@jbrowse/product-core 2.18.0 → 3.0.0

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 (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 +3 -3
package/esm/Session/SessionTracks.d.ts CHANGED
@@ -11,1677 +11,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
11
11
  selection: unknown;
12
12
  hovered: unknown;
13
13
  } & {
14
- readonly root: {
15
- jbrowse: any;
16
- session: any;
17
- sessionPath: string;
18
- assemblyManager: {
19
- assemblies: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
20
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
21
- }, {
22
- error: unknown;
23
- loadingP: Promise<void> | undefined;
24
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
25
- refNameAliases: {
26
- [x: string]: string;
27
- } | undefined;
28
- lowerCaseRefNameAliases: {
29
- [x: string]: string;
30
- } | undefined;
31
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
32
- } & {
33
- getConf(arg: string): any;
34
- } & {
35
- readonly initialized: boolean;
36
- readonly name: string;
37
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
38
- readonly aliases: string[];
39
- readonly displayName: string | undefined;
40
- hasName(name: string): boolean;
41
- readonly allAliases: string[];
42
- readonly allRefNames: string[] | undefined;
43
- readonly lowerCaseRefNames: string[] | undefined;
44
- readonly allRefNamesWithLowerCase: string[] | undefined;
45
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
46
- readonly refNameColors: string[];
47
- } & {
48
- readonly refNames: string[] | undefined;
49
- } & {
50
- getCanonicalRefName(refName: string): string | undefined;
51
- getRefNameColor(refName: string): string | undefined;
52
- isValidRefName(refName: string): boolean;
53
- } & {
54
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
55
- regions: import("@jbrowse/core/util").Region[];
56
- refNameAliases: {
57
- [x: string]: string;
58
- };
59
- lowerCaseRefNameAliases: {
60
- [x: string]: string;
61
- };
62
- cytobands: import("@jbrowse/core/util").Feature[];
63
- }): void;
64
- setError(e: unknown): void;
65
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
66
- setRefNameAliases(aliases: {
67
- [x: string]: string;
68
- }, lowerCaseAliases: {
69
- [x: string]: string;
70
- }): void;
71
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
72
- setLoadingP(p?: Promise<void>): void;
73
- load(): Promise<void>;
74
- loadPre(): Promise<void>;
75
- } & {
76
- getAdapterMapEntry(adapterConf: {
77
- [x: string]: unknown;
78
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
79
- getRefNameMapForAdapter(adapterConf: {
80
- [x: string]: unknown;
81
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
82
- [x: string]: string;
83
- }>;
84
- getReverseRefNameMapForAdapter(adapterConf: {
85
- [x: string]: unknown;
86
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
87
- [x: string]: string;
88
- }>;
89
- }, 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<{
90
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
91
- }, {
92
- error: unknown;
93
- loadingP: Promise<void> | undefined;
94
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
95
- refNameAliases: {
96
- [x: string]: string;
97
- } | undefined;
98
- lowerCaseRefNameAliases: {
99
- [x: string]: string;
100
- } | undefined;
101
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
102
- } & {
103
- getConf(arg: string): any;
104
- } & {
105
- readonly initialized: boolean;
106
- readonly name: string;
107
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
108
- readonly aliases: string[];
109
- readonly displayName: string | undefined;
110
- hasName(name: string): boolean;
111
- readonly allAliases: string[];
112
- readonly allRefNames: string[] | undefined;
113
- readonly lowerCaseRefNames: string[] | undefined;
114
- readonly allRefNamesWithLowerCase: string[] | undefined;
115
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
116
- readonly refNameColors: string[];
117
- } & {
118
- readonly refNames: string[] | undefined;
119
- } & {
120
- getCanonicalRefName(refName: string): string | undefined;
121
- getRefNameColor(refName: string): string | undefined;
122
- isValidRefName(refName: string): boolean;
123
- } & {
124
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
125
- regions: import("@jbrowse/core/util").Region[];
126
- refNameAliases: {
127
- [x: string]: string;
128
- };
129
- lowerCaseRefNameAliases: {
130
- [x: string]: string;
131
- };
132
- cytobands: import("@jbrowse/core/util").Feature[];
133
- }): void;
134
- setError(e: unknown): void;
135
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
136
- setRefNameAliases(aliases: {
137
- [x: string]: string;
138
- }, lowerCaseAliases: {
139
- [x: string]: string;
140
- }): void;
141
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
142
- setLoadingP(p?: Promise<void>): void;
143
- load(): Promise<void>;
144
- loadPre(): Promise<void>;
145
- } & {
146
- getAdapterMapEntry(adapterConf: {
147
- [x: string]: unknown;
148
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
149
- getRefNameMapForAdapter(adapterConf: {
150
- [x: string]: unknown;
151
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
152
- [x: string]: string;
153
- }>;
154
- getReverseRefNameMapForAdapter(adapterConf: {
155
- [x: string]: unknown;
156
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
157
- [x: string]: string;
158
- }>;
159
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
160
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
161
- readonly assemblyNameMap: Record<string, {
162
- configuration: any;
163
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
164
- error: unknown;
165
- loadingP: Promise<void> | undefined;
166
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
167
- refNameAliases: {
168
- [x: string]: string;
169
- } | undefined;
170
- lowerCaseRefNameAliases: {
171
- [x: string]: string;
172
- } | undefined;
173
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
174
- } & {
175
- getConf(arg: string): any;
176
- } & {
177
- readonly initialized: boolean;
178
- readonly name: string;
179
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
180
- readonly aliases: string[];
181
- readonly displayName: string | undefined;
182
- hasName(name: string): boolean;
183
- readonly allAliases: string[];
184
- readonly allRefNames: string[] | undefined;
185
- readonly lowerCaseRefNames: string[] | undefined;
186
- readonly allRefNamesWithLowerCase: string[] | undefined;
187
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
188
- readonly refNameColors: string[];
189
- } & {
190
- readonly refNames: string[] | undefined;
191
- } & {
192
- getCanonicalRefName(refName: string): string | undefined;
193
- getRefNameColor(refName: string): string | undefined;
194
- isValidRefName(refName: string): boolean;
195
- } & {
196
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
197
- regions: import("@jbrowse/core/util").Region[];
198
- refNameAliases: {
199
- [x: string]: string;
200
- };
201
- lowerCaseRefNameAliases: {
202
- [x: string]: string;
203
- };
204
- cytobands: import("@jbrowse/core/util").Feature[];
205
- }): void;
206
- setError(e: unknown): void;
207
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
208
- setRefNameAliases(aliases: {
209
- [x: string]: string;
210
- }, lowerCaseAliases: {
211
- [x: string]: string;
212
- }): void;
213
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
214
- setLoadingP(p?: Promise<void>): void;
215
- load(): Promise<void>;
216
- loadPre(): Promise<void>;
217
- } & {
218
- getAdapterMapEntry(adapterConf: {
219
- [x: string]: unknown;
220
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
221
- getRefNameMapForAdapter(adapterConf: {
222
- [x: string]: unknown;
223
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
224
- [x: string]: string;
225
- }>;
226
- getReverseRefNameMapForAdapter(adapterConf: {
227
- [x: string]: unknown;
228
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
229
- [x: string]: string;
230
- }>;
231
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
