@jbrowse/react-circular-genome-view2 3.6.5 → 4.0.0

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 (55) hide show
  1. package/esm/JBrowseCircularGenomeView/JBrowseCircularGenomeView.d.ts +1 -1
  2. package/esm/JBrowseCircularGenomeView/JBrowseCircularGenomeView.js +1 -1
  3. package/esm/JBrowseCircularGenomeView/index.d.ts +1 -1
  4. package/esm/JBrowseCircularGenomeView/index.js +1 -1
  5. package/esm/corePlugins.d.ts +2 -2
  6. package/esm/createModel/createConfigModel.d.ts +25 -29
  7. package/esm/createModel/createConfigModel.js +1 -1
  8. package/esm/createModel/createModel.d.ts +524 -629
  9. package/esm/createModel/createModel.js +5 -5
  10. package/esm/createModel/createSessionModel.d.ts +250 -305
  11. package/esm/createModel/createSessionModel.js +5 -4
  12. package/esm/createModel/index.d.ts +3 -3
  13. package/esm/createModel/index.js +3 -3
  14. package/esm/createViewState.d.ts +1323 -1625
  15. package/esm/createViewState.js +3 -4
  16. package/esm/index.d.ts +4 -4
  17. package/esm/index.js +4 -4
  18. package/esm/loadPlugins.js +1 -1
  19. package/esm/types.d.ts +1 -1
  20. package/esm/version.d.ts +1 -1
  21. package/esm/version.js +1 -1
  22. package/esm/webpack.d.ts +4 -4
  23. package/esm/webpack.js +4 -4
  24. package/package.json +38 -40
  25. package/dist/JBrowseCircularGenomeView/JBrowseCircularGenomeView.d.ts +0 -5
  26. package/dist/JBrowseCircularGenomeView/JBrowseCircularGenomeView.js +0 -23
  27. package/dist/JBrowseCircularGenomeView/index.d.ts +0 -1
  28. package/dist/JBrowseCircularGenomeView/index.js +0 -8
  29. package/dist/corePlugins.d.ts +0 -3
  30. package/dist/corePlugins.js +0 -22
  31. package/dist/createModel/AboutDialog.d.ts +0 -1
  32. package/dist/createModel/AboutDialog.js +0 -5
  33. package/dist/createModel/createConfigModel.d.ts +0 -104
  34. package/dist/createModel/createConfigModel.js +0 -43
  35. package/dist/createModel/createModel.d.ts +0 -4530
  36. package/dist/createModel/createModel.js +0 -117
  37. package/dist/createModel/createSessionModel.d.ts +0 -1845
  38. package/dist/createModel/createSessionModel.js +0 -115
  39. package/dist/createModel/index.d.ts +0 -3
  40. package/dist/createModel/index.js +0 -12
  41. package/dist/createViewState.d.ts +0 -11620
  42. package/dist/createViewState.js +0 -64
  43. package/dist/index.d.ts +0 -4
  44. package/dist/index.js +0 -14
  45. package/dist/loadPlugins.d.ts +0 -13
  46. package/dist/loadPlugins.js +0 -12
  47. package/dist/react-circular-genome-view.umd.production.min.js +0 -229
  48. package/dist/react-circular-genome-view.umd.production.min.js.LICENSE.txt +0 -135
  49. package/dist/react-circular-genome-view.umd.production.min.js.map +0 -1
  50. package/dist/types.d.ts +0 -5
  51. package/dist/types.js +0 -2
  52. package/dist/version.d.ts +0 -1
  53. package/dist/version.js +0 -4
  54. package/dist/webpack.d.ts +0 -7
  55. package/dist/webpack.js +0 -53
package/dist/createModel/createModel.d.ts DELETED
@@ -1,4530 +0,0 @@
1
- import PluginManager from '@jbrowse/core/PluginManager';
2
- import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
3
- import RpcManager from '@jbrowse/core/rpc/RpcManager';
4
- import type { PluginConstructor } from '@jbrowse/core/Plugin';
5
- import type { UriLocation } from '@jbrowse/core/util';
6
- import type { Instance, SnapshotIn } from 'mobx-state-tree';
7
- export default function createModel(runtimePlugins: PluginConstructor[], makeWorkerInstance?: () => Worker): {
8
- model: import("mobx-state-tree").IModelType<{
9
- config: import("mobx-state-tree").IModelType<{
10
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
11
- rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
12
- defaultDriver: {
13
- type: string;
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- description: string;
15
- defaultValue: string;
16
- };
17
- drivers: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IMapType<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> | undefined, import("mobx-state-tree").ModelSnapshotType<Record<string, any>>, ({} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> & import("mobx-state-tree/dist/internal").NonEmptyObject) | undefined>>, [undefined]>;
18
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
19
- highResolutionScaling: {
20
- type: string;
21
- defaultValue: number;
22
- };
23
- formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
24
- feature: {
25
- type: string;
26
- description: string;
27
- defaultValue: {};
28
- contextVariable: string[];
29
- };
30
- subfeatures: {
31
- type: string;
32
- description: string;
33
- defaultValue: {};
34
- contextVariable: string[];
35
- };
36
- depth: {
37
- type: string;
38
- defaultValue: number;
39
- description: string;
40
- };
41
- maxDepth: {
42
- type: string;
43
- defaultValue: number;
44
- description: string;
45
- };
46
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
47
- formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
48
- config: {
49
- type: string;
50
- description: string;
51
- defaultValue: {};
52
- contextVariable: string[];
53
- };
54
- hideUris: {
55
- type: string;
56
- defaultValue: boolean;
57
- };
58
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
59
- hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
60
- sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
61
- trackNames: {
62
- type: string;
63
- defaultValue: boolean;
64
- };
65
- categories: {
66
- type: string;
67
- defaultValue: boolean;
68
- };
69
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
70
- defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
71
- categoryNames: {
72
- type: string;
73
- defaultValue: never[];
74
- };
75
- topLevelCategories: {
76
- type: string;
77
- defaultValue: boolean;
78
- };
79
- subCategories: {
80
- type: string;
81
- defaultValue: boolean;
82
- };
83
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
84
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
85
- theme: {
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- type: string;
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- defaultValue: {};
88
- };
89
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
90
- assembly: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
91
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
92
- internetAccounts: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
93
- connections: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
94
- aggregateTextSearchAdapters: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
95
- plugins: import("mobx-state-tree").IType<any, any, any>;
96
- }, {
97
- readonly assemblies: ({
98
- [x: string]: any;
99
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
100
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
101
- [x: string]: any;
102
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
103
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
104
- [x: string]: any;
105
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
106
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
107
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
108
- readonly assemblyName: string;
109
- readonly rpcManager: any;
110
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
111
- session: import("mobx-state-tree").IModelType<{
112
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
113
- name: import("mobx-state-tree").ISimpleType<string>;
114
- margin: import("mobx-state-tree").IType<number | undefined, number, number>;
115
- } & {
116
- drawerPosition: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
117
- drawerWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
118
- widgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyType>;
119
- activeWidgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>>;
120
- minimized: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
121
- } & {
122
- connectionInstances: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
123
- name: import("mobx-state-tree").ISimpleType<string>;
124
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
125
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
126
- name: {
127
- type: string;
128
- defaultValue: string;
129
- description: string;
130
- };
131
- assemblyNames: {
132
- type: string;
133
- defaultValue: never[];
134
- description: string;
135
- };
136
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
137
- }, {
138
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
139
- } & {
140
- afterAttach(): void;
141
- addTrackConf(trackConf: Record<string, unknown> | ({
142
- [x: string]: any;
143
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
144
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
145
- [x: string]: any;
146
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
147
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
148
- [x: string]: any;
149
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
150
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
151
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
152
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
153
- [x: string]: any;
154
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
155
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
156
- [x: string]: any;
157
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
158
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
159
- [x: string]: any;
160
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
161
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
162
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
163
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
164
- clear(): void;
165
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
166
- } & {
167
- view: import("mobx-state-tree").IAnyModelType;
168
- }, {
169
- selection: unknown;
170
- hovered: unknown;
171
- } & {
172
- readonly root: {
173
- jbrowse: any;
174
- session: any;
175
- sessionPath: string;
176
- assemblyManager: {
177
- assemblies: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
178
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
179
- }, {
180
- error: unknown;
181
- loadingP: Promise<void> | undefined;
182
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
183
- refNameAliases: {
184
- [x: string]: string;
185
- } | undefined;
186
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
187
- } & {
188
- getConf(arg: string): any;
189
- readonly lowerCaseRefNameAliases: {
190
- [k: string]: string;
191
- } | undefined;
192
- } & {
193
- readonly initialized: boolean;
194
- readonly name: string;
195
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
196
- readonly aliases: string[];
197
- readonly displayName: string;
198
- hasName(name: string): boolean;
199
- readonly allAliases: string[];
200
- readonly allRefNames: string[] | undefined;
201
- readonly lowerCaseRefNames: string[] | undefined;
202
- readonly allRefNamesWithLowerCase: string[] | undefined;
203
- readonly rpcManager: RpcManager;
204
- readonly refNameColors: string[];
205
- } & {
206
- readonly refNames: string[] | undefined;
207
- } & {
208
- getCanonicalRefName(refName: string): string | undefined;
209
- getRefNameColor(refName: string): string | undefined;
210
- isValidRefName(refName: string): boolean;
211
- } & {
212
- setLoaded({ regions, refNameAliases, cytobands, }: {
213
- regions: import("@jbrowse/core/util").Region[];
214
- refNameAliases: {
215
- [x: string]: string;
216
- };
217
- cytobands: import("@jbrowse/core/util").Feature[];
218
- }): void;
219
- setError(e: unknown): void;
220
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
221
- setRefNameAliases(aliases: {
222
- [x: string]: string;
223
- }): void;
224
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
225
- setLoadingP(p?: Promise<void>): void;
226
- load(): Promise<void>;
227
- loadPre(): Promise<void>;
228
- } & {
229
- getAdapterMapEntry(adapterConf: {
230
- [x: string]: unknown;
231
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
232
- getRefNameMapForAdapter(adapterConf: {
233
- [x: string]: unknown;
234
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
235
- [x: string]: string;
236
- }>;
237
- getReverseRefNameMapForAdapter(adapterConf: {
238
- [x: string]: unknown;
239
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
240
- [x: string]: string;
241
- }>;
242
- afterCreate(): void;
243
- }, 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<{
244
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
245
- }, {
246
- error: unknown;
247
- loadingP: Promise<void> | undefined;
248
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
249
- refNameAliases: {
250
- [x: string]: string;
251
- } | undefined;
252
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
253
- } & {
254
- getConf(arg: string): any;
255
- readonly lowerCaseRefNameAliases: {
256
- [k: string]: string;
257
- } | undefined;
258
- } & {
259
- readonly initialized: boolean;
260
- readonly name: string;
261
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
262
- readonly aliases: string[];
263
- readonly displayName: string;
264
- hasName(name: string): boolean;
265
- readonly allAliases: string[];
266
- readonly allRefNames: string[] | undefined;
267
- readonly lowerCaseRefNames: string[] | undefined;
268
- readonly allRefNamesWithLowerCase: string[] | undefined;
269
- readonly rpcManager: RpcManager;
270
- readonly refNameColors: string[];
271
- } & {
272
- readonly refNames: string[] | undefined;
273
- } & {
274
- getCanonicalRefName(refName: string): string | undefined;
275
- getRefNameColor(refName: string): string | undefined;
276
- isValidRefName(refName: string): boolean;
277
- } & {
278
- setLoaded({ regions, refNameAliases, cytobands, }: {
279
- regions: import("@jbrowse/core/util").Region[];
280
- refNameAliases: {
281
- [x: string]: string;
282
- };
283
- cytobands: import("@jbrowse/core/util").Feature[];
284
- }): void;
285
- setError(e: unknown): void;
286
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
287
- setRefNameAliases(aliases: {
288
- [x: string]: string;
289
- }): void;
290
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
291
- setLoadingP(p?: Promise<void>): void;
292
- load(): Promise<void>;
293
- loadPre(): Promise<void>;
294
- } & {
295
- getAdapterMapEntry(adapterConf: {
296
- [x: string]: unknown;
297
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
298
- getRefNameMapForAdapter(adapterConf: {
299
- [x: string]: unknown;
300
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
301
- [x: string]: string;
302
- }>;
303
- getReverseRefNameMapForAdapter(adapterConf: {
304
- [x: string]: unknown;
305
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
306
- [x: string]: string;
307
- }>;
308
- afterCreate(): void;
309
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
310
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
311
- readonly assemblyNameMap: Record<string, {
312
- configuration: any;
313
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
314
- error: unknown;
315
- loadingP: Promise<void> | undefined;
316
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
317
- refNameAliases: {
318
- [x: string]: string;
319
- } | undefined;
320
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
321
- } & {
322
- getConf(arg: string): any;
323
- readonly lowerCaseRefNameAliases: {
324
- [k: string]: string;
325
- } | undefined;
326
- } & {
327
- readonly initialized: boolean;
328
- readonly name: string;
329
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
330
- readonly aliases: string[];
331
- readonly displayName: string;
332
- hasName(name: string): boolean;
333
- readonly allAliases: string[];
334
- readonly allRefNames: string[] | undefined;
335
- readonly lowerCaseRefNames: string[] | undefined;
336
- readonly allRefNamesWithLowerCase: string[] | undefined;
337
- readonly rpcManager: RpcManager;
338
- readonly refNameColors: string[];
339
- } & {
340
- readonly refNames: string[] | undefined;
341
- } & {
342
- getCanonicalRefName(refName: string): string | undefined;
343
- getRefNameColor(refName: string): string | undefined;
344
- isValidRefName(refName: string): boolean;
345
- } & {
346
- setLoaded({ regions, refNameAliases, cytobands, }: {
347
- regions: import("@jbrowse/core/util").Region[];
348
- refNameAliases: {
349
- [x: string]: string;
350
- };
351
- cytobands: import("@jbrowse/core/util").Feature[];
352
- }): void;
353
- setError(e: unknown): void;
354
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
355
- setRefNameAliases(aliases: {
356
- [x: string]: string;
357
- }): void;
358
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
359
- setLoadingP(p?: Promise<void>): void;
360
- load(): Promise<void>;
361
- loadPre(): Promise<void>;
362
- } & {
363
- getAdapterMapEntry(adapterConf: {
364
- [x: string]: unknown;
365
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
366
- getRefNameMapForAdapter(adapterConf: {
367
- [x: string]: unknown;
368
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
369
- [x: string]: string;
370
- }>;
371
- getReverseRefNameMapForAdapter(adapterConf: {
372
- [x: string]: unknown;
373
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
374
- [x: string]: string;
375
- }>;
376
- afterCreate(): void;
377
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
378
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
379
- }, {
380
- error: unknown;
381
- loadingP: Promise<void> | undefined;
382
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
383
- refNameAliases: {
384
- [x: string]: string;
385
- } | undefined;
386
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
387
- } & {
388
- getConf(arg: string): any;
389
- readonly lowerCaseRefNameAliases: {
390
- [k: string]: string;
391
- } | undefined;
392
- } & {
393
- readonly initialized: boolean;
394
- readonly name: string;
395
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
396
- readonly aliases: string[];
397
- readonly displayName: string;
398
- hasName(name: string): boolean;
399
- readonly allAliases: string[];
400
- readonly allRefNames: string[] | undefined;
401
- readonly lowerCaseRefNames: string[] | undefined;
402
- readonly allRefNamesWithLowerCase: string[] | undefined;
403
- readonly rpcManager: RpcManager;
404
- readonly refNameColors: string[];
405
- } & {
406
- readonly refNames: string[] | undefined;
407
- } & {
408
- getCanonicalRefName(refName: string): string | undefined;
409
- getRefNameColor(refName: string): string | undefined;
410
- isValidRefName(refName: string): boolean;
411
- } & {
412
- setLoaded({ regions, refNameAliases, cytobands, }: {
413
- regions: import("@jbrowse/core/util").Region[];
414
- refNameAliases: {
415
- [x: string]: string;
416
- };
417
- cytobands: import("@jbrowse/core/util").Feature[];
418
- }): void;
419
- setError(e: unknown): void;
420
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
421
- setRefNameAliases(aliases: {
422
- [x: string]: string;
423
- }): void;
424
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
425
- setLoadingP(p?: Promise<void>): void;
426
- load(): Promise<void>;
427
- loadPre(): Promise<void>;
428
- } & {
429
- getAdapterMapEntry(adapterConf: {
430
- [x: string]: unknown;
431
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
432
- getRefNameMapForAdapter(adapterConf: {
433
- [x: string]: unknown;
434
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
435
- [x: string]: string;
436
- }>;
437
- getReverseRefNameMapForAdapter(adapterConf: {
438
- [x: string]: unknown;
439
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
440
- [x: string]: string;
441
- }>;
442
- afterCreate(): void;
443
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
444
- } & {
445
- getCanonicalAssemblyName(asmName: string): string | undefined;
446
- get(asmName: string): ({
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
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
456
- } & {
457
- getConf(arg: string): any;
458
- readonly lowerCaseRefNameAliases: {
459
- [k: string]: string;
460
- } | undefined;
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;
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: RpcManager;
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, cytobands, }: {
482
- regions: import("@jbrowse/core/util").Region[];
483
- refNameAliases: {
484
- [x: string]: string;
485
- };
486
- cytobands: import("@jbrowse/core/util").Feature[];
487
- }): void;
488
- setError(e: unknown): void;
489
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
490
- setRefNameAliases(aliases: {
491
- [x: string]: string;
492
- }): void;
493
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
494
- setLoadingP(p?: Promise<void>): void;
495
- load(): Promise<void>;
496
- loadPre(): Promise<void>;
497
- } & {
498
- getAdapterMapEntry(adapterConf: {
499
- [x: string]: unknown;
500
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
501
- getRefNameMapForAdapter(adapterConf: {
502
- [x: string]: unknown;
503
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
504
- [x: string]: string;
505
- }>;
506
- getReverseRefNameMapForAdapter(adapterConf: {
507
- [x: string]: unknown;
508
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
509
- [x: string]: string;
510
- }>;
511
- afterCreate(): void;
512
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
513
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
514
- }, {
515
- error: unknown;
516
- loadingP: Promise<void> | undefined;
