf(trackConf: AnyConfigurationModel): any;