232
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
233
- }, {
234
- error: unknown;
235
- loadingP: Promise<void> | undefined;
236
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
237
- refNameAliases: {
238
- [x: string]: string;
239
- } | undefined;
240
- lowerCaseRefNameAliases: {
241
- [x: string]: string;
242
- } | undefined;
243
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
244
- } & {
245
- getConf(arg: string): any;
246
- } & {
247
- readonly initialized: boolean;
248
- readonly name: string;
249
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
250
- readonly aliases: string[];
251
- readonly displayName: string | undefined;
252
- hasName(name: string): boolean;
253
- readonly allAliases: string[];
254
- readonly allRefNames: string[] | undefined;
255
- readonly lowerCaseRefNames: string[] | undefined;
256
- readonly allRefNamesWithLowerCase: string[] | undefined;
257
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
258
- readonly refNameColors: string[];
259
- } & {
260
- readonly refNames: string[] | undefined;
261
- } & {
262
- getCanonicalRefName(refName: string): string | undefined;
263
- getRefNameColor(refName: string): string | undefined;
264
- isValidRefName(refName: string): boolean;
265
- } & {
266
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
267
- regions: import("@jbrowse/core/util").Region[];
268
- refNameAliases: {
269
- [x: string]: string;
270
- };
271
- lowerCaseRefNameAliases: {
272
- [x: string]: string;
273
- };
274
- cytobands: import("@jbrowse/core/util").Feature[];
275
- }): void;
276
- setError(e: unknown): void;
277
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
278
- setRefNameAliases(aliases: {
279
- [x: string]: string;
280
- }, lowerCaseAliases: {
281
- [x: string]: string;
282
- }): void;
283
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
284
- setLoadingP(p?: Promise<void>): void;
285
- load(): Promise<void>;
286
- loadPre(): Promise<void>;
287
- } & {
288
- getAdapterMapEntry(adapterConf: {
289
- [x: string]: unknown;
290
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
291
- getRefNameMapForAdapter(adapterConf: {
292
- [x: string]: unknown;
293
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
294
- [x: string]: string;
295
- }>;
296
- getReverseRefNameMapForAdapter(adapterConf: {
297
- [x: string]: unknown;
298
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
299
- [x: string]: string;
300
- }>;
301
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
302
- } & {
303
- get(asmName: string): ({
304
- configuration: any;
305
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
306
- error: unknown;
307
- loadingP: Promise<void> | undefined;
308
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
309
- refNameAliases: {
310
- [x: string]: string;
311
- } | undefined;
312
- lowerCaseRefNameAliases: {
313
- [x: string]: string;
314
- } | undefined;
315
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
316
- } & {
317
- getConf(arg: string): any;
318
- } & {
319
- readonly initialized: boolean;
320
- readonly name: string;
321
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
322
- readonly aliases: string[];
323
- readonly displayName: string | undefined;
324
- hasName(name: string): boolean;
325
- readonly allAliases: string[];
326
- readonly allRefNames: string[] | undefined;
327
- readonly lowerCaseRefNames: string[] | undefined;
328
- readonly allRefNamesWithLowerCase: string[] | undefined;
329
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
330
- readonly refNameColors: string[];
331
- } & {
332
- readonly refNames: string[] | undefined;
333
- } & {
334
- getCanonicalRefName(refName: string): string | undefined;
335
- getRefNameColor(refName: string): string | undefined;
336
- isValidRefName(refName: string): boolean;
337
- } & {
338
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
339
- regions: import("@jbrowse/core/util").Region[];
340
- refNameAliases: {
341
- [x: string]: string;
342
- };
343
- lowerCaseRefNameAliases: {
344
- [x: string]: string;
345
- };
346
- cytobands: import("@jbrowse/core/util").Feature[];
347
- }): void;
348
- setError(e: unknown): void;
349
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
350
- setRefNameAliases(aliases: {
351
- [x: string]: string;
352
- }, lowerCaseAliases: {
353
- [x: string]: string;
354
- }): void;
355
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
356
- setLoadingP(p?: Promise<void>): void;
357
- load(): Promise<void>;
358
- loadPre(): Promise<void>;
359
- } & {
360
- getAdapterMapEntry(adapterConf: {
361
- [x: string]: unknown;
362
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
363
- getRefNameMapForAdapter(adapterConf: {
364
- [x: string]: unknown;
365
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
366
- [x: string]: string;
367
- }>;
368
- getReverseRefNameMapForAdapter(adapterConf: {
369
- [x: string]: unknown;
370
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
371
- [x: string]: string;
372
- }>;
373
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
374
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
375
- }, {
376
- error: unknown;
377
- loadingP: Promise<void> | undefined;
378
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
379
- refNameAliases: {
380
- [x: string]: string;
381
- } | undefined;
382
- lowerCaseRefNameAliases: {
383
- [x: string]: string;
384
- } | undefined;
385
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
386
- } & {
387
- getConf(arg: string): any;
388
- } & {
389
- readonly initialized: boolean;
390
- readonly name: string;
391
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
392
- readonly aliases: string[];
393
- readonly displayName: string | undefined;
394
- hasName(name: string): boolean;
395
- readonly allAliases: string[];
396
- readonly allRefNames: string[] | undefined;
397
- readonly lowerCaseRefNames: string[] | undefined;
398
- readonly allRefNamesWithLowerCase: string[] | undefined;
399
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
400
- readonly refNameColors: string[];
401
- } & {
402
- readonly refNames: string[] | undefined;
403
- } & {
404
- getCanonicalRefName(refName: string): string | undefined;
405
- getRefNameColor(refName: string): string | undefined;
406
- isValidRefName(refName: string): boolean;
407
- } & {
408
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
409
- regions: import("@jbrowse/core/util").Region[];
410
- refNameAliases: {
411
- [x: string]: string;
412
- };
413
- lowerCaseRefNameAliases: {
414
- [x: string]: string;
415
- };
416
- cytobands: import("@jbrowse/core/util").Feature[];
417
- }): void;
418
- setError(e: unknown): void;
419
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
420
- setRefNameAliases(aliases: {
421
- [x: string]: string;
422
- }, lowerCaseAliases: {
423
- [x: string]: string;
424
- }): void;
425
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
426
- setLoadingP(p?: Promise<void>): void;
427
- load(): Promise<void>;
428
- loadPre(): Promise<void>;
429
- } & {
430
- getAdapterMapEntry(adapterConf: {
431
- [x: string]: unknown;
432
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
433
- getRefNameMapForAdapter(adapterConf: {
434
- [x: string]: unknown;
435
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
436
- [x: string]: string;
437
- }>;
438
- getReverseRefNameMapForAdapter(adapterConf: {
439
- [x: string]: unknown;
440
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
441
- [x: string]: string;
442
- }>;
443
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
444
- readonly assemblyNamesList: any[];
445
- readonly assemblyList: AnyConfigurationModel[];
446
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
447
- } & {
448
- waitForAssembly(assemblyName: string): Promise<({
449
- configuration: any;
450
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
451
- error: unknown;
452
- loadingP: Promise<void> | undefined;
453
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
454
- refNameAliases: {
455
- [x: string]: string;
456