517
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
518
- refNameAliases: {
519
- [x: string]: string;
520
- } | undefined;
521
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
522
- } & {
523
- getConf(arg: string): any;
524
- readonly lowerCaseRefNameAliases: {
525
- [k: string]: string;
526
- } | undefined;
527
- } & {
528
- readonly initialized: boolean;
529
- readonly name: string;
530
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
531
- readonly aliases: string[];
532
- readonly displayName: string;
533
- hasName(name: string): boolean;
534
- readonly allAliases: string[];
535
- readonly allRefNames: string[] | undefined;
536
- readonly lowerCaseRefNames: string[] | undefined;
537
- readonly allRefNamesWithLowerCase: string[] | undefined;
538
- readonly rpcManager: RpcManager;
539
- readonly refNameColors: string[];
540
- } & {
541
- readonly refNames: string[] | undefined;
542
- } & {
543
- getCanonicalRefName(refName: string): string | undefined;
544
- getRefNameColor(refName: string): string | undefined;
545
- isValidRefName(refName: string): boolean;
546
- } & {
547
- setLoaded({ regions, refNameAliases, cytobands, }: {
548
- regions: import("@jbrowse/core/util").Region[];
549
- refNameAliases: {
550
- [x: string]: string;
551
- };
552
- cytobands: import("@jbrowse/core/util").Feature[];
553
- }): void;
554
- setError(e: unknown): void;
555
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
556
- setRefNameAliases(aliases: {
557
- [x: string]: string;
558
- }): void;
559
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
560
- setLoadingP(p?: Promise<void>): void;
561
- load(): Promise<void>;
562
- loadPre(): Promise<void>;
563
- } & {
564
- getAdapterMapEntry(adapterConf: {
565
- [x: string]: unknown;
566
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
567
- getRefNameMapForAdapter(adapterConf: {
568
- [x: string]: unknown;
569
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
570
- [x: string]: string;
571
- }>;
572
- getReverseRefNameMapForAdapter(adapterConf: {
573
- [x: string]: unknown;
574
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
575
- [x: string]: string;
576
- }>;
577
- afterCreate(): void;
578
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
579
- readonly assemblyNamesList: any[];
580
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
581
- readonly rpcManager: RpcManager;
582
- } & {
583
- waitForAssembly(assemblyName: string): Promise<({
584
- configuration: any;
585
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
586
- error: unknown;
587
- loadingP: Promise<void> | undefined;
588
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
589
- refNameAliases: {
590
- [x: string]: string;
591
- } | undefined;
592
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
593
- } & {
594
- getConf(arg: string): any;
595
- readonly lowerCaseRefNameAliases: {
596
- [k: string]: string;
597
- } | undefined;
598
- } & {
599
- readonly initialized: boolean;
600
- readonly name: string;
601
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
602
- readonly aliases: string[];
603
- readonly displayName: string;
604
- hasName(name: string): boolean;
605
- readonly allAliases: string[];
606
- readonly allRefNames: string[] | undefined;
607
- readonly lowerCaseRefNames: string[] | undefined;
608
- readonly allRefNamesWithLowerCase: string[] | undefined;
609
- readonly rpcManager: RpcManager;
610
- readonly refNameColors: string[];
611
- } & {
612
- readonly refNames: string[] | undefined;
613
- } & {
614
- getCanonicalRefName(refName: string): string | undefined;
615
- getRefNameColor(refName: string): string | undefined;
616
- isValidRefName(refName: string): boolean;
617
- } & {
618
- setLoaded({ regions, refNameAliases, cytobands, }: {
619
- regions: import("@jbrowse/core/util").Region[];
620
- refNameAliases: {
621
- [x: string]: string;
622
- };
623
- cytobands: import("@jbrowse/core/util").Feature[];
624
- }): void;
625
- setError(e: unknown): void;
626
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
627
- setRefNameAliases(aliases: {
628
- [x: string]: string;
629
- }): void;
630
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
631
- setLoadingP(p?: Promise<void>): void;
632
- load(): Promise<void>;
633
- loadPre(): Promise<void>;
634
- } & {
635
- getAdapterMapEntry(adapterConf: {
636
- [x: string]: unknown;
637
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
638
- getRefNameMapForAdapter(adapterConf: {
639
- [x: string]: unknown;
640
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
641
- [x: string]: string;
642
- }>;
643
- getReverseRefNameMapForAdapter(adapterConf: {
644
- [x: string]: unknown;
645
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
646
- [x: string]: string;
647
- }>;
648
- afterCreate(): void;
649
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
650
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
651
- }, {
652
- error: unknown;
653
- loadingP: Promise<void> | undefined;
654
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
655
- refNameAliases: {
656
- [x: string]: string;
657
- } | undefined;
658
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
659
- } & {
660
- getConf(arg: string): any;
661
- readonly lowerCaseRefNameAliases: {
662
- [k: string]: string;
663
- } | undefined;
664
- } & {
665
- readonly initialized: boolean;
666
- readonly name: string;
667
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
668
- readonly aliases: string[];
669
- readonly displayName: string;
670
- hasName(name: string): boolean;
671
- readonly allAliases: string[];
672
- readonly allRefNames: string[] | undefined;
673
- readonly lowerCaseRefNames: string[] | undefined;
674
- readonly allRefNamesWithLowerCase: string[] | undefined;
675
- readonly rpcManager: RpcManager;
676
- readonly refNameColors: string[];
677
- } & {
678
- readonly refNames: string[] | undefined;
679
- } & {
680
- getCanonicalRefName(refName: string): string | undefined;
681
- getRefNameColor(refName: string): string | undefined;
682
- isValidRefName(refName: string): boolean;
683
- } & {
684
- setLoaded({ regions, refNameAliases, cytobands, }: {
685
- regions: import("@jbrowse/core/util").Region[];
686
- refNameAliases: {
687
- [x: string]: string;
688
- };
689
- cytobands: import("@jbrowse/core/util").Feature[];
690
- }): void;
691
- setError(e: unknown): void;
692
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
693
- setRefNameAliases(aliases: {
694
- [x: string]: string;
695
- }): void;
696
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
697
- setLoadingP(p?: Promise<void>): void;
698
- load(): Promise<void>;
699
- loadPre(): Promise<void>;
700
- } & {
701
- getAdapterMapEntry(adapterConf: {
702
- [x: string]: unknown;
703
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
704
- getRefNameMapForAdapter(adapterConf: {
705
- [x: string]: unknown;
706
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
707
- [x: string]: string;
708
- }>;
709
- getReverseRefNameMapForAdapter(adapterConf: {
710
- [x: string]: unknown;
711
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
712
- [x: string]: string;
713
- }>;
714
- afterCreate(): void;
715
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
716
- getRefNameMapForAdapter(adapterConf: {
717
- [x: string]: unknown;
718
- }, assemblyName: string | undefined, opts: {
719
- stopToken?: string;
720
- sessionId: string;
721
- }): Promise<{
722
- [x: string]: string;
723
- } | undefined>;
724
- getReverseRefNameMapForAdapter(adapterConf: {
725
- [x: string]: unknown;
726
- }, assemblyName: string | undefined, opts: {
727
- stopToken?: string;
728
- sessionId: string;
729
- }): Promise<{
730
- [x: string]: string;
731
- } | undefined>;
732
- isValidRefName(refName: string, assemblyName: string): boolean;
733
- } & {
734
- afterAttach(): void;
735
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
736
- addAssembly(configuration: any): void;
737
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
738
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
739
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
740
- }, {
741
- error: unknown;
742
- loadingP: Promise<void> | undefined;
743
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
744
- refNameAliases: {
745
- [x: string]: string;
746
- } | undefined;
747
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
748
- } & {
749
- getConf(arg: string): any;
750
- readonly lowerCaseRefNameAliases: {
751
- [k: string]: string;
752
- } | undefined;
753
- } & {
754
- readonly initialized: boolean;
755
- readonly name: string;
756
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
757
- readonly aliases: string[];
758
- readonly displayName: string;
759
- hasName(name: string): boolean;
760
- readonly allAliases: string[];
761
- readonly allRefNames: string[] | undefined;
762
- readonly lowerCaseRefNames: string[] | undefined;
763
- readonly allRefNamesWithLowerCase: string[] | undefined;
764
- readonly rpcManager: RpcManager;
765
- readonly refNameColors: string[];
766
- } & {
767
- readonly refNames: string[] | undefined;
768
- } & {
769
- getCanonicalRefName(refName: string): string | undefined;
770
- getRefNameColor(refName: string): string | undefined;
771
- isValidRefName(refName: string): boolean;
772
- } & {
773
- setLoaded({ regions, refNameAliases, cytobands, }: {
774
- regions: import("@jbrowse/core/util").Region[];
775
- refNameAliases: {
776
- [x: string]: string;
777
- };
778
- cytobands: import("@jbrowse/core/util").Feature[];
779
- }): void;
780
- setError(e: unknown): void;
781
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
782
- setRefNameAliases(aliases: {
783
- [x: string]: string;
784
- }): void;
785
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
786
- setLoadingP(p?: Promise<void>): void;
787
- load(): Promise<void>;
788
- loadPre(): Promise<void>;
789
- } & {
790
- getAdapterMapEntry(adapterConf: {
791
- [x: string]: unknown;
792
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
793
- getRefNameMapForAdapter(adapterConf: {
794
- [x: string]: unknown;
795
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
796
- [x: string]: string;
797
- }>;
798
- getReverseRefNameMapForAdapter(adapterConf: {
799
- [x: string]: unknown;
800
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
801
- [x: string]: string;
802
- }>;
803
- afterCreate(): void;
804
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
805
- }, {
806
- readonly assemblyNameMap: Record<string, {
807
- configuration: any;
808
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
809
- error: unknown;
810
- loadingP: Promise<void> | undefined;
811
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
812
- refNameAliases: {
813
- [x: string]: string;
814
- } | undefined;
815
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
816
- } & {
817
- getConf(arg: string): any;
818
- readonly lowerCaseRefNameAliases: {
819
- [k: string]: string;
820
- } | undefined;
821
- } & {
822
- readonly initialized: boolean;
823
- readonly name: string;
824
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
825
- readonly aliases: string[];
826
- readonly displayName: string;
827
- hasName(name: string): boolean;
828
- readonly allAliases: string[];
829
- readonly allRefNames: string[] | undefined;
830
- readonly lowerCaseRefNames: string[] | undefined;
831
- readonly allRefNamesWithLowerCase: string[] | undefined;
832
- readonly rpcManager: RpcManager;
833
- readonly refNameColors: string[];
834
- } & {
835
- readonly refNames: string[] | undefined;
836
- } & {
837
- getCanonicalRefName(refName: string): string | undefined;
838
- getRefNameColor(refName: string): string | undefined;
839
- isValidRefName(refName: string): boolean;
840
- } & {
841
- setLoaded({ regions, refNameAliases, cytobands, }: {
842
- regions: import("@jbrowse/core/util").Region[];
843
- refNameAliases: {
844
- [x: string]: string;
845
- };
846
- cytobands: import("@jbrowse/core/util").Feature[];
847
- }): void;
848
- setError(e: unknown): void;
849
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
850
- setRefNameAliases(aliases: {
851
- [x: string]: string;
852
- }): void;
853
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
854
- setLoadingP(p?: Promise<void>): void;
855
- load(): Promise<void>;
856
- loadPre(): Promise<void>;
857
- } & {
858
- getAdapterMapEntry(adapterConf: {
859
- [x: string]: unknown;
860
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
861
- getRefNameMapForAdapter(adapterConf: {
862
- [x: string]: unknown;
863
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
864
- [x: string]: string;
865
- }>;
866
- getReverseRefNameMapForAdapter(adapterConf: {
867
- [x: string]: unknown;
868
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
869
- [x: string]: string;
870
- }>;
871
- afterCreate(): void;
872
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
873
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
874
- }, {
875
- error: unknown;
876
- loadingP: Promise<void> | undefined;
877
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
878
- refNameAliases: {
879
- [x: string]: string;
880
- } | undefined;
881
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
882
- } & {
883
- getConf(arg: string): any;
884
- readonly lowerCaseRefNameAliases: {
885
- [k: string]: string;
886
- } | undefined;
887
- } & {
888
- readonly initialized: boolean;
889
- readonly name: string;
890
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
891
- readonly aliases: string[];
892
- readonly displayName: string;
893
- hasName(name: string): boolean;
894
- readonly allAliases: string[];
895
- readonly allRefNames: string[] | undefined;
896
- readonly lowerCaseRefNames: string[] | undefined;
897
- readonly allRefNamesWithLowerCase: string[] | undefined;
898
- readonly rpcManager: RpcManager;
899
- readonly refNameColors: string[];
900
- } & {
901
- readonly refNames: string[] | undefined;
902
- } & {
903
- getCanonicalRefName(refName: string): string | undefined;
904
- getRefNameColor(refName: string): string | undefined;
905
- isValidRefName(refName: string): boolean;
906
- } & {
907
- setLoaded({ regions, refNameAliases, cytobands, }: {
908
- regions: import("@jbrowse/core/util").Region[];
909
- refNameAliases: {
910
- [x: string]: string;
911
- };
912
- cytobands: import("@jbrowse/core/util").Feature[];
913
- }): void;
914
- setError(e: unknown): void;
915
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
916
- setRefNameAliases(aliases: {
917
- [x: string]: string;
918
- }): void;
919
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
920
- setLoadingP(p?: Promise<void>): void;
921
- load(): Promise<void>;
922
- loadPre(): Promise<void>;
923
- } & {
924
- getAdapterMapEntry(adapterConf: {
925
- [x: string]: unknown;
926
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
927
- getRefNameMapForAdapter(adapterConf: {
928
- [x: string]: unknown;
929
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
930
- [x: string]: string;
931
- }>;
932
- getReverseRefNameMapForAdapter(adapterConf: {
933
- [x: string]: unknown;
934
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
935
- [x: string]: string;
936
- }>;
937
- afterCreate(): void;
938
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
939
- } & {
940
- getCanonicalAssemblyName(asmName: string): string | undefined;
941
- get(asmName: string): ({
942
- configuration: any;
943
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
944
- error: unknown;
945
- loadingP: Promise<void> | undefined;
946
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
947
- refNameAliases: {
948
- [x: string]: string;
949
- } | undefined;
950
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
951
- } & {
952
- getConf(arg: string): any;
953
- readonly lowerCaseRefNameAliases: {
954
- [k: string]: string;
955
- } | undefined;
956
- } & {
957
- readonly initialized: boolean;
958
- readonly name: string;
959
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
960
- readonly aliases: string[];
961
- readonly displayName: string;
962
- hasName(name: string): boolean;
963
- readonly allAliases: string[];
964
- readonly allRefNames: string[] | undefined;
965
- readonly lowerCaseRefNames: string[] | undefined;
966
- readonly allRefNamesWithLowerCase: string[] | undefined;
967
- readonly rpcManager: RpcManager;
968
- readonly refNameColors: string[];
969
- } & {
970
- readonly refNames: string[] | undefined;
971
- } & {
972
- getCanonicalRefName(refName: string): string | undefined;
973
- getRefNameColor(refName: string): string | undefined;
974
- isValidRefName(refName: string): boolean;
975
- } & {
976
- setLoaded({ regions, refNameAliases, cytobands, }: {
977
- regions: import("@jbrowse/core/util").Region[];
978
- refNameAliases: {
979
- [x: string]: string;
980
- };
981
- cytobands: import("@jbrowse/core/util").Feature[];
982
- }): void;
983
- setError(e: unknown): void;
984
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
985
- setRefNameAliases(aliases: {
986
- [x: string]: string;
987
- }): void;
988
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
989
- setLoadingP(p?: Promise<void>): void;
990
- load(): Promise<void>;
991
- loadPre(): Promise<void>;
992
- } & {
993
- getAdapterMapEntry(adapterConf: {
994
- [x: string]: unknown;
995
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
996
- getRefNameMapForAdapter(adapterConf: {
997
- [x: string]: unknown;
998
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
999
- [x: string]: string;
1000
- }>;
1001
- getReverseRefNameMapForAdapter(adapterConf: {
1002
- [x: string]: unknown;
1003
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1004
- [x: string]: string;
1005
- }>;
1006
- afterCreate(): void;
1007
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1008
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1009
- }, {
1010
- error: unknown;
1011
- loadingP: Promise<void> | undefined;
1012
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1013
- refNameAliases: {
1014
- [x: string]: string;
1015
- } | undefined;
1016
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1017
- } & {
1018
- getConf(arg: string): any;
1019
- readonly lowerCaseRefNameAliases: {
1020
- [k: string]: string;
1021
- } | undefined;
1022
- } & {
1023
- readonly initialized: boolean;
1024
- readonly name: string;
1025
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1026
- readonly aliases: string[];
1027
- readonly displayName: string;
1028
- hasName(name: string): boolean;
1029
- readonly allAliases: string[];
1030
- readonly allRefNames: string[] | undefined;
1031
- readonly lowerCaseRefNames: string[] | undefined;
1032
- readonly allRefNamesWithLowerCase: string[] | undefined;
1033
- readonly rpcManager: RpcManager;
1034
- readonly refNameColors: string[];
1035
- } & {
1036
- readonly refNames: string[] | undefined;
1037
- } & {
1038
- getCanonicalRefName(refName: string): string | undefined;
1039
- getRefNameColor(refName: string): string | undefined;
1040
- isValidRefName(refName: string): boolean;
1041
- } & {
1042
- setLoaded({ regions, refNameAliases, cytobands, }: {
1043
- regions: import("@jbrowse/core/util").Region[];
1044
- refNameAliases: {
1045
- [x: string]: string;
1046
- };
1047
- cytobands: import("@jbrowse/core/util").Feature[];
1048
- }): void;
1049
- setError(e: unknown): void;
1050
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1051
- setRefNameAliases(aliases: {
1052
- [x: string]: string;
1053
- }): void;
1054
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1055
- setLoadingP(p?: Promise<void>): void;
1056
- load(): Promise<void>;
1057
- loadPre(): Promise<void>;
1058
- } & {
1059
- getAdapterMapEntry(adapterConf: {
1060
- [x: string]: unknown;
1061
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1062
- getRefNameMapForAdapter(adapterConf: {
1063
- [x: string]: unknown;
1064
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1065
- [x: string]: string;
1066
- }>;
1067
- getReverseRefNameMapForAdapter(adapterConf: {
1068
- [x: string]: unknown;
1069
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1070
- [x: string]: string;
1071
- }>;
1072
- afterCreate(): void;
1073
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1074
- readonly assemblyNamesList: any[];
1075
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1076
- readonly rpcManager: RpcManager;
1077
- } & {
1078
- waitForAssembly(assemblyName: string): Promise<({
1079
- configuration: any;
1080
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1081
- error: unknown;
1082
- loadingP: Promise<void> | undefined;
1083
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1084
- refNameAliases: {
1085
- [x: string]: string;
1086
- } | undefined;
1087
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1088
- } & {
1089
- getConf(arg: string): any;
1090
- readonly lowerCaseRefNameAliases: {
1091
- [k: string]: string;
1092
- } | undefined;
1093
- } & {
1094
- readonly initialized: boolean;
1095
- readonly name: string;
1096
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1097
- readonly aliases: string[];
1098
- readonly displayName: string;
1099
- hasName(name: string): boolean;
1100
- readonly allAliases: string[];
1101
- readonly allRefNames: string[] | undefined;
1102
- readonly lowerCaseRefNames: string[] | undefined;
1103
- readonly allRefNamesWithLowerCase: string[] | undefined;
1104
- readonly rpcManager: RpcManager;
1105
- readonly refNameColors: string[];