- } | undefined;
457
- lowerCaseRefNameAliases: {
458
- [x: string]: string;
459
- } | undefined;
460
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
461
- } & {
462
- getConf(arg: string): any;
463
- } & {
464
- readonly initialized: boolean;
465
- readonly name: string;
466
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
467
- readonly aliases: string[];
468
- readonly displayName: string | undefined;
469
- hasName(name: string): boolean;
470
- readonly allAliases: string[];
471
- readonly allRefNames: string[] | undefined;
472
- readonly lowerCaseRefNames: string[] | undefined;
473
- readonly allRefNamesWithLowerCase: string[] | undefined;
474
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
475
- readonly refNameColors: string[];
476
- } & {
477
- readonly refNames: string[] | undefined;
478
- } & {
479
- getCanonicalRefName(refName: string): string | undefined;
480
- getRefNameColor(refName: string): string | undefined;
481
- isValidRefName(refName: string): boolean;
482
- } & {
483
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
484
- regions: import("@jbrowse/core/util").Region[];
485
- refNameAliases: {
486
- [x: string]: string;
487
- };
488
- lowerCaseRefNameAliases: {
489
- [x: string]: string;
490
- };
491
- cytobands: import("@jbrowse/core/util").Feature[];
492
- }): void;
493
- setError(e: unknown): void;
494
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
495
- setRefNameAliases(aliases: {
496
- [x: string]: string;
497
- }, lowerCaseAliases: {
498
- [x: string]: string;
499
- }): void;
500
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
501
- setLoadingP(p?: Promise<void>): void;
502
- load(): Promise<void>;
503
- loadPre(): Promise<void>;
504
- } & {
505
- getAdapterMapEntry(adapterConf: {
506
- [x: string]: unknown;
507
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
508
- getRefNameMapForAdapter(adapterConf: {
509
- [x: string]: unknown;
510
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
511
- [x: string]: string;
512
- }>;
513
- getReverseRefNameMapForAdapter(adapterConf: {
514
- [x: string]: unknown;
515
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
516
- [x: string]: string;
517
- }>;
518
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
519
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
520
- }, {
521
- error: unknown;
522
- loadingP: Promise<void> | undefined;
523
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
524
- refNameAliases: {
525
- [x: string]: string;
526
- } | undefined;
527
- lowerCaseRefNameAliases: {
528
- [x: string]: string;
529
- } | undefined;
530
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
531
- } & {
532
- getConf(arg: string): any;
533
- } & {
534
- readonly initialized: boolean;
535
- readonly name: string;
536
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
537
- readonly aliases: string[];
538
- readonly displayName: string | undefined;
539
- hasName(name: string): boolean;
540
- readonly allAliases: string[];
541
- readonly allRefNames: string[] | undefined;
542
- readonly lowerCaseRefNames: string[] | undefined;
543
- readonly allRefNamesWithLowerCase: string[] | undefined;
544
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
545
- readonly refNameColors: string[];
546
- } & {
547
- readonly refNames: string[] | undefined;
548
- } & {
549
- getCanonicalRefName(refName: string): string | undefined;
550
- getRefNameColor(refName: string): string | undefined;
551
- isValidRefName(refName: string): boolean;
552
- } & {
553
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
554
- regions: import("@jbrowse/core/util").Region[];
555
- refNameAliases: {
556
- [x: string]: string;
557
- };
558
- lowerCaseRefNameAliases: {
559
- [x: string]: string;
560
- };
561
- cytobands: import("@jbrowse/core/util").Feature[];
562
- }): void;
563
- setError(e: unknown): void;
564
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
565
- setRefNameAliases(aliases: {
566
- [x: string]: string;
567
- }, lowerCaseAliases: {
568
- [x: string]: string;
569
- }): void;
570
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
571
- setLoadingP(p?: Promise<void>): void;
572
- load(): Promise<void>;
573
- loadPre(): Promise<void>;
574
- } & {
575
- getAdapterMapEntry(adapterConf: {
576
- [x: string]: unknown;
577
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
578
- getRefNameMapForAdapter(adapterConf: {
579
- [x: string]: unknown;
580
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
581
- [x: string]: string;
582
- }>;
583
- getReverseRefNameMapForAdapter(adapterConf: {
584
- [x: string]: unknown;
585
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
586
- [x: string]: string;
587
- }>;
588
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
589
- getRefNameMapForAdapter(adapterConf: {
590
- [x: string]: unknown;
591
- }, assemblyName: string | undefined, opts: {
592
- stopToken?: string;
593
- sessionId: string;
594
- }): Promise<{
595
- [x: string]: string;
596
- } | undefined>;
597
- getReverseRefNameMapForAdapter(adapterConf: {
598
- [x: string]: unknown;
599
- }, assemblyName: string | undefined, opts: {
600
- stopToken?: string;
601
- sessionId: string;
602
- }): Promise<{
603
- [x: string]: string;
604
- } | undefined>;
605
- isValidRefName(refName: string, assemblyName: string): boolean;
606
- } & {
607
- afterAttach(): void;
608
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
609
- addAssembly(configuration: any): void;
610
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
611
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
612
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
613
- }, {
614
- error: unknown;
615
- loadingP: Promise<void> | undefined;
616
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
617
- refNameAliases: {
618
- [x: string]: string;
619
- } | undefined;
620
- lowerCaseRefNameAliases: {
621
- [x: string]: string;
622
- } | undefined;
623
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
624
- } & {
625
- getConf(arg: string): any;
626
- } & {
627
- readonly initialized: boolean;
628
- readonly name: string;
629
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
630
- readonly aliases: string[];
631
- readonly displayName: string | undefined;
632
- hasName(name: string): boolean;
633
- readonly allAliases: string[];
634
- readonly allRefNames: string[] | undefined;
635
- readonly lowerCaseRefNames: string[] | undefined;
636
- readonly allRefNamesWithLowerCase: string[] | undefined;
637
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
638
- readonly refNameColors: string[];
639
- } & {
640
- readonly refNames: string[] | undefined;
641
- } & {
642
- getCanonicalRefName(refName: string): string | undefined;
643
- getRefNameColor(refName: string): string | undefined;
644
- isValidRefName(refName: string): boolean;
645
- } & {
646
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
647
- regions: import("@jbrowse/core/util").Region[];
648
- refNameAliases: {
649
- [x: string]: string;
650
- };
651
- lowerCaseRefNameAliases: {
652
- [x: string]: string;
653
- };
654
- cytobands: import("@jbrowse/core/util").Feature[];
655
- }): void;
656
- setError(e: unknown): void;
657
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
658
- setRefNameAliases(aliases: {
659
- [x: string]: string;
660
- }, lowerCaseAliases: {
661
- [x: string]: string;
662
- }): void;
663
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
664
- setLoadingP(p?: Promise<void>): void;
665
- load(): Promise<void>;
666
- loadPre(): Promise<void>;
667
- } & {
668
- getAdapterMapEntry(adapterConf: {
669
- [x: string]: unknown;
670
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
671
- getRefNameMapForAdapter(adapterConf: {
672
- [x: string]: unknown;
673
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
674
- [x: string]: string;
675
- }>;
676
- getReverseRefNameMapForAdapter(adapterConf: {
677
- [x: string]: unknown;
678
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
679
- [x: string]: string;
680
- }>;
681
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