1106
- } & {
1107
- readonly refNames: string[] | undefined;
1108
- } & {
1109
- getCanonicalRefName(refName: string): string | undefined;
1110
- getRefNameColor(refName: string): string | undefined;
1111
- isValidRefName(refName: string): boolean;
1112
- } & {
1113
- setLoaded({ regions, refNameAliases, cytobands, }: {
1114
- regions: import("@jbrowse/core/util").Region[];
1115
- refNameAliases: {
1116
- [x: string]: string;
1117
- };
1118
- cytobands: import("@jbrowse/core/util").Feature[];
1119
- }): void;
1120
- setError(e: unknown): void;
1121
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1122
- setRefNameAliases(aliases: {
1123
- [x: string]: string;
1124
- }): void;
1125
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1126
- setLoadingP(p?: Promise<void>): void;
1127
- load(): Promise<void>;
1128
- loadPre(): Promise<void>;
1129
- } & {
1130
- getAdapterMapEntry(adapterConf: {
1131
- [x: string]: unknown;
1132
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1133
- getRefNameMapForAdapter(adapterConf: {
1134
- [x: string]: unknown;
1135
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1136
- [x: string]: string;
1137
- }>;
1138
- getReverseRefNameMapForAdapter(adapterConf: {
1139
- [x: string]: unknown;
1140
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1141
- [x: string]: string;
1142
- }>;
1143
- afterCreate(): void;
1144
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1145
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1146
- }, {
1147
- error: unknown;
1148
- loadingP: Promise<void> | undefined;
1149
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1150
- refNameAliases: {
1151
- [x: string]: string;
1152
- } | undefined;
1153
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1154
- } & {
1155
- getConf(arg: string): any;
1156
- readonly lowerCaseRefNameAliases: {
1157
- [k: string]: string;
1158
- } | undefined;
1159
- } & {
1160
- readonly initialized: boolean;
1161
- readonly name: string;
1162
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1163
- readonly aliases: string[];
1164
- readonly displayName: string;
1165
- hasName(name: string): boolean;
1166
- readonly allAliases: string[];
1167
- readonly allRefNames: string[] | undefined;
1168
- readonly lowerCaseRefNames: string[] | undefined;
1169
- readonly allRefNamesWithLowerCase: string[] | undefined;
1170
- readonly rpcManager: RpcManager;
1171
- readonly refNameColors: string[];
1172
- } & {
1173
- readonly refNames: string[] | undefined;
1174
- } & {
1175
- getCanonicalRefName(refName: string): string | undefined;
1176
- getRefNameColor(refName: string): string | undefined;
1177
- isValidRefName(refName: string): boolean;
1178
- } & {
1179
- setLoaded({ regions, refNameAliases, cytobands, }: {
1180
- regions: import("@jbrowse/core/util").Region[];
1181
- refNameAliases: {
1182
- [x: string]: string;
1183
- };
1184
- cytobands: import("@jbrowse/core/util").Feature[];
1185
- }): void;
1186
- setError(e: unknown): void;
1187
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1188
- setRefNameAliases(aliases: {
1189
- [x: string]: string;
1190
- }): void;
1191
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1192
- setLoadingP(p?: Promise<void>): void;
1193
- load(): Promise<void>;
1194
- loadPre(): Promise<void>;
1195
- } & {
1196
- getAdapterMapEntry(adapterConf: {
1197
- [x: string]: unknown;
1198
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1199
- getRefNameMapForAdapter(adapterConf: {
1200
- [x: string]: unknown;
1201
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1202
- [x: string]: string;
1203
- }>;
1204
- getReverseRefNameMapForAdapter(adapterConf: {
1205
- [x: string]: unknown;
1206
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1207
- [x: string]: string;
1208
- }>;
1209
- afterCreate(): void;
1210
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1211
- getRefNameMapForAdapter(adapterConf: {
1212
- [x: string]: unknown;
1213
- }, assemblyName: string | undefined, opts: {
1214
- stopToken?: string;
1215
- sessionId: string;
1216
- }): Promise<{
1217
- [x: string]: string;
1218
- } | undefined>;
1219
- getReverseRefNameMapForAdapter(adapterConf: {
1220
- [x: string]: unknown;
1221
- }, assemblyName: string | undefined, opts: {
1222
- stopToken?: string;
1223
- sessionId: string;
1224
- }): Promise<{
1225
- [x: string]: string;
1226
- } | undefined>;
1227
- isValidRefName(refName: string, assemblyName: string): boolean;
1228
- } & {
1229
- afterAttach(): void;
1230
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1231
- addAssembly(configuration: any): void;
1232
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
1233
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1234
- rpcManager: RpcManager;
1235
- adminMode: boolean;
1236
- error: unknown;
1237
- textSearchManager: TextSearchManager;
1238
- pluginManager: PluginManager;
1239
- } & {
1240
- setError(error: unknown): void;
1241
- setSession(sessionSnapshot?: SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1242
- setDefaultSession(): void;
1243
- setSessionPath(path: string): void;
1244
- renameCurrentSession(newName: string): void;
1245
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1246
- jbrowse: import("mobx-state-tree").IAnyType;
1247
- session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
1248
- sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1249
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1250
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1251
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1252
- }, {
1253
- error: unknown;
1254
- loadingP: Promise<void> | undefined;
1255
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1256
- refNameAliases: {
1257
- [x: string]: string;
1258
- } | undefined;
1259
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1260
- } & {
1261
- getConf(arg: string): any;
1262
- readonly lowerCaseRefNameAliases: {
1263
- [k: string]: string;
1264
- } | undefined;
1265
- } & {
1266
- readonly initialized: boolean;
1267
- readonly name: string;
1268
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1269
- readonly aliases: string[];
1270
- readonly displayName: string;
1271
- hasName(name: string): boolean;
1272
- readonly allAliases: string[];
1273
- readonly allRefNames: string[] | undefined;
1274
- readonly lowerCaseRefNames: string[] | undefined;
1275
- readonly allRefNamesWithLowerCase: string[] | undefined;
1276
- readonly rpcManager: RpcManager;
1277
- readonly refNameColors: string[];
1278
- } & {
1279
- readonly refNames: string[] | undefined;
1280
- } & {
1281
- getCanonicalRefName(refName: string): string | undefined;
1282
- getRefNameColor(refName: string): string | undefined;
1283
- isValidRefName(refName: string): boolean;
1284
- } & {
1285
- setLoaded({ regions, refNameAliases, cytobands, }: {
1286
- regions: import("@jbrowse/core/util").Region[];
1287
- refNameAliases: {
1288
- [x: string]: string;
1289
- };
1290
- cytobands: import("@jbrowse/core/util").Feature[];
1291
- }): void;
1292
- setError(e: unknown): void;
1293
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1294
- setRefNameAliases(aliases: {
1295
- [x: string]: string;
1296
- }): void;
1297
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1298
- setLoadingP(p?: Promise<void>): void;
1299
- load(): Promise<void>;
1300
- loadPre(): Promise<void>;
1301
- } & {
1302
- getAdapterMapEntry(adapterConf: {
1303
- [x: string]: unknown;
1304
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1305
- getRefNameMapForAdapter(adapterConf: {
1306
- [x: string]: unknown;
1307
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1308
- [x: string]: string;
1309
- }>;
1310
- getReverseRefNameMapForAdapter(adapterConf: {
1311
- [x: string]: unknown;
1312
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1313
- [x: string]: string;
1314
- }>;
1315
- afterCreate(): void;
1316
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1317
- }, {
1318
- readonly assemblyNameMap: Record<string, {
1319
- configuration: any;
1320
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1321
- error: unknown;
1322
- loadingP: Promise<void> | undefined;
1323
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1324
- refNameAliases: {
1325
- [x: string]: string;
1326
- } | undefined;
1327
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1328
- } & {
1329
- getConf(arg: string): any;
1330
- readonly lowerCaseRefNameAliases: {
1331
- [k: string]: string;
1332
- } | undefined;
1333
- } & {
1334
- readonly initialized: boolean;
1335
- readonly name: string;
1336
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1337
- readonly aliases: string[];
1338
- readonly displayName: string;
1339
- hasName(name: string): boolean;
1340
- readonly allAliases: string[];
1341
- readonly allRefNames: string[] | undefined;
1342
- readonly lowerCaseRefNames: string[] | undefined;
1343
- readonly allRefNamesWithLowerCase: string[] | undefined;
1344
- readonly rpcManager: RpcManager;
1345
- readonly refNameColors: string[];
1346
- } & {
1347
- readonly refNames: string[] | undefined;
1348
- } & {
1349
- getCanonicalRefName(refName: string): string | undefined;
1350
- getRefNameColor(refName: string): string | undefined;
1351
- isValidRefName(refName: string): boolean;
1352
- } & {
1353
- setLoaded({ regions, refNameAliases, cytobands, }: {
1354
- regions: import("@jbrowse/core/util").Region[];
1355
- refNameAliases: {
1356
- [x: string]: string;
1357
- };
1358
- cytobands: import("@jbrowse/core/util").Feature[];
1359
- }): void;
1360
- setError(e: unknown): void;
1361
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1362
- setRefNameAliases(aliases: {
1363
- [x: string]: string;
1364
- }): void;
1365
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1366
- setLoadingP(p?: Promise<void>): void;
1367
- load(): Promise<void>;
1368
- loadPre(): Promise<void>;
1369
- } & {
1370
- getAdapterMapEntry(adapterConf: {
1371
- [x: string]: unknown;
1372
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1373
- getRefNameMapForAdapter(adapterConf: {
1374
- [x: string]: unknown;
1375
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1376
- [x: string]: string;
1377
- }>;
1378
- getReverseRefNameMapForAdapter(adapterConf: {
1379
- [x: string]: unknown;
1380
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1381
- [x: string]: string;
1382
- }>;
1383
- afterCreate(): void;
1384
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1385
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1386
- }, {
1387
- error: unknown;
1388
- loadingP: Promise<void> | undefined;
1389
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1390
- refNameAliases: {
1391
- [x: string]: string;
1392
- } | undefined;
1393
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1394
- } & {
1395
- getConf(arg: string): any;
1396
- readonly lowerCaseRefNameAliases: {
1397
- [k: string]: string;
1398
- } | undefined;
1399
- } & {
1400
- readonly initialized: boolean;
1401
- readonly name: string;
1402
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1403
- readonly aliases: string[];
1404
- readonly displayName: string;
1405
- hasName(name: string): boolean;
1406
- readonly allAliases: string[];
1407
- readonly allRefNames: string[] | undefined;
1408
- readonly lowerCaseRefNames: string[] | undefined;
1409
- readonly allRefNamesWithLowerCase: string[] | undefined;
1410
- readonly rpcManager: RpcManager;
1411
- readonly refNameColors: string[];
1412
- } & {
1413
- readonly refNames: string[] | undefined;
1414
- } & {
1415
- getCanonicalRefName(refName: string): string | undefined;
1416
- getRefNameColor(refName: string): string | undefined;
1417
- isValidRefName(refName: string): boolean;
1418
- } & {
1419
- setLoaded({ regions, refNameAliases, cytobands, }: {
1420
- regions: import("@jbrowse/core/util").Region[];
1421
- refNameAliases: {
1422
- [x: string]: string;
1423
- };
1424
- cytobands: import("@jbrowse/core/util").Feature[];
1425
- }): void;
1426
- setError(e: unknown): void;
1427
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1428
- setRefNameAliases(aliases: {
1429
- [x: string]: string;
1430
- }): void;
1431
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1432
- setLoadingP(p?: Promise<void>): void;
1433
- load(): Promise<void>;
1434
- loadPre(): Promise<void>;
1435
- } & {
1436
- getAdapterMapEntry(adapterConf: {
1437
- [x: string]: unknown;
1438
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1439
- getRefNameMapForAdapter(adapterConf: {
1440
- [x: string]: unknown;
1441
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1442
- [x: string]: string;
1443
- }>;
1444
- getReverseRefNameMapForAdapter(adapterConf: {
1445
- [x: string]: unknown;
1446
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1447
- [x: string]: string;
1448
- }>;
1449
- afterCreate(): void;
1450
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
1451
- } & {
1452
- getCanonicalAssemblyName(asmName: string): string | undefined;
1453
- get(asmName: string): ({
1454
- configuration: any;
1455
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1456
- error: unknown;
1457
- loadingP: Promise<void> | undefined;
1458
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1459
- refNameAliases: {
1460
- [x: string]: string;
1461
- } | undefined;
1462
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1463
- } & {
1464
- getConf(arg: string): any;
1465
- readonly lowerCaseRefNameAliases: {
1466
- [k: string]: string;
1467
- } | undefined;
1468
- } & {
1469
- readonly initialized: boolean;
1470
- readonly name: string;
1471
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1472
- readonly aliases: string[];
1473
- readonly displayName: string;
1474
- hasName(name: string): boolean;
1475
- readonly allAliases: string[];
1476
- readonly allRefNames: string[] | undefined;
1477
- readonly lowerCaseRefNames: string[] | undefined;
1478
- readonly allRefNamesWithLowerCase: string[] | undefined;
1479
- readonly rpcManager: RpcManager;
1480
- readonly refNameColors: string[];
1481
- } & {
1482
- readonly refNames: string[] | undefined;
1483
- } & {
1484
- getCanonicalRefName(refName: string): string | undefined;
1485
- getRefNameColor(refName: string): string | undefined;
1486
- isValidRefName(refName: string): boolean;
1487
- } & {
1488
- setLoaded({ regions, refNameAliases, cytobands, }: {
1489
- regions: import("@jbrowse/core/util").Region[];
1490
- refNameAliases: {
1491
- [x: string]: string;
1492
- };
1493
- cytobands: import("@jbrowse/core/util").Feature[];
1494
- }): void;
1495
- setError(e: unknown): void;
1496
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1497
- setRefNameAliases(aliases: {
1498
- [x: string]: string;
1499
- }): void;
1500
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1501
- setLoadingP(p?: Promise<void>): void;
1502
- load(): Promise<void>;
1503
- loadPre(): Promise<void>;
1504
- } & {
1505
- getAdapterMapEntry(adapterConf: {
1506
- [x: string]: unknown;
1507
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1508
- getRefNameMapForAdapter(adapterConf: {
1509
- [x: string]: unknown;
1510
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1511
- [x: string]: string;
1512
- }>;
1513
- getReverseRefNameMapForAdapter(adapterConf: {
1514
- [x: string]: unknown;
1515
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1516
- [x: string]: string;
1517
- }>;
1518
- afterCreate(): void;
1519
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1520
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1521
- }, {
1522
- error: unknown;
1523
- loadingP: Promise<void> | undefined;
1524
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1525
- refNameAliases: {
1526
- [x: string]: string;
1527
- } | undefined;
1528
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1529
- } & {
1530
- getConf(arg: string): any;
1531
- readonly lowerCaseRefNameAliases: {
1532
- [k: string]: string;
1533
- } | undefined;
1534
- } & {
1535
- readonly initialized: boolean;
1536
- readonly name: string;
1537
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1538
- readonly aliases: string[];
1539
- readonly displayName: string;
1540
- hasName(name: string): boolean;
1541
- readonly allAliases: string[];
1542
- readonly allRefNames: string[] | undefined;
1543
- readonly lowerCaseRefNames: string[] | undefined;
1544
- readonly allRefNamesWithLowerCase: string[] | undefined;
1545
- readonly rpcManager: RpcManager;
1546
- readonly refNameColors: string[];
1547
- } & {
1548
- readonly refNames: string[] | undefined;
1549
- } & {
1550
- getCanonicalRefName(refName: string): string | undefined;
1551
- getRefNameColor(refName: string): string | undefined;
1552
- isValidRefName(refName: string): boolean;
1553
- } & {
1554
- setLoaded({ regions, refNameAliases, cytobands, }: {
1555
- regions: import("@jbrowse/core/util").Region[];
1556
- refNameAliases: {
1557
- [x: string]: string;
1558
- };
1559
- cytobands: import("@jbrowse/core/util").Feature[];
1560
- }): void;
1561
- setError(e: unknown): void;
1562
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1563
- setRefNameAliases(aliases: {
1564
- [x: string]: string;
1565
- }): void;
1566
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1567
- setLoadingP(p?: Promise<void>): void;
1568
- load(): Promise<void>;
1569
- loadPre(): Promise<void>;
1570
- } & {
1571
- getAdapterMapEntry(adapterConf: {
1572
- [x: string]: unknown;
1573
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1574
- getRefNameMapForAdapter(adapterConf: {
1575
- [x: string]: unknown;
1576
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1577
- [x: string]: string;
1578
- }>;
1579
- getReverseRefNameMapForAdapter(adapterConf: {
1580
- [x: string]: unknown;
1581
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1582
- [x: string]: string;
1583
- }>;
1584
- afterCreate(): void;
1585
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1586
- readonly assemblyNamesList: any[];
1587
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1588
- readonly rpcManager: RpcManager;
1589
- } & {
1590
- waitForAssembly(assemblyName: string): Promise<({
1591
- configuration: any;
1592
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1593
- error: unknown;
1594
- loadingP: Promise<void> | undefined;
1595
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1596
- refNameAliases: {
1597
- [x: string]: string;
1598
- } | undefined;
1599
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1600
- } & {
1601
- getConf(arg: string): any;
1602
- readonly lowerCaseRefNameAliases: {
1603
- [k: string]: string;
1604
- } | undefined;
1605
- } & {
1606
- readonly initialized: boolean;
1607
- readonly name: string;
1608
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1609
- readonly aliases: string[];
1610
- readonly displayName: string;
1611
- hasName(name: string): boolean;
1612
- readonly allAliases: string[];
1613
- readonly allRefNames: string[] | undefined;
1614
- readonly lowerCaseRefNames: string[] | undefined;
1615
- readonly allRefNamesWithLowerCase: string[] | undefined;
1616
- readonly rpcManager: RpcManager;
1617
- readonly refNameColors: string[];
1618
- } & {
1619
- readonly refNames: string[] | undefined;
1620
- } & {
1621
- getCanonicalRefName(refName: string): string | undefined;
1622
- getRefNameColor(refName: string): string | undefined;
1623
- isValidRefName(refName: string): boolean;
1624
- } & {
1625
- setLoaded({ regions, refNameAliases, cytobands, }: {
1626
- regions: import("@jbrowse/core/util").Region[];
1627
- refNameAliases: {
1628
- [x: string]: string;
1629
- };
1630
- cytobands: import("@jbrowse/core/util").Feature[];
1631
- }): void;
1632
- setError(e: unknown): void;
1633
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1634
- setRefNameAliases(aliases: {
1635
- [x: string]: string;
1636
- }): void;
1637
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1638
- setLoadingP(p?: Promise<void>): void;
1639
- load(): Promise<void>;
1640
- loadPre(): Promise<void>;
1641
- } & {
1642
- getAdapterMapEntry(adapterConf: {
1643
- [x: string]: unknown;
1644
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1645
- getRefNameMapForAdapter(adapterConf: {
1646
- [x: string]: unknown;
1647
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1648
- [x: string]: string;
1649
- }>;
1650
- getReverseRefNameMapForAdapter(adapterConf: {
1651
- [x: string]: unknown;
1652
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1653
- [x: string]: string;
1654
- }>;
1655
- afterCreate(): void;
1656
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1657
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1658
- }, {
1659
- error: unknown;
1660
- loadingP: Promise<void> | undefined;
1661
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1662
- refNameAliases: {
1663
- [x: string]: string;
1664
- } | undefined;
1665
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1666
- } & {
1667
- getConf(arg: string): any;
1668
- readonly lowerCaseRefNameAliases: {
1669
- [k: string]: string;
1670
- } | undefined;
1671
- } & {
1672
- readonly initialized: boolean;
1673
- readonly name: string;
1674
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1675
- readonly aliases: string[];
1676
- readonly displayName: string;
1677
- hasName(name: string): boolean;
1678
- readonly allAliases: string[];
1679
- readonly allRefNames: string[] | undefined;
1680
- readonly lowerCaseRefNames: string[] | undefined;
1681