682
- }, {
683
- readonly assemblyNameMap: Record<string, {
684
- configuration: any;
685
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
686
- error: unknown;
687
- loadingP: Promise<void> | undefined;
688
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
689
- refNameAliases: {
690
- [x: string]: string;
691
- } | undefined;
692
- lowerCaseRefNameAliases: {
693
- [x: string]: string;
694
- } | undefined;
695
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
696
- } & {
697
- getConf(arg: string): any;
698
- } & {
699
- readonly initialized: boolean;
700
- readonly name: string;
701
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
702
- readonly aliases: string[];
703
- readonly displayName: string | undefined;
704
- hasName(name: string): boolean;
705
- readonly allAliases: string[];
706
- readonly allRefNames: string[] | undefined;
707
- readonly lowerCaseRefNames: string[] | undefined;
708
- readonly allRefNamesWithLowerCase: string[] | undefined;
709
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
710
- readonly refNameColors: string[];
711
- } & {
712
- readonly refNames: string[] | undefined;
713
- } & {
714
- getCanonicalRefName(refName: string): string | undefined;
715
- getRefNameColor(refName: string): string | undefined;
716
- isValidRefName(refName: string): boolean;
717
- } & {
718
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
719
- regions: import("@jbrowse/core/util").Region[];
720
- refNameAliases: {
721
- [x: string]: string;
722
- };
723
- lowerCaseRefNameAliases: {
724
- [x: string]: string;
725
- };
726
- cytobands: import("@jbrowse/core/util").Feature[];
727
- }): void;
728
- setError(e: unknown): void;
729
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
730
- setRefNameAliases(aliases: {
731
- [x: string]: string;
732
- }, lowerCaseAliases: {
733
- [x: string]: string;
734
- }): void;
735
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
736
- setLoadingP(p?: Promise<void>): void;
737
- load(): Promise<void>;
738
- loadPre(): Promise<void>;
739
- } & {
740
- getAdapterMapEntry(adapterConf: {
741
- [x: string]: unknown;
742
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
743
- getRefNameMapForAdapter(adapterConf: {
744
- [x: string]: unknown;
745
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
746
- [x: string]: string;
747
- }>;
748
- getReverseRefNameMapForAdapter(adapterConf: {
749
- [x: string]: unknown;
750
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
751
- [x: string]: string;
752
- }>;
753
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
754
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
755
- }, {
756
- error: unknown;
757
- loadingP: Promise<void> | undefined;
758
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
759
- refNameAliases: {
760
- [x: string]: string;
761
- } | undefined;
762
- lowerCaseRefNameAliases: {
763
- [x: string]: string;
764
- } | undefined;
765
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
766
- } & {
767
- getConf(arg: string): any;
768
- } & {
769
- readonly initialized: boolean;
770
- readonly name: string;
771
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
772
- readonly aliases: string[];
773
- readonly displayName: string | undefined;
774
- hasName(name: string): boolean;
775
- readonly allAliases: string[];
776
- readonly allRefNames: string[] | undefined;
777
- readonly lowerCaseRefNames: string[] | undefined;
778
- readonly allRefNamesWithLowerCase: string[] | undefined;
779
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
780
- readonly refNameColors: string[];
781
- } & {
782
- readonly refNames: string[] | undefined;
783
- } & {
784
- getCanonicalRefName(refName: string): string | undefined;
785
- getRefNameColor(refName: string): string | undefined;
786
- isValidRefName(refName: string): boolean;
787
- } & {
788
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
789
- regions: import("@jbrowse/core/util").Region[];
790
- refNameAliases: {
791
- [x: string]: string;
792
- };
793
- lowerCaseRefNameAliases: {
794
- [x: string]: string;
795
- };
796
- cytobands: import("@jbrowse/core/util").Feature[];
797
- }): void;
798
- setError(e: unknown): void;
799
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
800
- setRefNameAliases(aliases: {
801
- [x: string]: string;
802
- }, lowerCaseAliases: {
803
- [x: string]: string;
804
- }): void;
805
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
806
- setLoadingP(p?: Promise<void>): void;
807
- load(): Promise<void>;
808
- loadPre(): Promise<void>;
809
- } & {
810
- getAdapterMapEntry(adapterConf: {
811
- [x: string]: unknown;
812
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
813
- getRefNameMapForAdapter(adapterConf: {
814
- [x: string]: unknown;
815
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
816
- [x: string]: string;
817
- }>;
818
- getReverseRefNameMapForAdapter(adapterConf: {
819
- [x: string]: unknown;
820
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
821
- [x: string]: string;
822
- }>;
823
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
824
- } & {
825
- get(asmName: string): ({
826
- configuration: any;
827
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
828
- error: unknown;
829
- loadingP: Promise<void> | undefined;
830
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
831
- refNameAliases: {
832
- [x: string]: string;
833
- } | undefined;
834
- lowerCaseRefNameAliases: {
835
- [x: string]: string;
836
- } | undefined;
837
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
838
- } & {
839
- getConf(arg: string): any;
840
- } & {
841
- readonly initialized: boolean;
842
- readonly name: string;
843
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
844
- readonly aliases: string[];
845
- readonly displayName: string | undefined;
846
- hasName(name: string): boolean;
847
- readonly allAliases: string[];
848
- readonly allRefNames: string[] | undefined;
849
- readonly lowerCaseRefNames: string[] | undefined;
850
- readonly allRefNamesWithLowerCase: string[] | undefined;
851
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
852
- readonly refNameColors: string[];
853
- } & {
854
- readonly refNames: string[] | undefined;
855
- } & {
856
- getCanonicalRefName(refName: string): string | undefined;
857
- getRefNameColor(refName: string): string | undefined;
858
- isValidRefName(refName: string): boolean;
859
- } & {
860
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
861
- regions: import("@jbrowse/core/util").Region[];
862
- refNameAliases: {
863
- [x: string]: string;
864
- };
865
- lowerCaseRefNameAliases: {
866
- [x: string]: string;
867
- };
868
- cytobands: import("@jbrowse/core/util").Feature[];
869
- }): void;
870
- setError(e: unknown): void;
871
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
872
- setRefNameAliases(aliases: {
873
- [x: string]: string;
874
- }, lowerCaseAliases: {
875
- [x: string]: string;
876
- }): void;
877
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
878
- setLoadingP(p?: Promise<void>): void;
879
- load(): Promise<void>;
880
- loadPre(): Promise<void>;
881
- } & {
882
- getAdapterMapEntry(adapterConf: {
883
- [x: string]: unknown;
884
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
885
- getRefNameMapForAdapter(adapterConf: {
886
- [x: string]: unknown;
887
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
888
- [x: string]: string;
889
- }>;
890
- getReverseRefNameMapForAdapter(adapterConf: {
891
- [x: string]: unknown;
892
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
893
- [x: string]: string;
894
- }>;
895
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
896
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
897
- }, {
898
- error: unknown;
899
- loadingP: Promise<void> | undefined;
900
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
901
- refNameAliases: {
902
- [x: string]: string;
903
- } | undefined;
904
- lowerCaseRefNameAliases: {
905
- [x: string]: string;
906
- } | undefined;
907
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
908