- readonly allRefNamesWithLowerCase: string[] | undefined;
1682
- readonly rpcManager: RpcManager;
1683
- readonly refNameColors: string[];
1684
- } & {
1685
- readonly refNames: string[] | undefined;
1686
- } & {
1687
- getCanonicalRefName(refName: string): string | undefined;
1688
- getRefNameColor(refName: string): string | undefined;
1689
- isValidRefName(refName: string): boolean;
1690
- } & {
1691
- setLoaded({ regions, refNameAliases, cytobands, }: {
1692
- regions: import("@jbrowse/core/util").Region[];
1693
- refNameAliases: {
1694
- [x: string]: string;
1695
- };
1696
- cytobands: import("@jbrowse/core/util").Feature[];
1697
- }): void;
1698
- setError(e: unknown): void;
1699
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1700
- setRefNameAliases(aliases: {
1701
- [x: string]: string;
1702
- }): void;
1703
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1704
- setLoadingP(p?: Promise<void>): void;
1705
- load(): Promise<void>;
1706
- loadPre(): Promise<void>;
1707
- } & {
1708
- getAdapterMapEntry(adapterConf: {
1709
- [x: string]: unknown;
1710
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1711
- getRefNameMapForAdapter(adapterConf: {
1712
- [x: string]: unknown;
1713
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1714
- [x: string]: string;
1715
- }>;
1716
- getReverseRefNameMapForAdapter(adapterConf: {
1717
- [x: string]: unknown;
1718
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1719
- [x: string]: string;
1720
- }>;
1721
- afterCreate(): void;
1722
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1723
- getRefNameMapForAdapter(adapterConf: {
1724
- [x: string]: unknown;
1725
- }, assemblyName: string | undefined, opts: {
1726
- stopToken?: string;
1727
- sessionId: string;
1728
- }): Promise<{
1729
- [x: string]: string;
1730
- } | undefined>;
1731
- getReverseRefNameMapForAdapter(adapterConf: {
1732
- [x: string]: unknown;
1733
- }, assemblyName: string | undefined, opts: {
1734
- stopToken?: string;
1735
- sessionId: string;
1736
- }): Promise<{
1737
- [x: string]: string;
1738
- } | undefined>;
1739
- isValidRefName(refName: string, assemblyName: string): boolean;
1740
- } & {
1741
- afterAttach(): void;
1742
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1743
- addAssembly(configuration: any): void;
1744
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
1745
- }, {
1746
- rpcManager: RpcManager;
1747
- adminMode: boolean;
1748
- error: unknown;
1749
- textSearchManager: TextSearchManager;
1750
- pluginManager: PluginManager;
1751
- } & {
1752
- setError(error: unknown): void;
1753
- setSession(sessionSnapshot?: SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1754
- setDefaultSession(): void;
1755
- setSessionPath(path: string): void;
1756
- renameCurrentSession(newName: string): void;
1757
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1758
- } & {
1759
- readonly jbrowse: any;
1760
- readonly rpcManager: RpcManager;
1761
- readonly configuration: {
1762
- [x: string]: any;
1763
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1764
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1765
- [x: string]: any;
1766
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1767
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1768
- [x: string]: any;
1769
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1770
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1771
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1772
- readonly adminMode: boolean;
1773
- readonly textSearchManager: TextSearchManager;
1774
- } & {
1775
- readonly assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
1776
- } & {
1777
- setSelection(thing: unknown): void;
1778
- clearSelection(): void;
1779
- setHovered(thing: unknown): void;
1780
- } & {
1781
- readonly visibleWidget: any;
1782
- } & {
1783
- setDrawerPosition(arg: string): void;
1784
- updateDrawerWidth(drawerWidth: number): number;
1785
- resizeDrawer(distance: number): number;
1786
- addWidget(typeName: string, id: string, initialState?: {}, conf?: unknown): any;
1787
- showWidget(widget: any): void;
1788
- hasWidget(widget: any): boolean;
1789
- hideWidget(widget: any): void;
1790
- minimizeWidgetDrawer(): void;
1791
- showWidgetDrawer(): void;
1792
- hideAllWidgets(): void;
1793
- editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1794
- afterAttach(): void;
1795
- } & {
1796
- readonly connections: import("@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig").BaseConnectionConfigModel[];
1797
- } & {
1798
- makeConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: {}): ({
1799
- name: string;
1800
- tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
1801
- configuration: {
1802
- [x: string]: any;
1803
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1804
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1805
- [x: string]: any;
1806
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1807
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1808
- [x: string]: any;
1809
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1810
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1811
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1812
- name: {
1813
- type: string;
1814
- defaultValue: string;
1815
- description: string;
1816
- };
1817
- assemblyNames: {
1818
- type: string;
1819
- defaultValue: never[];
1820
- description: string;
1821
- };
1822
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>;
1823
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1824
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1825
- } & {
1826
- afterAttach(): void;
1827
- addTrackConf(trackConf: Record<string, unknown> | ({
1828
- [x: string]: any;
1829
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1830
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1831
- [x: string]: any;
1832
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1833
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1834
- [x: string]: any;
1835
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1836
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1837
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
1838
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
1839
- [x: string]: any;
1840
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1841
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1842
- [x: string]: any;
1843
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1844
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1845
- [x: string]: any;
1846
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1847
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1848
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
1849
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
1850
- clear(): void;
1851
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1852
- name: import("mobx-state-tree").ISimpleType<string>;
1853
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
1854
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1855
- name: {
1856
- type: string;
1857
- defaultValue: string;
1858
- description: string;
1859
- };
1860
- assemblyNames: {
1861
- type: string;
1862
- defaultValue: never[];
1863
- description: string;
1864
- };
1865
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
1866
- }, {
1867
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1868
- } & {
1869
- afterAttach(): void;
1870
- addTrackConf(trackConf: Record<string, unknown> | ({
1871
- [x: string]: any;
1872
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1873
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1874
- [x: string]: any;
1875
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1876
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1877
- [x: string]: any;
1878
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1879
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1880
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
1881
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
1882
- [x: string]: any;
1883
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1884
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1885
- [x: string]: any;
1886
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1887
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1888
- [x: string]: any;
1889
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1890
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1891
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
1892
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
1893
- clear(): void;
1894
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1895
- prepareToBreakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): (Record<string, number> | (() => void))[] | undefined;
1896
- breakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1897
- deleteConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1898
- addConnectionConf(connectionConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1899
- clearConnections(): void;
1900
- } & {
1901
- queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, unknown][];
1902
- } & {
1903
- readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType | undefined;
1904
- readonly DialogProps: unknown;
1905
- } & {
1906
- removeActiveDialog(): void;
1907
- queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, unknown]): void;
1908
- } & {
1909
- getReferring(object: import("mobx-state-tree").IAnyStateTreeNode): import("@jbrowse/product-core").ReferringNode[];
1910
- } & {
1911
- removeReferring(referring: import("@jbrowse/product-core").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
1912
- } & {
1913
- readonly tracks: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1914
- } & {
1915
- addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfiguration): any;
1916
- deleteTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1917
- } & {
1918
- snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1919
- } & {
1920
- readonly snackbarMessageSet: Map<string, import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1921
- } & {
1922
- notify(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction): void;
1923
- notifyError(errorMessage: string, error?: unknown, extra?: unknown): void;
1924
- pushSnackbarMessage(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction): void;
1925
- popSnackbarMessage(): import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage | undefined;
1926
- removeSnackbarMessage(message: string): void;
1927
- } & {
1928
- task: undefined;
1929
- } & {
1930
- readonly version: any;
1931
- readonly assemblies: any[];
1932
- readonly assemblyNames: any[];
1933
- readonly connections: any;
1934
- readonly assemblyManager: any;
1935
- readonly views: any[];
1936
- renderProps(): {
1937
- theme: any;
1938
- highResolutionScaling: any;
1939
- };
1940
- } & {
1941
- addView(typeName: string, initialState?: {}): any;
1942
- removeView(): void;
1943
- } & {
1944
- getTrackActionMenuItems(config: any): {
1945
- label: string;
1946
- onClick: () => void;
1947
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
1948
- muiName: string;
1949
- };
1950
- }[];
1951
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
1952
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1953
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1954
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1955
- }, {
1956
- error: unknown;
1957
- loadingP: Promise<void> | undefined;
1958
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1959
- refNameAliases: {
1960
- [x: string]: string;
1961
- } | undefined;
1962
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1963
- } & {
1964
- getConf(arg: string): any;
1965
- readonly lowerCaseRefNameAliases: {
1966
- [k: string]: string;
1967
- } | undefined;
1968
- } & {
1969
- readonly initialized: boolean;
1970
- readonly name: string;
1971
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1972
- readonly aliases: string[];
1973
- readonly displayName: string;
1974
- hasName(name: string): boolean;
1975
- readonly allAliases: string[];
1976
- readonly allRefNames: string[] | undefined;
1977
- readonly lowerCaseRefNames: string[] | undefined;
1978
- readonly allRefNamesWithLowerCase: string[] | undefined;
1979
- readonly rpcManager: RpcManager;
1980
- readonly refNameColors: string[];
1981
- } & {
1982
- readonly refNames: string[] | undefined;
1983
- } & {
1984
- getCanonicalRefName(refName: string): string | undefined;
1985
- getRefNameColor(refName: string): string | undefined;
1986
- isValidRefName(refName: string): boolean;
1987
- } & {
1988
- setLoaded({ regions, refNameAliases, cytobands, }: {
1989
- regions: import("@jbrowse/core/util").Region[];
1990
- refNameAliases: {
1991
- [x: string]: string;
1992
- };
1993
- cytobands: import("@jbrowse/core/util").Feature[];
1994
- }): void;
1995
- setError(e: unknown): void;
1996
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1997
- setRefNameAliases(aliases: {
1998
- [x: string]: string;
1999
- }): void;
2000
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2001
- setLoadingP(p?: Promise<void>): void;
2002
- load(): Promise<void>;
2003
- loadPre(): Promise<void>;
2004
- } & {
2005
- getAdapterMapEntry(adapterConf: {
2006
- [x: string]: unknown;
2007
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2008
- getRefNameMapForAdapter(adapterConf: {
2009
- [x: string]: unknown;
2010
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2011
- [x: string]: string;
2012
- }>;
2013
- getReverseRefNameMapForAdapter(adapterConf: {
2014
- [x: string]: unknown;
2015
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2016
- [x: string]: string;
2017
- }>;
2018
- afterCreate(): void;
2019
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
2020
- }, {
2021
- readonly assemblyNameMap: Record<string, {
2022
- configuration: any;
2023
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2024
- error: unknown;
2025
- loadingP: Promise<void> | undefined;
2026
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2027
- refNameAliases: {
2028
- [x: string]: string;
2029
- } | undefined;
2030
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2031
- } & {
2032
- getConf(arg: string): any;
2033
- readonly lowerCaseRefNameAliases: {
2034
- [k: string]: string;
2035
- } | undefined;
2036
- } & {
2037
- readonly initialized: boolean;
2038
- readonly name: string;
2039
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2040
- readonly aliases: string[];
2041
- readonly displayName: string;
2042
- hasName(name: string): boolean;
2043
- readonly allAliases: string[];
2044
- readonly allRefNames: string[] | undefined;
2045
- readonly lowerCaseRefNames: string[] | undefined;
2046
- readonly allRefNamesWithLowerCase: string[] | undefined;
2047
- readonly rpcManager: RpcManager;
2048
- readonly refNameColors: string[];
2049
- } & {
2050
- readonly refNames: string[] | undefined;
2051
- } & {
2052
- getCanonicalRefName(refName: string): string | undefined;
2053
- getRefNameColor(refName: string): string | undefined;
2054
- isValidRefName(refName: string): boolean;
2055
- } & {
2056
- setLoaded({ regions, refNameAliases, cytobands, }: {
2057
- regions: import("@jbrowse/core/util").Region[];
2058
- refNameAliases: {
2059
- [x: string]: string;
2060
- };
2061
- cytobands: import("@jbrowse/core/util").Feature[];
2062
- }): void;
2063
- setError(e: unknown): void;
2064
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2065
- setRefNameAliases(aliases: {
2066
- [x: string]: string;
2067
- }): void;
2068
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2069
- setLoadingP(p?: Promise<void>): void;
2070
- load(): Promise<void>;
2071
- loadPre(): Promise<void>;
2072
- } & {
2073
- getAdapterMapEntry(adapterConf: {
2074
- [x: string]: unknown;
2075
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2076
- getRefNameMapForAdapter(adapterConf: {
2077
- [x: string]: unknown;
2078
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2079
- [x: string]: string;
2080
- }>;
2081
- getReverseRefNameMapForAdapter(adapterConf: {
2082
- [x: string]: unknown;
2083
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2084
- [x: string]: string;
2085
- }>;
2086
- afterCreate(): void;
2087
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2088
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2089
- }, {
2090
- error: unknown;
2091
- loadingP: Promise<void> | undefined;
2092
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2093
- refNameAliases: {
2094
- [x: string]: string;
2095
- } | undefined;
2096
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2097
- } & {
2098
- getConf(arg: string): any;
2099
- readonly lowerCaseRefNameAliases: {
2100
- [k: string]: string;
2101
- } | undefined;
2102
- } & {
2103
- readonly initialized: boolean;
2104
- readonly name: string;
2105
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2106
- readonly aliases: string[];
2107
- readonly displayName: string;
2108
- hasName(name: string): boolean;
2109
- readonly allAliases: string[];
2110
- readonly allRefNames: string[] | undefined;
2111
- readonly lowerCaseRefNames: string[] | undefined;
2112
- readonly allRefNamesWithLowerCase: string[] | undefined;
2113
- readonly rpcManager: RpcManager;
2114
- readonly refNameColors: string[];
2115
- } & {
2116
- readonly refNames: string[] | undefined;
2117
- } & {
2118
- getCanonicalRefName(refName: string): string | undefined;
2119
- getRefNameColor(refName: string): string | undefined;
2120
- isValidRefName(refName: string): boolean;
2121
- } & {
2122
- setLoaded({ regions, refNameAliases, cytobands, }: {
2123
- regions: import("@jbrowse/core/util").Region[];
2124
- refNameAliases: {
2125
- [x: string]: string;
2126
- };
2127
- cytobands: import("@jbrowse/core/util").Feature[];
2128
- }): void;
2129
- setError(e: unknown): void;
2130
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2131
- setRefNameAliases(aliases: {
2132
- [x: string]: string;
2133
- }): void;
2134
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2135
- setLoadingP(p?: Promise<void>): void;
2136
- load(): Promise<void>;
2137
- loadPre(): Promise<void>;
2138
- } & {
2139
- getAdapterMapEntry(adapterConf: {
2140
- [x: string]: unknown;
2141
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2142
- getRefNameMapForAdapter(adapterConf: {
2143
- [x: string]: unknown;
2144
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2145
- [x: string]: string;
2146
- }>;
2147
- getReverseRefNameMapForAdapter(adapterConf: {
2148
- [x: string]: unknown;
2149
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2150
- [x: string]: string;
2151
- }>;
2152
- afterCreate(): void;
2153
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
2154
- } & {
2155
- getCanonicalAssemblyName(asmName: string): string | undefined;
2156
- get(asmName: string): ({
2157
- configuration: any;
2158
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2159
- error: unknown;
2160
- loadingP: Promise<void> | undefined;
2161
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2162
- refNameAliases: {
2163
- [x: string]: string;
2164
- } | undefined;
2165
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2166
- } & {
2167
- getConf(arg: string): any;
2168
- readonly lowerCaseRefNameAliases: {
2169
- [k: string]: string;
2170
- } | undefined;
2171
- } & {
2172
- readonly initialized: boolean;
2173
- readonly name: string;
2174
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2175
- readonly aliases: string[];
2176
- readonly displayName: string;
2177
- hasName(name: string): boolean;
2178
- readonly allAliases: string[];
2179
- readonly allRefNames: string[] | undefined;
2180
- readonly lowerCaseRefNames: string[] | undefined;
2181
- readonly allRefNamesWithLowerCase: string[] | undefined;
2182
- readonly rpcManager: RpcManager;
2183
- readonly refNameColors: string[];
2184
- } & {
2185
- readonly refNames: string[] | undefined;
2186
- } & {
2187
- getCanonicalRefName(refName: string): string | undefined;
2188
- getRefNameColor(refName: string): string | undefined;
2189
- isValidRefName(refName: string): boolean;
2190
- } & {
2191
- setLoaded({ regions, refNameAliases, cytobands, }: {
2192
- regions: import("@jbrowse/core/util").Region[];
2193
- refNameAliases: {
2194
- [x: string]: string;
2195
- };
2196
- cytobands: import("@jbrowse/core/util").Feature[];
2197
- }): void;
2198
- setError(e: unknown): void;
2199
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2200
- setRefNameAliases(aliases: {
2201
- [x: string]: string;
2202
- }): void;
2203
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2204
- setLoadingP(p?: Promise<void>): void;
2205
- load(): Promise<void>;
2206
- loadPre(): Promise<void>;
2207
- } & {
2208
- getAdapterMapEntry(adapterConf: {
2209
- [x: string]: unknown;
2210
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2211
- getRefNameMapForAdapter(adapterConf: {
2212
- [x: string]: unknown;
2213
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2214
- [x: string]: string;
2215
- }>;
2216
- getReverseRefNameMapForAdapter(adapterConf: {
2217
- [x: string]: unknown;
2218
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2219
- [x: string]: string;
2220
- }>;
2221
- afterCreate(): void;
2222
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2223
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2224
- }, {
2225
- error: unknown;
2226
- loadingP: Promise<void> | undefined;
2227