- } & {
909
- getConf(arg: string): any;
910
- } & {
911
- readonly initialized: boolean;
912
- readonly name: string;
913
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
914
- readonly aliases: string[];
915
- readonly displayName: string | undefined;
916
- hasName(name: string): boolean;
917
- readonly allAliases: string[];
918
- readonly allRefNames: string[] | undefined;
919
- readonly lowerCaseRefNames: string[] | undefined;
920
- readonly allRefNamesWithLowerCase: string[] | undefined;
921
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
922
- readonly refNameColors: string[];
923
- } & {
924
- readonly refNames: string[] | undefined;
925
- } & {
926
- getCanonicalRefName(refName: string): string | undefined;
927
- getRefNameColor(refName: string): string | undefined;
928
- isValidRefName(refName: string): boolean;
929
- } & {
930
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
931
- regions: import("@jbrowse/core/util").Region[];
932
- refNameAliases: {
933
- [x: string]: string;
934
- };
935
- lowerCaseRefNameAliases: {
936
- [x: string]: string;
937
- };
938
- cytobands: import("@jbrowse/core/util").Feature[];
939
- }): void;
940
- setError(e: unknown): void;
941
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
942
- setRefNameAliases(aliases: {
943
- [x: string]: string;
944
- }, lowerCaseAliases: {
945
- [x: string]: string;
946
- }): void;
947
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
948
- setLoadingP(p?: Promise<void>): void;
949
- load(): Promise<void>;
950
- loadPre(): Promise<void>;
951
- } & {
952
- getAdapterMapEntry(adapterConf: {
953
- [x: string]: unknown;
954
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
955
- getRefNameMapForAdapter(adapterConf: {
956
- [x: string]: unknown;
957
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
958
- [x: string]: string;
959
- }>;
960
- getReverseRefNameMapForAdapter(adapterConf: {
961
- [x: string]: unknown;
962
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
963
- [x: string]: string;
964
- }>;
965
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
966
- readonly assemblyNamesList: any[];
967
- readonly assemblyList: AnyConfigurationModel[];
968
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
969
- } & {
970
- waitForAssembly(assemblyName: string): Promise<({
971
- configuration: any;
972
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
973
- error: unknown;
974
- loadingP: Promise<void> | undefined;
975
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
976
- refNameAliases: {
977
- [x: string]: string;
978
- } | undefined;
979
- lowerCaseRefNameAliases: {
980
- [x: string]: string;
981
- } | undefined;
982
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
983
- } & {
984
- getConf(arg: string): any;
985
- } & {
986
- readonly initialized: boolean;
987
- readonly name: string;
988
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
989
- readonly aliases: string[];
990
- readonly displayName: string | undefined;
991
- hasName(name: string): boolean;
992
- readonly allAliases: string[];
993
- readonly allRefNames: string[] | undefined;
994
- readonly lowerCaseRefNames: string[] | undefined;
995
- readonly allRefNamesWithLowerCase: string[] | undefined;
996
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
997
- readonly refNameColors: string[];
998
- } & {
999
- readonly refNames: string[] | undefined;
1000
- } & {
1001
- getCanonicalRefName(refName: string): string | undefined;
1002
- getRefNameColor(refName: string): string | undefined;
1003
- isValidRefName(refName: string): boolean;
1004
- } & {
1005
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1006
- regions: import("@jbrowse/core/util").Region[];
1007
- refNameAliases: {
1008
- [x: string]: string;
1009
- };
1010
- lowerCaseRefNameAliases: {
1011
- [x: string]: string;
1012
- };
1013
- cytobands: import("@jbrowse/core/util").Feature[];
1014
- }): void;
1015
- setError(e: unknown): void;
1016
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1017
- setRefNameAliases(aliases: {
1018
- [x: string]: string;
1019
- }, lowerCaseAliases: {
1020
- [x: string]: string;
1021
- }): void;
1022
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1023
- setLoadingP(p?: Promise<void>): void;
1024
- load(): Promise<void>;
1025
- loadPre(): Promise<void>;
1026
- } & {
1027
- getAdapterMapEntry(adapterConf: {
1028
- [x: string]: unknown;
1029
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1030
- getRefNameMapForAdapter(adapterConf: {
1031
- [x: string]: unknown;
1032
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1033
- [x: string]: string;
1034
- }>;
1035
- getReverseRefNameMapForAdapter(adapterConf: {
1036
- [x: string]: unknown;
1037
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1038
- [x: string]: string;
1039
- }>;
1040
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1041
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1042
- }, {
1043
- error: unknown;
1044
- loadingP: Promise<void> | undefined;
1045
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1046
- refNameAliases: {
1047
- [x: string]: string;
1048
- } | undefined;
1049
- lowerCaseRefNameAliases: {
1050
- [x: string]: string;
1051
- } | undefined;
1052
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1053
- } & {
1054
- getConf(arg: string): any;
1055
- } & {
1056
- readonly initialized: boolean;
1057
- readonly name: string;
1058
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1059
- readonly aliases: string[];
1060
- readonly displayName: string | undefined;
1061
- hasName(name: string): boolean;
1062
- readonly allAliases: string[];
1063
- readonly allRefNames: string[] | undefined;
1064
- readonly lowerCaseRefNames: string[] | undefined;
1065
- readonly allRefNamesWithLowerCase: string[] | undefined;
1066
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1067
- readonly refNameColors: string[];
1068
- } & {
1069
- readonly refNames: string[] | undefined;
1070
- } & {
1071
- getCanonicalRefName(refName: string): string | undefined;
1072
- getRefNameColor(refName: string): string | undefined;
1073
- isValidRefName(refName: string): boolean;
1074
- } & {
1075
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1076
- regions: import("@jbrowse/core/util").Region[];
1077
- refNameAliases: {
1078
- [x: string]: string;
1079
- };
1080
- lowerCaseRefNameAliases: {
1081
- [x: string]: string;
1082
- };
1083
- cytobands: import("@jbrowse/core/util").Feature[];
1084
- }): void;
1085
- setError(e: unknown): void;
1086
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1087
- setRefNameAliases(aliases: {
1088
- [x: string]: string;
1089
- }, lowerCaseAliases: {
1090
- [x: string]: string;
1091
- }): void;
1092
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1093
- setLoadingP(p?: Promise<void>): void;
1094
- load(): Promise<void>;
1095
- loadPre(): Promise<void>;
1096
- } & {
1097
- getAdapterMapEntry(adapterConf: {
1098
- [x: string]: unknown;
1099
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1100
- getRefNameMapForAdapter(adapterConf: {
1101
- [x: string]: unknown;
1102
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1103
- [x: string]: string;
1104
- }>;
1105
- getReverseRefNameMapForAdapter(adapterConf: {
1106
- [x: string]: unknown;
1107
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1108
- [x: string]: string;
1109
- }>;
1110
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1111
- getRefNameMapForAdapter(adapterConf: {
1112
- [x: string]: unknown;
1113
- }, assemblyName: string | undefined, opts: {
1114
- stopToken?: string;
1115
- sessionId: string;
1116
- }): Promise<{
1117
- [x: string]: string;
1118
- } | undefined>;
1119
- getReverseRefNameMapForAdapter(adapterConf: {
1120
- [x: string]: unknown;
1121
- }, assemblyName: string | undefined, opts: {
1122
- stopToken?: string;
1123
- sessionId: string;
1124
- }): Promise<{
1125
- [x: string]: string;
1126
- } | undefined>;
1127
- isValidRefName(refName: string, assemblyName: string): boolean;
1128
- } & {
1129
- afterAttach(): void;
1130