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2228
- refNameAliases: {
2229
- [x: string]: string;
2230
- } | undefined;
2231
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2232
- } & {
2233
- getConf(arg: string): any;
2234
- readonly lowerCaseRefNameAliases: {
2235
- [k: string]: string;
2236
- } | undefined;
2237
- } & {
2238
- readonly initialized: boolean;
2239
- readonly name: string;
2240
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2241
- readonly aliases: string[];
2242
- readonly displayName: string;
2243
- hasName(name: string): boolean;
2244
- readonly allAliases: string[];
2245
- readonly allRefNames: string[] | undefined;
2246
- readonly lowerCaseRefNames: string[] | undefined;
2247
- readonly allRefNamesWithLowerCase: string[] | undefined;
2248
- readonly rpcManager: RpcManager;
2249
- readonly refNameColors: string[];
2250
- } & {
2251
- readonly refNames: string[] | undefined;
2252
- } & {
2253
- getCanonicalRefName(refName: string): string | undefined;
2254
- getRefNameColor(refName: string): string | undefined;
2255
- isValidRefName(refName: string): boolean;
2256
- } & {
2257
- setLoaded({ regions, refNameAliases, cytobands, }: {
2258
- regions: import("@jbrowse/core/util").Region[];
2259
- refNameAliases: {
2260
- [x: string]: string;
2261
- };
2262
- cytobands: import("@jbrowse/core/util").Feature[];
2263
- }): void;
2264
- setError(e: unknown): void;
2265
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2266
- setRefNameAliases(aliases: {
2267
- [x: string]: string;
2268
- }): void;
2269
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2270
- setLoadingP(p?: Promise<void>): void;
2271
- load(): Promise<void>;
2272
- loadPre(): Promise<void>;
2273
- } & {
2274
- getAdapterMapEntry(adapterConf: {
2275
- [x: string]: unknown;
2276
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2277
- getRefNameMapForAdapter(adapterConf: {
2278
- [x: string]: unknown;
2279
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2280
- [x: string]: string;
2281
- }>;
2282
- getReverseRefNameMapForAdapter(adapterConf: {
2283
- [x: string]: unknown;
2284
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2285
- [x: string]: string;
2286
- }>;
2287
- afterCreate(): void;
2288
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
2289
- readonly assemblyNamesList: any[];
2290
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
2291
- readonly rpcManager: RpcManager;
2292
- } & {
2293
- waitForAssembly(assemblyName: string): Promise<({
2294
- configuration: any;
2295
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2296
- error: unknown;
2297
- loadingP: Promise<void> | undefined;
2298
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2299
- refNameAliases: {
2300
- [x: string]: string;
2301
- } | undefined;
2302
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2303
- } & {
2304
- getConf(arg: string): any;
2305
- readonly lowerCaseRefNameAliases: {
2306
- [k: string]: string;
2307
- } | undefined;
2308
- } & {
2309
- readonly initialized: boolean;
2310
- readonly name: string;
2311
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2312
- readonly aliases: string[];
2313
- readonly displayName: string;
2314
- hasName(name: string): boolean;
2315
- readonly allAliases: string[];
2316
- readonly allRefNames: string[] | undefined;
2317
- readonly lowerCaseRefNames: string[] | undefined;
2318
- readonly allRefNamesWithLowerCase: string[] | undefined;
2319
- readonly rpcManager: RpcManager;
2320
- readonly refNameColors: string[];
2321
- } & {
2322
- readonly refNames: string[] | undefined;
2323
- } & {
2324
- getCanonicalRefName(refName: string): string | undefined;
2325
- getRefNameColor(refName: string): string | undefined;
2326
- isValidRefName(refName: string): boolean;
2327
- } & {
2328
- setLoaded({ regions, refNameAliases, cytobands, }: {
2329
- regions: import("@jbrowse/core/util").Region[];
2330
- refNameAliases: {
2331
- [x: string]: string;
2332
- };
2333
- cytobands: import("@jbrowse/core/util").Feature[];
2334
- }): void;
2335
- setError(e: unknown): void;
2336
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2337
- setRefNameAliases(aliases: {
2338
- [x: string]: string;
2339
- }): void;
2340
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2341
- setLoadingP(p?: Promise<void>): void;
2342
- load(): Promise<void>;
2343
- loadPre(): Promise<void>;
2344
- } & {
2345
- getAdapterMapEntry(adapterConf: {
2346
- [x: string]: unknown;
2347
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2348
- getRefNameMapForAdapter(adapterConf: {
2349
- [x: string]: unknown;
2350
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2351
- [x: string]: string;
2352
- }>;
2353
- getReverseRefNameMapForAdapter(adapterConf: {
2354
- [x: string]: unknown;
2355
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2356
- [x: string]: string;
2357
- }>;
2358
- afterCreate(): void;
2359
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2360
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2361
- }, {
2362
- error: unknown;
2363
- loadingP: Promise<void> | undefined;
2364
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2365
- refNameAliases: {
2366
- [x: string]: string;
2367
- } | undefined;
2368
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2369
- } & {
2370
- getConf(arg: string): any;
2371
- readonly lowerCaseRefNameAliases: {
2372
- [k: string]: string;
2373
- } | undefined;
2374
- } & {
2375
- readonly initialized: boolean;
2376
- readonly name: string;
2377
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2378
- readonly aliases: string[];
2379
- readonly displayName: string;
2380
- hasName(name: string): boolean;
2381
- readonly allAliases: string[];
2382
- readonly allRefNames: string[] | undefined;
2383
- readonly lowerCaseRefNames: string[] | undefined;
2384
- readonly allRefNamesWithLowerCase: string[] | undefined;
2385
- readonly rpcManager: RpcManager;
2386
- readonly refNameColors: string[];
2387
- } & {
2388
- readonly refNames: string[] | undefined;
2389
- } & {
2390
- getCanonicalRefName(refName: string): string | undefined;
2391
- getRefNameColor(refName: string): string | undefined;
2392
- isValidRefName(refName: string): boolean;
2393
- } & {
2394
- setLoaded({ regions, refNameAliases, cytobands, }: {
2395
- regions: import("@jbrowse/core/util").Region[];
2396
- refNameAliases: {
2397
- [x: string]: string;
2398
- };
2399
- cytobands: import("@jbrowse/core/util").Feature[];
2400
- }): void;
2401
- setError(e: unknown): void;
2402
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2403
- setRefNameAliases(aliases: {
2404
- [x: string]: string;
2405
- }): void;
2406
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2407
- setLoadingP(p?: Promise<void>): void;
2408
- load(): Promise<void>;
2409
- loadPre(): Promise<void>;
2410
- } & {
2411
- getAdapterMapEntry(adapterConf: {
2412
- [x: string]: unknown;
2413
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2414
- getRefNameMapForAdapter(adapterConf: {
2415
- [x: string]: unknown;
2416
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2417
- [x: string]: string;
2418
- }>;
2419
- getReverseRefNameMapForAdapter(adapterConf: {
2420
- [x: string]: unknown;
2421
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2422
- [x: string]: string;
2423
- }>;
2424
- afterCreate(): void;
2425
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
2426
- getRefNameMapForAdapter(adapterConf: {
2427
- [x: string]: unknown;
2428
- }, assemblyName: string | undefined, opts: {
2429
- stopToken?: string;
2430
- sessionId: string;
2431
- }): Promise<{
2432
- [x: string]: string;
2433
- } | undefined>;
2434
- getReverseRefNameMapForAdapter(adapterConf: {
2435
- [x: string]: unknown;
2436
- }, assemblyName: string | undefined, opts: {
2437
- stopToken?: string;
2438
- sessionId: string;
2439
- }): Promise<{
2440
- [x: string]: string;
2441
- } | undefined>;
2442
- isValidRefName(refName: string, assemblyName: string): boolean;
2443
- } & {
2444
- afterAttach(): void;
2445
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
2446
- addAssembly(configuration: any): void;
2447
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
2448
- internetAccounts: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
2449
- }, {
2450
- error: unknown;
2451
- adminMode: boolean;
2452
- version: string;
2453
- rpcManager: RpcManager;
2454
- textSearchManager: TextSearchManager;
2455
- } & {
2456
- setSession(sessionSnapshot: SnapshotIn<import("mobx-state-tree").IModelType<{
2457
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2458
- name: import("mobx-state-tree").ISimpleType<string>;
2459
- margin: import("mobx-state-tree").IType<number | undefined, number, number>;
2460
- } & {
2461
- drawerPosition: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2462
- drawerWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
2463
- widgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyType>;
2464
- activeWidgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>>;
2465
- minimized: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2466
- } & {
2467
- connectionInstances: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
2468
- name: import("mobx-state-tree").ISimpleType<string>;
2469
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
2470
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2471
- name: {
2472
- type: string;
2473
- defaultValue: string;
2474
- description: string;
2475
- };
2476
- assemblyNames: {
2477
- type: string;
2478
- defaultValue: never[];
2479
- description: string;
2480
- };
2481
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
2482
- }, {
2483
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
2484
- } & {
2485
- afterAttach(): void;
2486
- addTrackConf(trackConf: Record<string, unknown> | ({
2487
- [x: string]: any;
2488
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2489
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
2490
- [x: string]: any;
2491
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2492
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
2493
- [x: string]: any;
2494
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
2495
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
2496
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
2497
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
2498
- [x: string]: any;
2499
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2500
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
2501
- [x: string]: any;
2502
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2503
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
2504
- [x: string]: any;
2505
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
2506
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
2507
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
2508
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
2509
- clear(): void;
2510
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
2511
- } & {
2512
- view: import("mobx-state-tree").IAnyModelType;
2513
- }, {
2514
- selection: unknown;
2515
- hovered: unknown;
2516
- } & {
2517
- readonly root: {
2518
- jbrowse: any;
2519
- session: any;
2520
- sessionPath: string;
2521
- assemblyManager: {
2522
- assemblies: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
2523
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2524
- }, {
2525
- error: unknown;
2526
- loadingP: Promise<void> | undefined;
2527
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2528
- refNameAliases: {
2529
- [x: string]: string;
2530
- } | undefined;
2531
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2532
- } & {
2533
- getConf(arg: string): any;
2534
- readonly lowerCaseRefNameAliases: {
2535
- [k: string]: string;
2536
- } | undefined;
2537
- } & {
2538
- readonly initialized: boolean;
2539
- readonly name: string;
2540
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2541
- readonly aliases: string[];
2542
- readonly displayName: string;
2543
- hasName(name: string): boolean;
2544
- readonly allAliases: string[];
2545
- readonly allRefNames: string[] | undefined;
2546
- readonly lowerCaseRefNames: string[] | undefined;
2547
- readonly allRefNamesWithLowerCase: string[] | undefined;
2548
- readonly rpcManager: RpcManager;
2549
- readonly refNameColors: string[];
2550
- } & {
2551
- readonly refNames: string[] | undefined;
2552
- } & {
2553
- getCanonicalRefName(refName: string): string | undefined;
2554
- getRefNameColor(refName: string): string | undefined;
2555
- isValidRefName(refName: string): boolean;
2556
- } & {
2557
- setLoaded({ regions, refNameAliases, cytobands, }: {
2558
- regions: import("@jbrowse/core/util").Region[];
2559
- refNameAliases: {
2560
- [x: string]: string;
2561
- };
2562
- cytobands: import("@jbrowse/core/util").Feature[];
2563
- }): void;
2564
- setError(e: unknown): void;
2565
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2566
- setRefNameAliases(aliases: {
2567
- [x: string]: string;
2568
- }): void;
2569
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2570
- setLoadingP(p?: Promise<void>): void;
2571
- load(): Promise<void>;
2572
- loadPre(): Promise<void>;
2573
- } & {
2574
- getAdapterMapEntry(adapterConf: {
2575
- [x: string]: unknown;
2576
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2577
- getRefNameMapForAdapter(adapterConf: {
2578
- [x: string]: unknown;
2579
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2580
- [x: string]: string;
2581
- }>;
2582
- getReverseRefNameMapForAdapter(adapterConf: {
2583
- [x: string]: unknown;
2584
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2585
- [x: string]: string;
2586
- }>;
2587
- afterCreate(): void;
2588
- }, 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<{
2589
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2590
- }, {
2591
- error: unknown;
2592
- loadingP: Promise<void> | undefined;
2593
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2594
- refNameAliases: {
2595
- [x: string]: string;
2596
- } | undefined;
2597
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2598
- } & {
2599
- getConf(arg: string): any;
2600
- readonly lowerCaseRefNameAliases: {
2601
- [k: string]: string;
2602
- } | undefined;
2603
- } & {
2604
- readonly initialized: boolean;
2605
- readonly name: string;
2606
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2607
- readonly aliases: string[];
2608
- readonly displayName: string;
2609
- hasName(name: string): boolean;
2610
- readonly allAliases: string[];
2611
- readonly allRefNames: string[] | undefined;
2612
- readonly lowerCaseRefNames: string[] | undefined;
2613
- readonly allRefNamesWithLowerCase: string[] | undefined;
2614
- readonly rpcManager: RpcManager;
2615
- readonly refNameColors: string[];
2616
- } & {
2617
- readonly refNames: string[] | undefined;
2618
- } & {
2619
- getCanonicalRefName(refName: string): string | undefined;
2620
- getRefNameColor(refName: string): string | undefined;
2621
- isValidRefName(refName: string): boolean;
2622
- } & {
2623
- setLoaded({ regions, refNameAliases, cytobands, }: {
2624
- regions: import("@jbrowse/core/util").Region[];
2625
- refNameAliases: {
2626
- [x: string]: string;
2627
- };
2628
- cytobands: import("@jbrowse/core/util").Feature[];
2629
- }): void;
2630
- setError(e: unknown): void;
2631
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2632
- setRefNameAliases(aliases: {
2633
- [x: string]: string;
2634
- }): void;
2635
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2636
- setLoadingP(p?: Promise<void>): void;
2637
- load(): Promise<void>;
2638
- loadPre(): Promise<void>;
2639
- } & {
2640
- getAdapterMapEntry(adapterConf: {
2641
- [x: string]: unknown;
2642
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2643
- getRefNameMapForAdapter(adapterConf: {
2644
- [x: string]: unknown;
2645
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2646
- [x: string]: string;
2647
- }>;
2648
- getReverseRefNameMapForAdapter(adapterConf: {
2649
- [x: string]: unknown;
2650
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2651
- [x: string]: string;
2652
- }>;
2653
- afterCreate(): void;
2654
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
2655
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2656
- readonly assemblyNameMap: Record<string, {
2657
- configuration: any;
2658
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2659
- error: unknown;
2660
- loadingP: Promise<void> | undefined;
2661
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2662
- refNameAliases: {
2663
- [x: string]: string;
2664
- } | undefined;
2665
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2666
- } & {
2667
- getConf(arg: string): any;
2668
- readonly lowerCaseRefNameAliases: {
2669
- [k: string]: string;
2670
- } | undefined;
2671
- } & {
2672
- readonly initialized: boolean;
2673
- readonly name: string;
2674
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2675
- readonly aliases: string[];
2676
- readonly displayName: string;
2677
- hasName(name: string): boolean;
2678
- readonly allAliases: string[];
2679
- readonly allRefNames: string[] | undefined;
2680
- readonly lowerCaseRefNames: string[] | undefined;
2681
- readonly allRefNamesWithLowerCase: string[] | undefined;
2682
- readonly rpcManager: RpcManager;
2683
- readonly refNameColors: string[];
2684
- } & {
2685
- readonly refNames: string[] | undefined;
2686
- } & {
2687
- getCanonicalRefName(refName: string): string | undefined;
2688
- getRefNameColor(refName: string): string | undefined;
2689
- isValidRefName(refName: string): boolean;
2690
- } & {
2691
- setLoaded({ regions, refNameAliases, cytobands, }: {
2692
- regions: import("@jbrowse/core/util").Region[];
2693
- refNameAliases: {
2694
- [x: string]: string;
2695
- };
2696
- cytobands: import("@jbrowse/core/util").Feature[];
2697
- }): void;
2698
- setError(e: unknown): void;
2699
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2700
- setRefNameAliases(aliases: {
2701
- [x: string]: string;
2702
- }): void;
2703
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2704
- setLoadingP(p?: Promise<void>): void;
2705
- load(): Promise<void>;
2706
- loadPre(): Promise<void>;
2707
- } & {
2708
- getAdapterMapEntry(adapterConf: {
2709
- [x: string]: unknown;
2710
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2711
- getRefNameMapForAdapter(adapterConf: {
2712
- [x: string]: unknown;
2713
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2714
- [x: string]: string;
2715
- }>;
2716
- getReverseRefNameMapForAdapter(adapterConf: {
2717
- [x: string]: unknown;
2718
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2719
- [x: string]: string;
2720
- }>;
2721
- afterCreate(): void;
2722
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2723
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2724
- }, {
2725
- error: unknown;
2726
- loadingP: Promise<void> | undefined;
2727
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2728
- refNameAliases: {
2729
- [x: string]: string;
2730
- } | undefined;
2731
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2732
- } & {
2733
- getConf(arg: string): any;
2734
- readonly lowerCaseRefNameAliases: {
2735
- [k: string]: string;
2736
- } | undefined;
2737
- } & {
2738
- readonly initialized: boolean;
2739
- readonly name: string;
2740
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2741
- readonly aliases: string[];
2742
- readonly displayName: string;
2743
- hasName(name: string): boolean;
2744
- readonly allAliases: string[];
2745
- readonly allRefNames: string[] | undefined;
2746
- readonly lowerCaseRefNames: string[] | undefined;
2747
- readonly allRefNamesWithLowerCase: string[] | undefined;
2748
- readonly rpcManager: RpcManager;
2749
- readonly refNameColors: string[];
2750
- } & {
2751
- readonly refNames: string[] | undefined;
2752
- } & {
2753
- getCanonicalRefName(refName: string): string | undefined;
2754
- getRefNameColor(refName: string): string | undefined;
2755
- isValidRefName(refName: string): boolean;
2756
- } & {
2757
- setLoaded({ regions, refNameAliases, cytobands, }: {
2758
- regions: import("@jbrowse/core/util").Region[];
2759
- refNameAliases: {
2760
- [x: string]: string;
2761
- };
2762
- cytobands: import("@jbrowse/core/util").Feature[];
2763
- }): void;
2764
- setError(e: unknown): void;
2765
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2766
- setRefNameAliases(aliases: {
2767
- [x: string]: string;
2768
- }): void;
2769
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2770
- setLoadingP(p?: Promise<void>): void;
2771
- load(): Promise<void>;
2772
- loadPre(): Promise<void>;
2773
- } & {
2774
- getAdapterMapEntry(adapterConf: {
2775
- [x: string]: unknown;
2776
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2777
- getRefNameMapForAdapter(adapterConf: {
2778
- [x: string]: unknown;
2779
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2780
- [x: string]: string;
2781
- }>;
2782
- getReverseRefNameMapForAdapter(adapterConf: {
2783
- [x: string]: unknown;
2784
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2785
- [x: string]: string;
2786
- }>;
2787
- afterCreate(): void;
2788
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
2789
- } & {
2790
- getCanonicalAssemblyName(asmName: string): string | undefined;
2791
- get(asmName: string): ({
2792
- configuration: any;
2793
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2794
- error: unknown;
2795
- loadingP: Promise<void> | undefined;
2796