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1131
- addAssembly(configuration: any): void;
1132
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
1133
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1134
- rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1135
- adminMode: boolean;
1136
- error: unknown;
1137
- textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1138
- pluginManager: PluginManager;
1139
- } & {
1140
- setError(error: unknown): void;
1141
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1142
- setDefaultSession(): void;
1143
- setSessionPath(path: string): void;
1144
- renameCurrentSession(newName: string): void;
1145
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1146
- jbrowse: import("mobx-state-tree").IAnyType;
1147
- session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
1148
- sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1149
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1150
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1151
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1152
- }, {
1153
- error: unknown;
1154
- loadingP: Promise<void> | undefined;
1155
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1156
- refNameAliases: {
1157
- [x: string]: string;
1158
- } | undefined;
1159
- lowerCaseRefNameAliases: {
1160
- [x: string]: string;
1161
- } | undefined;
1162
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1163
- } & {
1164
- getConf(arg: string): any;
1165
- } & {
1166
- readonly initialized: boolean;
1167
- readonly name: string;
1168
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1169
- readonly aliases: string[];
1170
- readonly displayName: string | undefined;
1171
- hasName(name: string): boolean;
1172
- readonly allAliases: string[];
1173
- readonly allRefNames: string[] | undefined;
1174
- readonly lowerCaseRefNames: string[] | undefined;
1175
- readonly allRefNamesWithLowerCase: string[] | undefined;
1176
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1177
- readonly refNameColors: string[];
1178
- } & {
1179
- readonly refNames: string[] | undefined;
1180
- } & {
1181
- getCanonicalRefName(refName: string): string | undefined;
1182
- getRefNameColor(refName: string): string | undefined;
1183
- isValidRefName(refName: string): boolean;
1184
- } & {
1185
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1186
- regions: import("@jbrowse/core/util").Region[];
1187
- refNameAliases: {
1188
- [x: string]: string;
1189
- };
1190
- lowerCaseRefNameAliases: {
1191
- [x: string]: string;
1192
- };
1193
- cytobands: import("@jbrowse/core/util").Feature[];
1194
- }): void;
1195
- setError(e: unknown): void;
1196
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1197
- setRefNameAliases(aliases: {
1198
- [x: string]: string;
1199
- }, lowerCaseAliases: {
1200
- [x: string]: string;
1201
- }): void;
1202
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1203
- setLoadingP(p?: Promise<void>): void;
1204
- load(): Promise<void>;
1205
- loadPre(): Promise<void>;
1206
- } & {
1207
- getAdapterMapEntry(adapterConf: {
1208
- [x: string]: unknown;
1209
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1210
- getRefNameMapForAdapter(adapterConf: {
1211
- [x: string]: unknown;
1212
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1213
- [x: string]: string;
1214
- }>;
1215
- getReverseRefNameMapForAdapter(adapterConf: {
1216
- [x: string]: unknown;
1217
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1218
- [x: string]: string;
1219
- }>;
1220
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1221
- }, {
1222
- readonly assemblyNameMap: Record<string, {
1223
- configuration: any;
1224
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1225
- error: unknown;
1226
- loadingP: Promise<void> | undefined;
1227
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1228
- refNameAliases: {
1229
- [x: string]: string;
1230
- } | undefined;
1231
- lowerCaseRefNameAliases: {
1232
- [x: string]: string;
1233
- } | undefined;
1234
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1235
- } & {
1236
- getConf(arg: string): any;
1237
- } & {
1238
- readonly initialized: boolean;
1239
- readonly name: string;
1240
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1241
- readonly aliases: string[];
1242
- readonly displayName: string | undefined;
1243
- hasName(name: string): boolean;
1244
- readonly allAliases: string[];
1245
- readonly allRefNames: string[] | undefined;
1246
- readonly lowerCaseRefNames: string[] | undefined;
1247
- readonly allRefNamesWithLowerCase: string[] | undefined;
1248
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1249
- readonly refNameColors: string[];
1250
- } & {
1251
- readonly refNames: string[] | undefined;
1252
- } & {
1253
- getCanonicalRefName(refName: string): string | undefined;
1254
- getRefNameColor(refName: string): string | undefined;
1255
- isValidRefName(refName: string): boolean;
1256
- } & {
1257
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1258
- regions: import("@jbrowse/core/util").Region[];
1259
- refNameAliases: {
1260
- [x: string]: string;
1261
- };
1262
- lowerCaseRefNameAliases: {
1263
- [x: string]: string;
1264
- };
1265
- cytobands: import("@jbrowse/core/util").Feature[];
1266
- }): void;
1267
- setError(e: unknown): void;
1268
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1269
- setRefNameAliases(aliases: {
1270
- [x: string]: string;
1271
- }, lowerCaseAliases: {
1272
- [x: string]: string;
1273
- }): void;
1274
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1275
- setLoadingP(p?: Promise<void>): void;
1276
- load(): Promise<void>;
1277
- loadPre(): Promise<void>;
1278
- } & {
1279
- getAdapterMapEntry(adapterConf: {
1280
- [x: string]: unknown;
1281
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1282
- getRefNameMapForAdapter(adapterConf: {
1283
- [x: string]: unknown;
1284
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1285
- [x: string]: string;
1286
- }>;
1287
- getReverseRefNameMapForAdapter(adapterConf: {
1288
- [x: string]: unknown;
1289
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1290
- [x: string]: string;
1291
- }>;
1292
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1293
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1294
- }, {
1295
- error: unknown;
1296
- loadingP: Promise<void> | undefined;
1297
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1298
- refNameAliases: {
1299
- [x: string]: string;
1300
- } | undefined;
1301
- lowerCaseRefNameAliases: {
1302
- [x: string]: string;
1303
- } | undefined;
1304
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1305
- } & {
1306
- getConf(arg: string): any;
1307
- } & {
1308
- readonly initialized: boolean;
1309
- readonly name: string;
1310
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1311
- readonly aliases: string[];
1312
- readonly displayName: string | undefined;
1313
- hasName(name: string): boolean;
1314
- readonly allAliases: string[];
1315
- readonly allRefNames: string[] | undefined;
1316
- readonly lowerCaseRefNames: string[] | undefined;
1317
- readonly allRefNamesWithLowerCase: string[] | undefined;
1318
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1319
- readonly refNameColors: string[];
1320
- } & {
1321
- readonly refNames: string[] | undefined;
1322
- } & {
1323
- getCanonicalRefName(refName: string): string | undefined;
1324
- getRefNameColor(refName: string): string | undefined;
1325
- isValidRefName(refName: string): boolean;
1326
- } & {
1327
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1328
- regions: import("@jbrowse/core/util").Region[];
1329
- refNameAliases: {
1330
- [x: string]: string;
1331
- };
1332
- lowerCaseRefNameAliases: {
1333
- [x: string]: string;
1334
- };
1335
- cytobands: import("@jbrowse/core/util").Feature[];
1336
- }): void;
1337
- setError(e: unknown): void;
1338
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1339
- setRefNameAliases(aliases: {
1340
- [x: string]: string;
1341
- }, lowerCaseAliases: {
1342
- [x: string]: string;
1343
- }): void;
1344