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2797
- refNameAliases: {
2798
- [x: string]: string;
2799
- } | undefined;
2800
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2801
- } & {
2802
- getConf(arg: string): any;
2803
- readonly lowerCaseRefNameAliases: {
2804
- [k: string]: string;
2805
- } | undefined;
2806
- } & {
2807
- readonly initialized: boolean;
2808
- readonly name: string;
2809
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2810
- readonly aliases: string[];
2811
- readonly displayName: string;
2812
- hasName(name: string): boolean;
2813
- readonly allAliases: string[];
2814
- readonly allRefNames: string[] | undefined;
2815
- readonly lowerCaseRefNames: string[] | undefined;
2816
- readonly allRefNamesWithLowerCase: string[] | undefined;
2817
- readonly rpcManager: RpcManager;
2818
- readonly refNameColors: string[];
2819
- } & {
2820
- readonly refNames: string[] | undefined;
2821
- } & {
2822
- getCanonicalRefName(refName: string): string | undefined;
2823
- getRefNameColor(refName: string): string | undefined;
2824
- isValidRefName(refName: string): boolean;
2825
- } & {
2826
- setLoaded({ regions, refNameAliases, cytobands, }: {
2827
- regions: import("@jbrowse/core/util").Region[];
2828
- refNameAliases: {
2829
- [x: string]: string;
2830
- };
2831
- cytobands: import("@jbrowse/core/util").Feature[];
2832
- }): void;
2833
- setError(e: unknown): void;
2834
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2835
- setRefNameAliases(aliases: {
2836
- [x: string]: string;
2837
- }): void;
2838
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2839
- setLoadingP(p?: Promise<void>): void;
2840
- load(): Promise<void>;
2841
- loadPre(): Promise<void>;
2842
- } & {
2843
- getAdapterMapEntry(adapterConf: {
2844
- [x: string]: unknown;
2845
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2846
- getRefNameMapForAdapter(adapterConf: {
2847
- [x: string]: unknown;
2848
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2849
- [x: string]: string;
2850
- }>;
2851
- getReverseRefNameMapForAdapter(adapterConf: {
2852
- [x: string]: unknown;
2853
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2854
- [x: string]: string;
2855
- }>;
2856
- afterCreate(): void;
2857
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2858
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2859
- }, {
2860
- error: unknown;
2861
- loadingP: Promise<void> | undefined;
2862
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2863
- refNameAliases: {
2864
- [x: string]: string;
2865
- } | undefined;
2866
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2867
- } & {
2868
- getConf(arg: string): any;
2869
- readonly lowerCaseRefNameAliases: {
2870
- [k: string]: string;
2871
- } | undefined;
2872
- } & {
2873
- readonly initialized: boolean;
2874
- readonly name: string;
2875
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2876
- readonly aliases: string[];
2877
- readonly displayName: string;
2878
- hasName(name: string): boolean;
2879
- readonly allAliases: string[];
2880
- readonly allRefNames: string[] | undefined;
2881
- readonly lowerCaseRefNames: string[] | undefined;
2882
- readonly allRefNamesWithLowerCase: string[] | undefined;
2883
- readonly rpcManager: RpcManager;
2884
- readonly refNameColors: string[];
2885
- } & {
2886
- readonly refNames: string[] | undefined;
2887
- } & {
2888
- getCanonicalRefName(refName: string): string | undefined;
2889
- getRefNameColor(refName: string): string | undefined;
2890
- isValidRefName(refName: string): boolean;
2891
- } & {
2892
- setLoaded({ regions, refNameAliases, cytobands, }: {
2893
- regions: import("@jbrowse/core/util").Region[];
2894
- refNameAliases: {
2895
- [x: string]: string;
2896
- };
2897
- cytobands: import("@jbrowse/core/util").Feature[];
2898
- }): void;
2899
- setError(e: unknown): void;
2900
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2901
- setRefNameAliases(aliases: {
2902
- [x: string]: string;
2903
- }): void;
2904
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2905
- setLoadingP(p?: Promise<void>): void;
2906
- load(): Promise<void>;
2907
- loadPre(): Promise<void>;
2908
- } & {
2909
- getAdapterMapEntry(adapterConf: {
2910
- [x: string]: unknown;
2911
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2912
- getRefNameMapForAdapter(adapterConf: {
2913
- [x: string]: unknown;
2914
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2915
- [x: string]: string;
2916
- }>;
2917
- getReverseRefNameMapForAdapter(adapterConf: {
2918
- [x: string]: unknown;
2919
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2920
- [x: string]: string;
2921
- }>;
2922
- afterCreate(): void;
2923
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
2924
- readonly assemblyNamesList: any[];
2925
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
2926
- readonly rpcManager: RpcManager;
2927
- } & {
2928
- waitForAssembly(assemblyName: string): Promise<({
2929
- configuration: any;
2930
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2931
- error: unknown;
2932
- loadingP: Promise<void> | undefined;
2933
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2934
- refNameAliases: {
2935
- [x: string]: string;
2936
- } | undefined;
2937
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2938
- } & {
2939
- getConf(arg: string): any;
2940
- readonly lowerCaseRefNameAliases: {
2941
- [k: string]: string;
2942
- } | undefined;
2943
- } & {
2944
- readonly initialized: boolean;
2945
- readonly name: string;
2946
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2947
- readonly aliases: string[];
2948
- readonly displayName: string;
2949
- hasName(name: string): boolean;
2950
- readonly allAliases: string[];
2951
- readonly allRefNames: string[] | undefined;
2952
- readonly lowerCaseRefNames: string[] | undefined;
2953
- readonly allRefNamesWithLowerCase: string[] | undefined;
2954
- readonly rpcManager: RpcManager;
2955
- readonly refNameColors: string[];
2956
- } & {
2957
- readonly refNames: string[] | undefined;
2958
- } & {
2959
- getCanonicalRefName(refName: string): string | undefined;
2960
- getRefNameColor(refName: string): string | undefined;
2961
- isValidRefName(refName: string): boolean;
2962
- } & {
2963
- setLoaded({ regions, refNameAliases, cytobands, }: {
2964
- regions: import("@jbrowse/core/util").Region[];
2965
- refNameAliases: {
2966
- [x: string]: string;
2967
- };
2968
- cytobands: import("@jbrowse/core/util").Feature[];
2969
- }): void;
2970
- setError(e: unknown): void;
2971
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2972
- setRefNameAliases(aliases: {
2973
- [x: string]: string;
2974
- }): void;
2975
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2976
- setLoadingP(p?: Promise<void>): void;
2977
- load(): Promise<void>;
2978
- loadPre(): Promise<void>;
2979
- } & {
2980
- getAdapterMapEntry(adapterConf: {
2981
- [x: string]: unknown;
2982
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2983
- getRefNameMapForAdapter(adapterConf: {
2984
- [x: string]: unknown;
2985
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2986
- [x: string]: string;
2987
- }>;
2988
- getReverseRefNameMapForAdapter(adapterConf: {
2989
- [x: string]: unknown;
2990
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2991
- [x: string]: string;
2992
- }>;
2993
- afterCreate(): void;
2994
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2995
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2996
- }, {
2997
- error: unknown;
2998
- loadingP: Promise<void> | undefined;
2999
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3000
- refNameAliases: {
3001
- [x: string]: string;
3002
- } | undefined;
3003
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3004
- } & {
3005
- getConf(arg: string): any;
3006
- readonly lowerCaseRefNameAliases: {
3007
- [k: string]: string;
3008
- } | undefined;
3009
- } & {
3010
- readonly initialized: boolean;
3011
- readonly name: string;
3012
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3013
- readonly aliases: string[];
3014
- readonly displayName: string;
3015
- hasName(name: string): boolean;
3016
- readonly allAliases: string[];
3017
- readonly allRefNames: string[] | undefined;
3018
- readonly lowerCaseRefNames: string[] | undefined;
3019
- readonly allRefNamesWithLowerCase: string[] | undefined;
3020
- readonly rpcManager: RpcManager;
3021
- readonly refNameColors: string[];
3022
- } & {
3023
- readonly refNames: string[] | undefined;
3024
- } & {
3025
- getCanonicalRefName(refName: string): string | undefined;
3026
- getRefNameColor(refName: string): string | undefined;
3027
- isValidRefName(refName: string): boolean;
3028
- } & {
3029
- setLoaded({ regions, refNameAliases, cytobands, }: {
3030
- regions: import("@jbrowse/core/util").Region[];
3031
- refNameAliases: {
3032
- [x: string]: string;
3033
- };
3034
- cytobands: import("@jbrowse/core/util").Feature[];
3035
- }): void;
3036
- setError(e: unknown): void;
3037
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3038
- setRefNameAliases(aliases: {
3039
- [x: string]: string;
3040
- }): void;
3041
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3042
- setLoadingP(p?: Promise<void>): void;
3043
- load(): Promise<void>;
3044
- loadPre(): Promise<void>;
3045
- } & {
3046
- getAdapterMapEntry(adapterConf: {
3047
- [x: string]: unknown;
3048
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3049
- getRefNameMapForAdapter(adapterConf: {
3050
- [x: string]: unknown;
3051
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3052
- [x: string]: string;
3053
- }>;
3054
- getReverseRefNameMapForAdapter(adapterConf: {
3055
- [x: string]: unknown;
3056
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3057
- [x: string]: string;
3058
- }>;
3059
- afterCreate(): void;
3060
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
3061
- getRefNameMapForAdapter(adapterConf: {
3062
- [x: string]: unknown;
3063
- }, assemblyName: string | undefined, opts: {
3064
- stopToken?: string;
3065
- sessionId: string;
3066
- }): Promise<{
3067
- [x: string]: string;
3068
- } | undefined>;
3069
- getReverseRefNameMapForAdapter(adapterConf: {
3070
- [x: string]: unknown;
3071
- }, assemblyName: string | undefined, opts: {
3072
- stopToken?: string;
3073
- sessionId: string;
3074
- }): Promise<{
3075
- [x: string]: string;
3076
- } | undefined>;
3077
- isValidRefName(refName: string, assemblyName: string): boolean;
3078
- } & {
3079
- afterAttach(): void;
3080
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
3081
- addAssembly(configuration: any): void;
3082
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
3083
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
3084
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3085
- }, {
3086
- error: unknown;
3087
- loadingP: Promise<void> | undefined;
3088
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3089
- refNameAliases: {
3090
- [x: string]: string;
3091
- } | undefined;
3092
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3093
- } & {
3094
- getConf(arg: string): any;
3095
- readonly lowerCaseRefNameAliases: {
3096
- [k: string]: string;
3097
- } | undefined;
3098
- } & {
3099
- readonly initialized: boolean;
3100
- readonly name: string;
3101
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3102
- readonly aliases: string[];
3103
- readonly displayName: string;
3104
- hasName(name: string): boolean;
3105
- readonly allAliases: string[];
3106
- readonly allRefNames: string[] | undefined;
3107
- readonly lowerCaseRefNames: string[] | undefined;
3108
- readonly allRefNamesWithLowerCase: string[] | undefined;
3109
- readonly rpcManager: RpcManager;
3110
- readonly refNameColors: string[];
3111
- } & {
3112
- readonly refNames: string[] | undefined;
3113
- } & {
3114
- getCanonicalRefName(refName: string): string | undefined;
3115
- getRefNameColor(refName: string): string | undefined;
3116
- isValidRefName(refName: string): boolean;
3117
- } & {
3118
- setLoaded({ regions, refNameAliases, cytobands, }: {
3119
- regions: import("@jbrowse/core/util").Region[];
3120
- refNameAliases: {
3121
- [x: string]: string;
3122
- };
3123
- cytobands: import("@jbrowse/core/util").Feature[];
3124
- }): void;
3125
- setError(e: unknown): void;
3126
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3127
- setRefNameAliases(aliases: {
3128
- [x: string]: string;
3129
- }): void;
3130
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3131
- setLoadingP(p?: Promise<void>): void;
3132
- load(): Promise<void>;
3133
- loadPre(): Promise<void>;
3134
- } & {
3135
- getAdapterMapEntry(adapterConf: {
3136
- [x: string]: unknown;
3137
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3138
- getRefNameMapForAdapter(adapterConf: {
3139
- [x: string]: unknown;
3140
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3141
- [x: string]: string;
3142
- }>;
3143
- getReverseRefNameMapForAdapter(adapterConf: {
3144
- [x: string]: unknown;
3145
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3146
- [x: string]: string;
3147
- }>;
3148
- afterCreate(): void;
3149
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
3150
- }, {
3151
- readonly assemblyNameMap: Record<string, {
3152
- configuration: any;
3153
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3154
- error: unknown;
3155
- loadingP: Promise<void> | undefined;
3156
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3157
- refNameAliases: {
3158
- [x: string]: string;
3159
- } | undefined;
3160
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3161
- } & {
3162
- getConf(arg: string): any;
3163
- readonly lowerCaseRefNameAliases: {
3164
- [k: string]: string;
3165
- } | undefined;
3166
- } & {
3167
- readonly initialized: boolean;
3168
- readonly name: string;
3169
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3170
- readonly aliases: string[];
3171
- readonly displayName: string;
3172
- hasName(name: string): boolean;
3173
- readonly allAliases: string[];
3174
- readonly allRefNames: string[] | undefined;
3175
- readonly lowerCaseRefNames: string[] | undefined;
3176
- readonly allRefNamesWithLowerCase: string[] | undefined;
3177
- readonly rpcManager: RpcManager;
3178
- readonly refNameColors: string[];
3179
- } & {
3180
- readonly refNames: string[] | undefined;
3181
- } & {
3182
- getCanonicalRefName(refName: string): string | undefined;
3183
- getRefNameColor(refName: string): string | undefined;
3184
- isValidRefName(refName: string): boolean;
3185
- } & {
3186
- setLoaded({ regions, refNameAliases, cytobands, }: {
3187
- regions: import("@jbrowse/core/util").Region[];
3188
- refNameAliases: {
3189
- [x: string]: string;
3190
- };
3191
- cytobands: import("@jbrowse/core/util").Feature[];
3192
- }): void;
3193
- setError(e: unknown): void;
3194
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3195
- setRefNameAliases(aliases: {
3196
- [x: string]: string;
3197
- }): void;
3198
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3199
- setLoadingP(p?: Promise<void>): void;
3200
- load(): Promise<void>;
3201
- loadPre(): Promise<void>;
3202
- } & {
3203
- getAdapterMapEntry(adapterConf: {
3204
- [x: string]: unknown;
3205
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3206
- getRefNameMapForAdapter(adapterConf: {
3207
- [x: string]: unknown;
3208
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3209
- [x: string]: string;
3210
- }>;
3211
- getReverseRefNameMapForAdapter(adapterConf: {
3212
- [x: string]: unknown;
3213
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3214
- [x: string]: string;
3215
- }>;
3216
- afterCreate(): void;
3217
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
3218
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3219
- }, {
3220
- error: unknown;
3221
- loadingP: Promise<void> | undefined;
3222
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3223
- refNameAliases: {
3224
- [x: string]: string;
3225
- } | undefined;
3226
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3227
- } & {
3228
- getConf(arg: string): any;
3229
- readonly lowerCaseRefNameAliases: {
3230
- [k: string]: string;
3231
- } | undefined;
3232
- } & {
3233
- readonly initialized: boolean;
3234
- readonly name: string;
3235
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3236
- readonly aliases: string[];
3237
- readonly displayName: string;
3238
- hasName(name: string): boolean;
3239
- readonly allAliases: string[];
3240
- readonly allRefNames: string[] | undefined;
3241
- readonly lowerCaseRefNames: string[] | undefined;
3242
- readonly allRefNamesWithLowerCase: string[] | undefined;
3243
- readonly rpcManager: RpcManager;
3244
- readonly refNameColors: string[];
3245
- } & {
3246
- readonly refNames: string[] | undefined;
3247
- } & {
3248
- getCanonicalRefName(refName: string): string | undefined;
3249
- getRefNameColor(refName: string): string | undefined;
3250
- isValidRefName(refName: string): boolean;
3251
- } & {
3252
- setLoaded({ regions, refNameAliases, cytobands, }: {
3253
- regions: import("@jbrowse/core/util").Region[];
3254
- refNameAliases: {
3255
- [x: string]: string;
3256
- };
3257
- cytobands: import("@jbrowse/core/util").Feature[];
3258
- }): void;
3259
- setError(e: unknown): void;
3260
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3261
- setRefNameAliases(aliases: {
3262
- [x: string]: string;
3263
- }): void;
3264
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3265
- setLoadingP(p?: Promise<void>): void;
3266
- load(): Promise<void>;
3267
- loadPre(): Promise<void>;
3268
- } & {
3269
- getAdapterMapEntry(adapterConf: {
3270
- [x: string]: unknown;
3271
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3272
- getRefNameMapForAdapter(adapterConf: {
3273
- [x: string]: unknown;
3274
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3275
- [x: string]: string;
3276
- }>;
3277
- getReverseRefNameMapForAdapter(adapterConf: {
3278
- [x: string]: unknown;
3279
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3280
- [x: string]: string;
3281
- }>;
3282
- afterCreate(): void;
3283
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
3284
- } & {
3285
- getCanonicalAssemblyName(asmName: string): string | undefined;
3286
- get(asmName: string): ({
3287
- configuration: any;
3288
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3289
- error: unknown;
3290
- loadingP: Promise<void> | undefined;
3291
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3292
- refNameAliases: {
3293
- [x: string]: string;
3294
- } | undefined;
3295
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3296
- } & {
3297
- getConf(arg: string): any;
3298
- readonly lowerCaseRefNameAliases: {
3299
- [k: string]: string;
3300
- } | undefined;
3301
- } & {
3302
- readonly initialized: boolean;
3303
- readonly name: string;
3304
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3305
- readonly aliases: string[];
3306
- readonly displayName: string;
3307
- hasName(name: string): boolean;
3308
- readonly allAliases: string[];
3309
- readonly allRefNames: string[] | undefined;
3310
- readonly lowerCaseRefNames: string[] | undefined;
3311
- readonly allRefNamesWithLowerCase: string[] | undefined;
3312
- readonly rpcManager: RpcManager;
3313
- readonly refNameColors: string[];
3314
- } & {
3315
- readonly refNames: string[] | undefined;
3316
- } & {
3317
- getCanonicalRefName(refName: string): string | undefined;
3318
- getRefNameColor(refName: string): string | undefined;
3319
- isValidRefName(refName: string): boolean;
3320
- } & {
3321
- setLoaded({ regions, refNameAliases, cytobands, }: {
3322
- regions: import("@jbrowse/core/util").Region[];
3323
- refNameAliases: {
3324
- [x: string]: string;
3325
- };
3326
- cytobands: import("@jbrowse/core/util").Feature[];
3327
- }): void;
3328
- setError(e: unknown): void;
3329
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3330
- setRefNameAliases(aliases: {
3331
- [x: string]: string;
3332
- }): void;
3333
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3334
- setLoadingP(p?: Promise<void>): void;
3335
- load(): Promise<void>;
3336
- loadPre(): Promise<void>;
3337
- } & {
3338
- getAdapterMapEntry(adapterConf: {
3339
- [x: string]: unknown;
3340
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3341
- getRefNameMapForAdapter(adapterConf: {
3342
- [x: string]: unknown;
3343
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3344
- [x: string]: string;
3345
- }>;
3346
- getReverseRefNameMapForAdapter(adapterConf: {
3347
- [x: string]: unknown;
3348
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3349
- [x: string]: string;
3350
- }>;
3351
- afterCreate(): void;
3352
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
3353
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3354
- }, {
3355
- error: unknown;
3356
- loadingP: Promise<void> | undefined;
3357
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3358
- refNameAliases: {
3359
- [x: string]: string;
3360
- } | undefined;
3361
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3362
- } & {
3363
- getConf(arg: string): any;
3364
- readonly lowerCaseRefNameAliases: {
3365
- [k: string]: string;
3366
- } | undefined;
3367
- } & {
3368
- readonly initialized: boolean;
3369
- readonly name: string;
3370
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3371
- readonly aliases: string[];
3372
- readonly displayName: string;
3373
- hasName(name: string): boolean;
3374
- readonly allAliases: string[];
3375
- readonly allRefNames: string[] | undefined;