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1345
- setLoadingP(p?: Promise<void>): void;
1346
- load(): Promise<void>;
1347
- loadPre(): Promise<void>;
1348
- } & {
1349
- getAdapterMapEntry(adapterConf: {
1350
- [x: string]: unknown;
1351
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1352
- getRefNameMapForAdapter(adapterConf: {
1353
- [x: string]: unknown;
1354
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1355
- [x: string]: string;
1356
- }>;
1357
- getReverseRefNameMapForAdapter(adapterConf: {
1358
- [x: string]: unknown;
1359
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1360
- [x: string]: string;
1361
- }>;
1362
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
1363
- } & {
1364
- get(asmName: string): ({
1365
- configuration: any;
1366
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1367
- error: unknown;
1368
- loadingP: Promise<void> | undefined;
1369
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1370
- refNameAliases: {
1371
- [x: string]: string;
1372
- } | undefined;
1373
- lowerCaseRefNameAliases: {
1374
- [x: string]: string;
1375
- } | undefined;
1376
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1377
- } & {
1378
- getConf(arg: string): any;
1379
- } & {
1380
- readonly initialized: boolean;
1381
- readonly name: string;
1382
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1383
- readonly aliases: string[];
1384
- readonly displayName: string | undefined;
1385
- hasName(name: string): boolean;
1386
- readonly allAliases: string[];
1387
- readonly allRefNames: string[] | undefined;
1388
- readonly lowerCaseRefNames: string[] | undefined;
1389
- readonly allRefNamesWithLowerCase: string[] | undefined;
1390
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1391
- readonly refNameColors: string[];
1392
- } & {
1393
- readonly refNames: string[] | undefined;
1394
- } & {
1395
- getCanonicalRefName(refName: string): string | undefined;
1396
- getRefNameColor(refName: string): string | undefined;
1397
- isValidRefName(refName: string): boolean;
1398
- } & {
1399
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1400
- regions: import("@jbrowse/core/util").Region[];
1401
- refNameAliases: {
1402
- [x: string]: string;
1403
- };
1404
- lowerCaseRefNameAliases: {
1405
- [x: string]: string;
1406
- };
1407
- cytobands: import("@jbrowse/core/util").Feature[];
1408
- }): void;
1409
- setError(e: unknown): void;
1410
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1411
- setRefNameAliases(aliases: {
1412
- [x: string]: string;
1413
- }, lowerCaseAliases: {
1414
- [x: string]: string;
1415
- }): void;
1416
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1417
- setLoadingP(p?: Promise<void>): void;
1418
- load(): Promise<void>;
1419
- loadPre(): Promise<void>;
1420
- } & {
1421
- getAdapterMapEntry(adapterConf: {
1422
- [x: string]: unknown;
1423
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1424
- getRefNameMapForAdapter(adapterConf: {
1425
- [x: string]: unknown;
1426
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1427
- [x: string]: string;
1428
- }>;
1429
- getReverseRefNameMapForAdapter(adapterConf: {
1430
- [x: string]: unknown;
1431
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1432
- [x: string]: string;
1433
- }>;
1434
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1435
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1436
- }, {
1437
- error: unknown;
1438
- loadingP: Promise<void> | undefined;
1439
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1440
- refNameAliases: {
1441
- [x: string]: string;
1442
- } | undefined;
1443
- lowerCaseRefNameAliases: {
1444
- [x: string]: string;
1445
- } | undefined;
1446
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1447
- } & {
1448
- getConf(arg: string): any;
1449
- } & {
1450
- readonly initialized: boolean;
1451
- readonly name: string;
1452
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1453
- readonly aliases: string[];
1454
- readonly displayName: string | undefined;
1455
- hasName(name: string): boolean;
1456
- readonly allAliases: string[];
1457
- readonly allRefNames: string[] | undefined;
1458
- readonly lowerCaseRefNames: string[] | undefined;
1459
- readonly allRefNamesWithLowerCase: string[] | undefined;
1460
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1461
- readonly refNameColors: string[];
1462
- } & {
1463
- readonly refNames: string[] | undefined;
1464
- } & {
1465
- getCanonicalRefName(refName: string): string | undefined;
1466
- getRefNameColor(refName: string): string | undefined;
1467
- isValidRefName(refName: string): boolean;
1468
- } & {
1469
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1470
- regions: import("@jbrowse/core/util").Region[];
1471
- refNameAliases: {
1472
- [x: string]: string;
1473
- };
1474
- lowerCaseRefNameAliases: {
1475
- [x: string]: string;
1476
- };
1477
- cytobands: import("@jbrowse/core/util").Feature[];
1478
- }): void;
1479
- setError(e: unknown): void;
1480
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1481
- setRefNameAliases(aliases: {
1482
- [x: string]: string;
1483
- }, lowerCaseAliases: {
1484
- [x: string]: string;
1485
- }): void;
1486
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1487
- setLoadingP(p?: Promise<void>): void;
1488
- load(): Promise<void>;
1489
- loadPre(): Promise<void>;
1490
- } & {
1491
- getAdapterMapEntry(adapterConf: {
1492
- [x: string]: unknown;
1493
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1494
- getRefNameMapForAdapter(adapterConf: {
1495
- [x: string]: unknown;
1496
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1497
- [x: string]: string;
1498
- }>;
1499
- getReverseRefNameMapForAdapter(adapterConf: {
1500
- [x: string]: unknown;
1501
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1502
- [x: string]: string;
1503
- }>;
1504
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1505
- readonly assemblyNamesList: any[];
1506
- readonly assemblyList: AnyConfigurationModel[];
1507
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1508
- } & {
1509
- waitForAssembly(assemblyName: string): Promise<({
1510
- configuration: any;
1511
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1512
- error: unknown;
1513
- loadingP: Promise<void> | undefined;
1514
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1515
- refNameAliases: {
1516
- [x: string]: string;
1517
- } | undefined;
1518
- lowerCaseRefNameAliases: {
1519
- [x: string]: string;
1520
- } | undefined;
1521
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1522
- } & {
1523
- getConf(arg: string): any;
1524
- } & {
1525
- readonly initialized: boolean;
1526
- readonly name: string;
1527
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1528
- readonly aliases: string[];
1529
- readonly displayName: string | undefined;
1530
- hasName(name: string): boolean;
1531
- readonly allAliases: string[];
1532
- readonly allRefNames: string[] | undefined;
1533
- readonly lowerCaseRefNames: string[] | undefined;
1534
- readonly allRefNamesWithLowerCase: string[] | undefined;
1535
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1536
- readonly refNameColors: string[];
1537
- } & {
1538
- readonly refNames: string[] | undefined;
1539
- } & {
1540
- getCanonicalRefName(refName: string): string | undefined;
1541
- getRefNameColor(refName: string): string | undefined;
1542
- isValidRefName(refName: string): boolean;
1543
- } & {
1544
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1545
- regions: import("@jbrowse/core/util").Region[];
1546
- refNameAliases: {
1547
- [x: string]: string;
1548
- };
1549
- lowerCaseRefNameAliases: {
1550
- [x: string]: string;
1551
- };
1552
- cytobands: import("@jbrowse/core/util").Feature[];
1553
- }): void;
1554
- setError(e: unknown): void;
1555
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1556
- setRefNameAliases(aliases: {
1557
- [x: string]: string;
1558
- }, lowerCaseAliases: {
1559
- [x: string]: string;
1560
- }): void;
1561
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1562
- setLoadingP(p?: Promise<void>): void;