3376
- readonly lowerCaseRefNames: string[] | undefined;
3377
- readonly allRefNamesWithLowerCase: string[] | undefined;
3378
- readonly rpcManager: RpcManager;
3379
- readonly refNameColors: string[];
3380
- } & {
3381
- readonly refNames: string[] | undefined;
3382
- } & {
3383
- getCanonicalRefName(refName: string): string | undefined;
3384
- getRefNameColor(refName: string): string | undefined;
3385
- isValidRefName(refName: string): boolean;
3386
- } & {
3387
- setLoaded({ regions, refNameAliases, cytobands, }: {
3388
- regions: import("@jbrowse/core/util").Region[];
3389
- refNameAliases: {
3390
- [x: string]: string;
3391
- };
3392
- cytobands: import("@jbrowse/core/util").Feature[];
3393
- }): void;
3394
- setError(e: unknown): void;
3395
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3396
- setRefNameAliases(aliases: {
3397
- [x: string]: string;
3398
- }): void;
3399
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3400
- setLoadingP(p?: Promise<void>): void;
3401
- load(): Promise<void>;
3402
- loadPre(): Promise<void>;
3403
- } & {
3404
- getAdapterMapEntry(adapterConf: {
3405
- [x: string]: unknown;
3406
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3407
- getRefNameMapForAdapter(adapterConf: {
3408
- [x: string]: unknown;
3409
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3410
- [x: string]: string;
3411
- }>;
3412
- getReverseRefNameMapForAdapter(adapterConf: {
3413
- [x: string]: unknown;
3414
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3415
- [x: string]: string;
3416
- }>;
3417
- afterCreate(): void;
3418
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
3419
- readonly assemblyNamesList: any[];
3420
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
3421
- readonly rpcManager: RpcManager;
3422
- } & {
3423
- waitForAssembly(assemblyName: string): Promise<({
3424
- configuration: any;
3425
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3426
- error: unknown;
3427
- loadingP: Promise<void> | undefined;
3428
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3429
- refNameAliases: {
3430
- [x: string]: string;
3431
- } | undefined;
3432
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3433
- } & {
3434
- getConf(arg: string): any;
3435
- readonly lowerCaseRefNameAliases: {
3436
- [k: string]: string;
3437
- } | undefined;
3438
- } & {
3439
- readonly initialized: boolean;
3440
- readonly name: string;
3441
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3442
- readonly aliases: string[];
3443
- readonly displayName: string;
3444
- hasName(name: string): boolean;
3445
- readonly allAliases: string[];
3446
- readonly allRefNames: string[] | undefined;
3447
- readonly lowerCaseRefNames: string[] | undefined;
3448
- readonly allRefNamesWithLowerCase: string[] | undefined;
3449
- readonly rpcManager: RpcManager;
3450
- readonly refNameColors: string[];
3451
- } & {
3452
- readonly refNames: string[] | undefined;
3453
- } & {
3454
- getCanonicalRefName(refName: string): string | undefined;
3455
- getRefNameColor(refName: string): string | undefined;
3456
- isValidRefName(refName: string): boolean;
3457
- } & {
3458
- setLoaded({ regions, refNameAliases, cytobands, }: {
3459
- regions: import("@jbrowse/core/util").Region[];
3460
- refNameAliases: {
3461
- [x: string]: string;
3462
- };
3463
- cytobands: import("@jbrowse/core/util").Feature[];
3464
- }): void;
3465
- setError(e: unknown): void;
3466
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3467
- setRefNameAliases(aliases: {
3468
- [x: string]: string;
3469
- }): void;
3470
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3471
- setLoadingP(p?: Promise<void>): void;
3472
- load(): Promise<void>;
3473
- loadPre(): Promise<void>;
3474
- } & {
3475
- getAdapterMapEntry(adapterConf: {
3476
- [x: string]: unknown;
3477
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3478
- getRefNameMapForAdapter(adapterConf: {
3479
- [x: string]: unknown;
3480
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3481
- [x: string]: string;
3482
- }>;
3483
- getReverseRefNameMapForAdapter(adapterConf: {
3484
- [x: string]: unknown;
3485
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3486
- [x: string]: string;
3487
- }>;
3488
- afterCreate(): void;
3489
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
3490
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3491
- }, {
3492
- error: unknown;
3493
- loadingP: Promise<void> | undefined;
3494
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3495
- refNameAliases: {
3496
- [x: string]: string;
3497
- } | undefined;
3498
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3499
- } & {
3500
- getConf(arg: string): any;
3501
- readonly lowerCaseRefNameAliases: {
3502
- [k: string]: string;
3503
- } | undefined;
3504
- } & {
3505
- readonly initialized: boolean;
3506
- readonly name: string;
3507
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3508
- readonly aliases: string[];
3509
- readonly displayName: string;
3510
- hasName(name: string): boolean;
3511
- readonly allAliases: string[];
3512
- readonly allRefNames: string[] | undefined;
3513
- readonly lowerCaseRefNames: string[] | undefined;
3514
- readonly allRefNamesWithLowerCase: string[] | undefined;
3515
- readonly rpcManager: RpcManager;
3516
- readonly refNameColors: string[];
3517
- } & {
3518
- readonly refNames: string[] | undefined;
3519
- } & {
3520
- getCanonicalRefName(refName: string): string | undefined;
3521
- getRefNameColor(refName: string): string | undefined;
3522
- isValidRefName(refName: string): boolean;
3523
- } & {
3524
- setLoaded({ regions, refNameAliases, cytobands, }: {
3525
- regions: import("@jbrowse/core/util").Region[];
3526
- refNameAliases: {
3527
- [x: string]: string;
3528
- };
3529
- cytobands: import("@jbrowse/core/util").Feature[];
3530
- }): void;
3531
- setError(e: unknown): void;
3532
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3533
- setRefNameAliases(aliases: {
3534
- [x: string]: string;
3535
- }): void;
3536
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3537
- setLoadingP(p?: Promise<void>): void;
3538
- load(): Promise<void>;
3539
- loadPre(): Promise<void>;
3540
- } & {
3541
- getAdapterMapEntry(adapterConf: {
3542
- [x: string]: unknown;
3543
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3544
- getRefNameMapForAdapter(adapterConf: {
3545
- [x: string]: unknown;
3546
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3547
- [x: string]: string;
3548
- }>;
3549
- getReverseRefNameMapForAdapter(adapterConf: {
3550
- [x: string]: unknown;
3551
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3552
- [x: string]: string;
3553
- }>;
3554
- afterCreate(): void;
3555
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
3556
- getRefNameMapForAdapter(adapterConf: {
3557
- [x: string]: unknown;
3558
- }, assemblyName: string | undefined, opts: {
3559
- stopToken?: string;
3560
- sessionId: string;
3561
- }): Promise<{
3562
- [x: string]: string;
3563
- } | undefined>;
3564
- getReverseRefNameMapForAdapter(adapterConf: {
3565
- [x: string]: unknown;
3566
- }, assemblyName: string | undefined, opts: {
3567
- stopToken?: string;
3568
- sessionId: string;
3569
- }): Promise<{
3570
- [x: string]: string;
3571
- } | undefined>;
3572
- isValidRefName(refName: string, assemblyName: string): boolean;
3573
- } & {
3574
- afterAttach(): void;
3575
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
3576
- addAssembly(configuration: any): void;
3577
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
3578
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3579
- rpcManager: RpcManager;
3580
- adminMode: boolean;
3581
- error: unknown;
3582
- textSearchManager: TextSearchManager;
3583
- pluginManager: PluginManager;
3584
- } & {
3585
- setError(error: unknown): void;
3586
- setSession(sessionSnapshot?: SnapshotIn<import("mobx-state-tree").IAnyType>): void;
3587
- setDefaultSession(): void;
3588
- setSessionPath(path: string): void;
3589
- renameCurrentSession(newName: string): void;
3590
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
3591
- jbrowse: import("mobx-state-tree").IAnyType;
3592
- session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
3593
- sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
3594
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
3595
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
3596
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3597
- }, {
3598
- error: unknown;
3599
- loadingP: Promise<void> | undefined;
3600
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3601
- refNameAliases: {
3602
- [x: string]: string;
3603
- } | undefined;
3604
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3605
- } & {
3606
- getConf(arg: string): any;
3607
- readonly lowerCaseRefNameAliases: {
3608
- [k: string]: string;
3609
- } | undefined;
3610
- } & {
3611
- readonly initialized: boolean;
3612
- readonly name: string;
3613
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3614
- readonly aliases: string[];
3615
- readonly displayName: string;
3616
- hasName(name: string): boolean;
3617
- readonly allAliases: string[];
3618
- readonly allRefNames: string[] | undefined;
3619
- readonly lowerCaseRefNames: string[] | undefined;
3620
- readonly allRefNamesWithLowerCase: string[] | undefined;
3621
- readonly rpcManager: RpcManager;
3622
- readonly refNameColors: string[];
3623
- } & {
3624
- readonly refNames: string[] | undefined;
3625
- } & {
3626
- getCanonicalRefName(refName: string): string | undefined;
3627
- getRefNameColor(refName: string): string | undefined;
3628
- isValidRefName(refName: string): boolean;
3629
- } & {
3630
- setLoaded({ regions, refNameAliases, cytobands, }: {
3631
- regions: import("@jbrowse/core/util").Region[];
3632
- refNameAliases: {
3633
- [x: string]: string;
3634
- };
3635
- cytobands: import("@jbrowse/core/util").Feature[];
3636
- }): void;
3637
- setError(e: unknown): void;
3638
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3639
- setRefNameAliases(aliases: {
3640
- [x: string]: string;
3641
- }): void;
3642
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3643
- setLoadingP(p?: Promise<void>): void;
3644
- load(): Promise<void>;
3645
- loadPre(): Promise<void>;
3646
- } & {
3647
- getAdapterMapEntry(adapterConf: {
3648
- [x: string]: unknown;
3649
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3650
- getRefNameMapForAdapter(adapterConf: {
3651
- [x: string]: unknown;
3652
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3653
- [x: string]: string;
3654
- }>;
3655
- getReverseRefNameMapForAdapter(adapterConf: {
3656
- [x: string]: unknown;
3657
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3658
- [x: string]: string;
3659
- }>;
3660
- afterCreate(): void;
3661
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
3662
- }, {
3663
- readonly assemblyNameMap: Record<string, {
3664
- configuration: any;
3665
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3666
- error: unknown;
3667
- loadingP: Promise<void> | undefined;
3668
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3669
- refNameAliases: {
3670
- [x: string]: string;
3671
- } | undefined;
3672
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3673
- } & {
3674
- getConf(arg: string): any;
3675
- readonly lowerCaseRefNameAliases: {
3676
- [k: string]: string;
3677
- } | undefined;
3678
- } & {
3679
- readonly initialized: boolean;
3680
- readonly name: string;
3681
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3682
- readonly aliases: string[];
3683
- readonly displayName: string;
3684
- hasName(name: string): boolean;
3685
- readonly allAliases: string[];
3686
- readonly allRefNames: string[] | undefined;
3687
- readonly lowerCaseRefNames: string[] | undefined;
3688
- readonly allRefNamesWithLowerCase: string[] | undefined;
3689
- readonly rpcManager: RpcManager;
3690
- readonly refNameColors: string[];
3691
- } & {
3692
- readonly refNames: string[] | undefined;
3693
- } & {
3694
- getCanonicalRefName(refName: string): string | undefined;
3695
- getRefNameColor(refName: string): string | undefined;
3696
- isValidRefName(refName: string): boolean;
3697
- } & {
3698
- setLoaded({ regions, refNameAliases, cytobands, }: {
3699
- regions: import("@jbrowse/core/util").Region[];
3700
- refNameAliases: {
3701
- [x: string]: string;
3702
- };
3703
- cytobands: import("@jbrowse/core/util").Feature[];
3704
- }): void;
3705
- setError(e: unknown): void;
3706
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3707
- setRefNameAliases(aliases: {
3708
- [x: string]: string;
3709
- }): void;
3710
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3711
- setLoadingP(p?: Promise<void>): void;
3712
- load(): Promise<void>;
3713
- loadPre(): Promise<void>;
3714
- } & {
3715
- getAdapterMapEntry(adapterConf: {
3716
- [x: string]: unknown;
3717
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3718
- getRefNameMapForAdapter(adapterConf: {
3719
- [x: string]: unknown;
3720
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3721
- [x: string]: string;
3722
- }>;
3723
- getReverseRefNameMapForAdapter(adapterConf: {
3724
- [x: string]: unknown;
3725
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3726
- [x: string]: string;
3727
- }>;
3728
- afterCreate(): void;
3729
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
3730
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3731
- }, {
3732
- error: unknown;
3733
- loadingP: Promise<void> | undefined;
3734
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3735
- refNameAliases: {
3736
- [x: string]: string;
3737
- } | undefined;
3738
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3739
- } & {
3740
- getConf(arg: string): any;
3741
- readonly lowerCaseRefNameAliases: {
3742
- [k: string]: string;
3743
- } | undefined;
3744
- } & {
3745
- readonly initialized: boolean;
3746
- readonly name: string;
3747
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3748
- readonly aliases: string[];
3749
- readonly displayName: string;
3750
- hasName(name: string): boolean;
3751
- readonly allAliases: string[];
3752
- readonly allRefNames: string[] | undefined;
3753
- readonly lowerCaseRefNames: string[] | undefined;
3754
- readonly allRefNamesWithLowerCase: string[] | undefined;
3755
- readonly rpcManager: RpcManager;
3756
- readonly refNameColors: string[];
3757
- } & {
3758
- readonly refNames: string[] | undefined;
3759
- } & {
3760
- getCanonicalRefName(refName: string): string | undefined;
3761
- getRefNameColor(refName: string): string | undefined;
3762
- isValidRefName(refName: string): boolean;
3763
- } & {
3764
- setLoaded({ regions, refNameAliases, cytobands, }: {
3765
- regions: import("@jbrowse/core/util").Region[];
3766
- refNameAliases: {
3767
- [x: string]: string;
3768
- };
3769
- cytobands: import("@jbrowse/core/util").Feature[];
3770
- }): void;
3771
- setError(e: unknown): void;
3772
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3773
- setRefNameAliases(aliases: {
3774
- [x: string]: string;
3775
- }): void;
3776
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3777
- setLoadingP(p?: Promise<void>): void;
3778
- load(): Promise<void>;
3779
- loadPre(): Promise<void>;
3780
- } & {
3781
- getAdapterMapEntry(adapterConf: {
3782
- [x: string]: unknown;
3783
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3784
- getRefNameMapForAdapter(adapterConf: {
3785
- [x: string]: unknown;
3786
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3787
- [x: string]: string;
3788
- }>;
3789
- getReverseRefNameMapForAdapter(adapterConf: {
3790
- [x: string]: unknown;
3791
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3792
- [x: string]: string;
3793
- }>;
3794
- afterCreate(): void;
3795
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
3796
- } & {
3797
- getCanonicalAssemblyName(asmName: string): string | undefined;
3798
- get(asmName: string): ({
3799
- configuration: any;
3800
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3801
- error: unknown;
3802
- loadingP: Promise<void> | undefined;
3803
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3804
- refNameAliases: {
3805
- [x: string]: string;
3806
- } | undefined;
3807
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3808
- } & {
3809
- getConf(arg: string): any;
3810
- readonly lowerCaseRefNameAliases: {
3811
- [k: string]: string;
3812
- } | undefined;
3813
- } & {
3814
- readonly initialized: boolean;
3815
- readonly name: string;
3816
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3817
- readonly aliases: string[];
3818
- readonly displayName: string;
3819
- hasName(name: string): boolean;
3820
- readonly allAliases: string[];
3821
- readonly allRefNames: string[] | undefined;
3822
- readonly lowerCaseRefNames: string[] | undefined;
3823
- readonly allRefNamesWithLowerCase: string[] | undefined;
3824
- readonly rpcManager: RpcManager;
3825
- readonly refNameColors: string[];
3826
- } & {
3827
- readonly refNames: string[] | undefined;
3828
- } & {
3829
- getCanonicalRefName(refName: string): string | undefined;
3830
- getRefNameColor(refName: string): string | undefined;
3831
- isValidRefName(refName: string): boolean;
3832
- } & {
3833
- setLoaded({ regions, refNameAliases, cytobands, }: {
3834
- regions: import("@jbrowse/core/util").Region[];
3835
- refNameAliases: {
3836
- [x: string]: string;
3837
- };
3838
- cytobands: import("@jbrowse/core/util").Feature[];
3839
- }): void;
3840
- setError(e: unknown): void;
3841
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3842
- setRefNameAliases(aliases: {
3843
- [x: string]: string;
3844
- }): void;
3845
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3846
- setLoadingP(p?: Promise<void>): void;
3847
- load(): Promise<void>;
3848
- loadPre(): Promise<void>;
3849
- } & {
3850
- getAdapterMapEntry(adapterConf: {
3851
- [x: string]: unknown;
3852
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3853
- getRefNameMapForAdapter(adapterConf: {
3854
- [x: string]: unknown;
3855
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3856
- [x: string]: string;
3857
- }>;
3858
- getReverseRefNameMapForAdapter(adapterConf: {
3859
- [x: string]: unknown;
3860
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3861
- [x: string]: string;
3862
- }>;
3863
- afterCreate(): void;
3864
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
3865
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3866
- }, {
3867
- error: unknown;
3868
- loadingP: Promise<void> | undefined;
3869
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3870
- refNameAliases: {
3871
- [x: string]: string;
3872
- } | undefined;
3873
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3874
- } & {
3875
- getConf(arg: string): any;
3876
- readonly lowerCaseRefNameAliases: {
3877
- [k: string]: string;
3878
- } | undefined;
3879
- } & {
3880
- readonly initialized: boolean;
3881
- readonly name: string;
3882
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3883
- readonly aliases: string[];
3884
- readonly displayName: string;
3885
- hasName(name: string): boolean;
3886
- readonly allAliases: string[];
3887
- readonly allRefNames: string[] | undefined;
3888
- readonly lowerCaseRefNames: string[] | undefined;
3889
- readonly allRefNamesWithLowerCase: string[] | undefined;
3890
- readonly rpcManager: RpcManager;
3891
- readonly refNameColors: string[];
3892
- } & {
3893
- readonly refNames: string[] | undefined;
3894
- } & {
3895
- getCanonicalRefName(refName: string): string | undefined;
3896
- getRefNameColor(refName: string): string | undefined;
3897
- isValidRefName(refName: string): boolean;
3898
- } & {
3899
- setLoaded({ regions, refNameAliases, cytobands, }: {
3900
- regions: import("@jbrowse/core/util").Region[];
3901
- refNameAliases: {
3902
- [x: string]: string;
3903
- };
3904
- cytobands: import("@jbrowse/core/util").Feature[];
3905
- }): void;
3906
- setError(e: unknown): void;
3907
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3908
- setRefNameAliases(aliases: {
3909
- [x: string]: string;
3910
- }): void;
3911
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3912
- setLoadingP(p?: Promise<void>): void;
3913
- load(): Promise<void>;
3914
- loadPre(): Promise<void>;
3915
- } & {
3916
- getAdapterMapEntry(adapterConf: {
3917
- [x: string]: unknown;
3918
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3919
- getRefNameMapForAdapter(adapterConf: {
3920
- [x: string]: unknown;
3921
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3922
- [x: string]: string;
3923
- }>;
3924
- getReverseRefNameMapForAdapter(adapterConf: {
3925
- [x: string]: unknown;
3926
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3927
- [x: string]: string;
3928
- }>;
3929
- afterCreate(): void;
3930
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
3931
- readonly assemblyNamesList: any[];
3932
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
3933
- readonly rpcManager: RpcManager;
3934
- } & {
3935
- waitForAssembly(assemblyName: string): Promise<({
3936
- configuration: any;
3937
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3938
- error: unknown;
3939
- loadingP: Promise<void> | undefined;
3940
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3941
- refNameAliases: {
3942
- [x: string]: string;
3943
- } | undefined;
3944
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3945
- } & {
3946
- getConf(arg: string): any;
3947
- readonly lowerCaseRefNameAliases: {
3948
- [k: string]: string;