1563
- load(): Promise<void>;
1564
- loadPre(): Promise<void>;
1565
- } & {
1566
- getAdapterMapEntry(adapterConf: {
1567
- [x: string]: unknown;
1568
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1569
- getRefNameMapForAdapter(adapterConf: {
1570
- [x: string]: unknown;
1571
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1572
- [x: string]: string;
1573
- }>;
1574
- getReverseRefNameMapForAdapter(adapterConf: {
1575
- [x: string]: unknown;
1576
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1577
- [x: string]: string;
1578
- }>;
1579
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1580
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1581
- }, {
1582
- error: unknown;
1583
- loadingP: Promise<void> | undefined;
1584
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1585
- refNameAliases: {
1586
- [x: string]: string;
1587
- } | undefined;
1588
- lowerCaseRefNameAliases: {
1589
- [x: string]: string;
1590
- } | undefined;
1591
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1592
- } & {
1593
- getConf(arg: string): any;
1594
- } & {
1595
- readonly initialized: boolean;
1596
- readonly name: string;
1597
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1598
- readonly aliases: string[];
1599
- readonly displayName: string | undefined;
1600
- hasName(name: string): boolean;
1601
- readonly allAliases: string[];
1602
- readonly allRefNames: string[] | undefined;
1603
- readonly lowerCaseRefNames: string[] | undefined;
1604
- readonly allRefNamesWithLowerCase: string[] | undefined;
1605
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1606
- readonly refNameColors: string[];
1607
- } & {
1608
- readonly refNames: string[] | undefined;
1609
- } & {
1610
- getCanonicalRefName(refName: string): string | undefined;
1611
- getRefNameColor(refName: string): string | undefined;
1612
- isValidRefName(refName: string): boolean;
1613
- } & {
1614
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1615
- regions: import("@jbrowse/core/util").Region[];
1616
- refNameAliases: {
1617
- [x: string]: string;
1618
- };
1619
- lowerCaseRefNameAliases: {
1620
- [x: string]: string;
1621
- };
1622
- cytobands: import("@jbrowse/core/util").Feature[];
1623
- }): void;
1624
- setError(e: unknown): void;
1625
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1626
- setRefNameAliases(aliases: {
1627
- [x: string]: string;
1628
- }, lowerCaseAliases: {
1629
- [x: string]: string;
1630
- }): void;
1631
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1632
- setLoadingP(p?: Promise<void>): void;
1633
- load(): Promise<void>;
1634
- loadPre(): Promise<void>;
1635
- } & {
1636
- getAdapterMapEntry(adapterConf: {
1637
- [x: string]: unknown;
1638
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1639
- getRefNameMapForAdapter(adapterConf: {
1640
- [x: string]: unknown;
1641
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1642
- [x: string]: string;
1643
- }>;
1644
- getReverseRefNameMapForAdapter(adapterConf: {
1645
- [x: string]: unknown;
1646
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1647
- [x: string]: string;
1648
- }>;
1649
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1650
- getRefNameMapForAdapter(adapterConf: {
1651
- [x: string]: unknown;
1652
- }, assemblyName: string | undefined, opts: {
1653
- stopToken?: string;
1654
- sessionId: string;
1655
- }): Promise<{
1656
- [x: string]: string;
1657
- } | undefined>;
1658
- getReverseRefNameMapForAdapter(adapterConf: {
1659
- [x: string]: unknown;
1660
- }, assemblyName: string | undefined, opts: {
1661
- stopToken?: string;
1662
- sessionId: string;
1663
- }): Promise<{
1664
- [x: string]: string;
1665
- } | undefined>;
1666
- isValidRefName(refName: string, assemblyName: string): boolean;
1667
- } & {
1668
- afterAttach(): void;
1669
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1670
- addAssembly(configuration: any): void;
1671
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
1672
- }, {
1673
- rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1674
- adminMode: boolean;
1675
- error: unknown;
1676
- textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1677
- pluginManager: PluginManager;
1678
- } & {
1679
- setError(error: unknown): void;
1680
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1681
- setDefaultSession(): void;
1682
- setSessionPath(path: string): void;
1683
- renameCurrentSession(newName: string): void;
1684
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
14
+ readonly root: import("mobx-state-tree").TypeOrStateTreeNodeToStateTreeNode<ROOT_MODEL_TYPE>;
1685
15
  } & {
1686
16
  readonly jbrowse: any;
1687
17
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1699,40 +29,7 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
1699
29
  readonly adminMode: boolean;
1700
30
  readonly textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1701
31
  } & {
1702
- readonly assemblies: ({
1703
- [x: string]: any;
1704
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1705
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1706
- [x: string]: any;
1707
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1708
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1709
- [x: string]: any;
1710
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1711
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1712
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1713
- aliases: {
1714
- type: string;
1715
- defaultValue: never[];
1716
- description: string;
1717
- };
1718
- sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1719
- refNameColors: {
1720
- type: string;
1721
- defaultValue: never[];
1722
- description: string;
1723
- };
1724
- refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1725
- adapter: import("mobx-state-tree").IAnyModelType;
1726
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
1727
- cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1728
- adapter: import("mobx-state-tree").IAnyModelType;
1729
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
1730
- displayName: {
1731
- type: string;
1732
- defaultValue: string;
1733
- description: string;
1734
- };
1735
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name">>>)[];
32
+ readonly assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
1736
33
  } & {
1737
34
  setSelection(thing: unknown): void;
1738
35
  clearSelection(): void;
@@ -1742,32 +39,12 @@ export declare function SessionTracksManagerSessionMixin(pluginManager: PluginMa
1742
39
  } & {
1743
40
  removeReferring(referring: import("./ReferenceManagement").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
1744
41
  } & {
1745
- readonly tracks: ({
1746
- [x: string]: any;
1747
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1748
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1749
- [x: string]: any;
1750
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1751
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1752
- [x: string]: any;
1753
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1754
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1755
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
42
+ readonly tracks: AnyConfigurationModel[];
1756
43
  } & {
1757
44
  addTrackConf(trackConf: AnyConfiguration): any;
1758
45
  deleteTrackConf(trackConf: AnyConfigurationModel): any;
1759
46
  } & {
1760
- readonly tracks: ({
1761
- [x: string]: any;
1762
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1763
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1764
- [x: string]: any;
1765
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1766
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1767
- [x: string]: any;
1768
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1769
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1770
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
47
+ readonly tracks: AnyConfigurationModel[];
1771
48
  } & {
1772
49
  addTrackConf(trackConf: AnyConfiguration): any;
1773
50
  deleteTrackConf(trackConf: AnyConfigurationModel): any;