3949
- } | undefined;
3950
- } & {
3951
- readonly initialized: boolean;
3952
- readonly name: string;
3953
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3954
- readonly aliases: string[];
3955
- readonly displayName: string;
3956
- hasName(name: string): boolean;
3957
- readonly allAliases: string[];
3958
- readonly allRefNames: string[] | undefined;
3959
- readonly lowerCaseRefNames: string[] | undefined;
3960
- readonly allRefNamesWithLowerCase: string[] | undefined;
3961
- readonly rpcManager: RpcManager;
3962
- readonly refNameColors: string[];
3963
- } & {
3964
- readonly refNames: string[] | undefined;
3965
- } & {
3966
- getCanonicalRefName(refName: string): string | undefined;
3967
- getRefNameColor(refName: string): string | undefined;
3968
- isValidRefName(refName: string): boolean;
3969
- } & {
3970
- setLoaded({ regions, refNameAliases, cytobands, }: {
3971
- regions: import("@jbrowse/core/util").Region[];
3972
- refNameAliases: {
3973
- [x: string]: string;
3974
- };
3975
- cytobands: import("@jbrowse/core/util").Feature[];
3976
- }): void;
3977
- setError(e: unknown): void;
3978
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3979
- setRefNameAliases(aliases: {
3980
- [x: string]: string;
3981
- }): void;
3982
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3983
- setLoadingP(p?: Promise<void>): void;
3984
- load(): Promise<void>;
3985
- loadPre(): Promise<void>;
3986
- } & {
3987
- getAdapterMapEntry(adapterConf: {
3988
- [x: string]: unknown;
3989
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3990
- getRefNameMapForAdapter(adapterConf: {
3991
- [x: string]: unknown;
3992
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3993
- [x: string]: string;
3994
- }>;
3995
- getReverseRefNameMapForAdapter(adapterConf: {
3996
- [x: string]: unknown;
3997
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3998
- [x: string]: string;
3999
- }>;
4000
- afterCreate(): void;
4001
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
4002
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
4003
- }, {
4004
- error: unknown;
4005
- loadingP: Promise<void> | undefined;
4006
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
4007
- refNameAliases: {
4008
- [x: string]: string;
4009
- } | undefined;
4010
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
4011
- } & {
4012
- getConf(arg: string): any;
4013
- readonly lowerCaseRefNameAliases: {
4014
- [k: string]: string;
4015
- } | undefined;
4016
- } & {
4017
- readonly initialized: boolean;
4018
- readonly name: string;
4019
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
4020
- readonly aliases: string[];
4021
- readonly displayName: string;
4022
- hasName(name: string): boolean;
4023
- readonly allAliases: string[];
4024
- readonly allRefNames: string[] | undefined;
4025
- readonly lowerCaseRefNames: string[] | undefined;
4026
- readonly allRefNamesWithLowerCase: string[] | undefined;
4027
- readonly rpcManager: RpcManager;
4028
- readonly refNameColors: string[];
4029
- } & {
4030
- readonly refNames: string[] | undefined;
4031
- } & {
4032
- getCanonicalRefName(refName: string): string | undefined;
4033
- getRefNameColor(refName: string): string | undefined;
4034
- isValidRefName(refName: string): boolean;
4035
- } & {
4036
- setLoaded({ regions, refNameAliases, cytobands, }: {
4037
- regions: import("@jbrowse/core/util").Region[];
4038
- refNameAliases: {
4039
- [x: string]: string;
4040
- };
4041
- cytobands: import("@jbrowse/core/util").Feature[];
4042
- }): void;
4043
- setError(e: unknown): void;
4044
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
4045
- setRefNameAliases(aliases: {
4046
- [x: string]: string;
4047
- }): void;
4048
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
4049
- setLoadingP(p?: Promise<void>): void;
4050
- load(): Promise<void>;
4051
- loadPre(): Promise<void>;
4052
- } & {
4053
- getAdapterMapEntry(adapterConf: {
4054
- [x: string]: unknown;
4055
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
4056
- getRefNameMapForAdapter(adapterConf: {
4057
- [x: string]: unknown;
4058
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
4059
- [x: string]: string;
4060
- }>;
4061
- getReverseRefNameMapForAdapter(adapterConf: {
4062
- [x: string]: unknown;
4063
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
4064
- [x: string]: string;
4065
- }>;
4066
- afterCreate(): void;
4067
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
4068
- getRefNameMapForAdapter(adapterConf: {
4069
- [x: string]: unknown;
4070
- }, assemblyName: string | undefined, opts: {
4071
- stopToken?: string;
4072
- sessionId: string;
4073
- }): Promise<{
4074
- [x: string]: string;
4075
- } | undefined>;
4076
- getReverseRefNameMapForAdapter(adapterConf: {
4077
- [x: string]: unknown;
4078
- }, assemblyName: string | undefined, opts: {
4079
- stopToken?: string;
4080
- sessionId: string;
4081
- }): Promise<{
4082
- [x: string]: string;
4083
- } | undefined>;
4084
- isValidRefName(refName: string, assemblyName: string): boolean;
4085
- } & {
4086
- afterAttach(): void;
4087
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
4088
- addAssembly(configuration: any): void;
4089
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
4090
- }, {
4091
- rpcManager: RpcManager;
4092
- adminMode: boolean;
4093
- error: unknown;
4094
- textSearchManager: TextSearchManager;
4095
- pluginManager: PluginManager;
4096
- } & {
4097
- setError(error: unknown): void;
4098
- setSession(sessionSnapshot?: SnapshotIn<import("mobx-state-tree").IAnyType>): void;
4099
- setDefaultSession(): void;
4100
- setSessionPath(path: string): void;
4101
- renameCurrentSession(newName: string): void;
4102
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
4103
- } & {
4104
- readonly jbrowse: any;
4105
- readonly rpcManager: RpcManager;
4106
- readonly configuration: {
4107
- [x: string]: any;
4108
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4109
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4110
- [x: string]: any;
4111
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4112
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4113
- [x: string]: any;
4114
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4115
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4116
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
4117
- readonly adminMode: boolean;
4118
- readonly textSearchManager: TextSearchManager;
4119
- } & {
4120
- readonly assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
4121
- } & {
4122
- setSelection(thing: unknown): void;
4123
- clearSelection(): void;
4124
- setHovered(thing: unknown): void;
4125
- } & {
4126
- readonly visibleWidget: any;
4127
- } & {
4128
- setDrawerPosition(arg: string): void;
4129
- updateDrawerWidth(drawerWidth: number): number;
4130
- resizeDrawer(distance: number): number;
4131
- addWidget(typeName: string, id: string, initialState?: {}, conf?: unknown): any;
4132
- showWidget(widget: any): void;
4133
- hasWidget(widget: any): boolean;
4134
- hideWidget(widget: any): void;
4135
- minimizeWidgetDrawer(): void;
4136
- showWidgetDrawer(): void;
4137
- hideAllWidgets(): void;
4138
- editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
4139
- afterAttach(): void;
4140
- } & {
4141
- readonly connections: import("@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig").BaseConnectionConfigModel[];
4142
- } & {
4143
- makeConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: {}): ({
4144
- name: string;
4145
- tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
4146
- configuration: {
4147
- [x: string]: any;
4148
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4149
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4150
- [x: string]: any;
4151
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4152
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4153
- [x: string]: any;
4154
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4155
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4156
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4157
- name: {
4158
- type: string;
4159
- defaultValue: string;
4160
- description: string;
4161
- };
4162
- assemblyNames: {
4163
- type: string;
4164
- defaultValue: never[];
4165
- description: string;
4166
- };
4167
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>;
4168
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4169
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
4170
- } & {
4171
- afterAttach(): void;
4172
- addTrackConf(trackConf: Record<string, unknown> | ({
4173
- [x: string]: any;
4174
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4175
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4176
- [x: string]: any;
4177
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4178
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4179
- [x: string]: any;
4180
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4181
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4182
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
4183
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
4184
- [x: string]: any;
4185
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4186
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4187
- [x: string]: any;
4188
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4189
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4190
- [x: string]: any;
4191
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4192
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4193
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
4194
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
4195
- clear(): void;
4196
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
4197
- name: import("mobx-state-tree").ISimpleType<string>;
4198
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
4199
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4200
- name: {
4201
- type: string;
4202
- defaultValue: string;
4203
- description: string;
4204
- };
4205
- assemblyNames: {
4206
- type: string;
4207
- defaultValue: never[];
4208
- description: string;
4209
- };
4210
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
4211
- }, {
4212
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
4213
- } & {
4214
- afterAttach(): void;
4215
- addTrackConf(trackConf: Record<string, unknown> | ({
4216
- [x: string]: any;
4217
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4218
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4219
- [x: string]: any;
4220
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4221
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4222
- [x: string]: any;
4223
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4224
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4225
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
4226
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
4227
- [x: string]: any;
4228
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4229
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4230
- [x: string]: any;
4231
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4232
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4233
- [x: string]: any;
4234
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4235
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4236
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
4237
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
4238
- clear(): void;
4239
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
4240
- prepareToBreakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): (Record<string, number> | (() => void))[] | undefined;
4241
- breakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
4242
- deleteConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
4243
- addConnectionConf(connectionConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
4244
- clearConnections(): void;
4245
- } & {
4246
- queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, unknown][];
4247
- } & {
4248
- readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType | undefined;
4249
- readonly DialogProps: unknown;
4250
- } & {
4251
- removeActiveDialog(): void;
4252
- queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, unknown]): void;
4253
- } & {
4254
- getReferring(object: import("mobx-state-tree").IAnyStateTreeNode): import("@jbrowse/product-core").ReferringNode[];
4255
- } & {
4256
- removeReferring(referring: import("@jbrowse/product-core").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
4257
- } & {
4258
- readonly tracks: import("@jbrowse/core/configuration").AnyConfigurationModel[];
4259
- } & {
4260
- addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfiguration): any;
4261
- deleteTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
4262
- } & {
4263
- snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
4264
- } & {
4265
- readonly snackbarMessageSet: Map<string, import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
4266
- } & {
4267
- notify(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction): void;
4268
- notifyError(errorMessage: string, error?: unknown, extra?: unknown): void;
4269
- pushSnackbarMessage(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction): void;
4270
- popSnackbarMessage(): import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage | undefined;
4271
- removeSnackbarMessage(message: string): void;
4272
- } & {
4273
- task: undefined;
4274
- } & {
4275
- readonly version: any;
4276
- readonly assemblies: any[];
4277
- readonly assemblyNames: any[];
4278
- readonly connections: any;
4279
- readonly assemblyManager: any;
4280
- readonly views: any[];
4281
- renderProps(): {
4282
- theme: any;
4283
- highResolutionScaling: any;
4284
- };
4285
- } & {
4286
- addView(typeName: string, initialState?: {}): any;
4287
- removeView(): void;
4288
- } & {
4289
- getTrackActionMenuItems(config: any): {
4290
- label: string;
4291
- onClick: () => void;
4292
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
4293
- muiName: string;
4294
- };
4295
- }[];
4296
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): void;
4297
- renameCurrentSession(sessionName: string): void;
4298
- setError(error: unknown): void;
4299
- addInternetAccount(internetAccount: SnapshotIn<any>): void;
4300
- findAppropriateInternetAccount(location: UriLocation): any;
4301
- } & {
4302
- readonly jbrowse: {
4303
- configuration: {
4304
- [x: string]: any;
4305
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4306
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4307
- [x: string]: any;
4308
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4309
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4310
- [x: string]: any;
4311
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4312
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4313
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4314
- rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4315
- defaultDriver: {
4316
- type: string;
4317
- description: string;
4318
- defaultValue: string;
4319
- };
4320
- drivers: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IMapType<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> | undefined, import("mobx-state-tree").ModelSnapshotType<Record<string, any>>, ({} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> & import("mobx-state-tree/dist/internal").NonEmptyObject) | undefined>>, [undefined]>;
4321
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4322
- highResolutionScaling: {
4323
- type: string;
4324
- defaultValue: number;
4325
- };
4326
- formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4327
- feature: {
4328
- type: string;
4329
- description: string;
4330
- defaultValue: {};
4331
- contextVariable: string[];
4332
- };
4333
- subfeatures: {
4334
- type: string;
4335
- description: string;
4336
- defaultValue: {};
4337
- contextVariable: string[];
4338
- };
4339
- depth: {
4340
- type: string;
4341
- defaultValue: number;
4342
- description: string;
4343
- };
4344
- maxDepth: {
4345
- type: string;
4346
- defaultValue: number;
4347
- description: string;
4348
- };
4349
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4350
- formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4351
- config: {
4352
- type: string;
4353
- description: string;
4354
- defaultValue: {};
4355
- contextVariable: string[];
4356
- };
4357
- hideUris: {
4358
- type: string;
4359
- defaultValue: boolean;
4360
- };
4361
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4362
- hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4363
- sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4364
- trackNames: {
4365
- type: string;
4366
- defaultValue: boolean;
4367
- };
4368
- categories: {
4369
- type: string;
4370
- defaultValue: boolean;
4371
- };
4372
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4373
- defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4374
- categoryNames: {
4375
- type: string;
4376
- defaultValue: never[];
4377
- };
4378
- topLevelCategories: {
4379
- type: string;
4380
- defaultValue: boolean;
4381
- };
4382
- subCategories: {
4383
- type: string;
4384
- defaultValue: boolean;
4385
- };
4386
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4387
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4388
- theme: {
4389
- type: string;
4390
- defaultValue: {};
4391
- };
4392
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>>;
4393
- assembly: {
4394
- [x: string]: any;
4395
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4396
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4397
- [x: string]: any;
4398
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4399
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4400
- [x: string]: any;
4401
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4402
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4403
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
4404
- tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
4405
- internetAccounts: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
4406
- connections: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
4407
- aggregateTextSearchAdapters: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
4408
- plugins: any;
4409
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4410
- readonly assemblies: ({
4411
- [x: string]: any;
4412
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4413
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4414
- [x: string]: any;
4415
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4416
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4417
- [x: string]: any;
4418
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4419
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4420
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
4421
- readonly assemblyName: string;
4422
- readonly rpcManager: any;
4423
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
4424
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4425
- rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4426
- defaultDriver: {
4427
- type: string;
4428
- description: string;
4429
- defaultValue: string;
4430
- };
4431
- drivers: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IMapType<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> | undefined, import("mobx-state-tree").ModelSnapshotType<Record<string, any>>, ({} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> & import("mobx-state-tree/dist/internal").NonEmptyObject) | undefined>>, [undefined]>;
4432
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4433
- highResolutionScaling: {
4434
- type: string;
4435
- defaultValue: number;
4436
- };
4437
- formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4438
- feature: {
4439
- type: string;
4440
- description: string;
4441
- defaultValue: {};
4442
- contextVariable: string[];
4443
- };
4444
- subfeatures: {
4445
- type: string;
4446
- description: string;
4447
- defaultValue: {};
4448
- contextVariable: string[];
4449
- };
4450
- depth: {
4451
- type: string;
4452
- defaultValue: number;
4453
- description: string;
4454
- };
4455
- maxDepth: {
4456
- type: string;
4457
- defaultValue: number;
4458
- description: string;
4459
- };
4460
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4461
- formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4462
- config: {
4463
- type: string;
4464
- description: string;
4465
- defaultValue: {};
4466
- contextVariable: string[];
4467
- };
4468
- hideUris: {
4469
- type: string;
4470
- defaultValue: boolean;
4471
- };
4472
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4473
- hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4474
- sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4475
- trackNames: {
4476
- type: string;
4477
- defaultValue: boolean;
4478
- };
4479
- categories: {
4480
- type: string;
4481
- defaultValue: boolean;
4482
- };
4483
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4484
- defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4485
- categoryNames: {
4486
- type: string;
4487
- defaultValue: never[];
4488
- };
4489
- topLevelCategories: {
4490
- type: string;
4491
- defaultValue: boolean;
4492
- };
4493
- subCategories: {
4494
- type: string;
4495
- defaultValue: boolean;
4496
- };
4497
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4498
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4499
- theme: {
4500
- type: string;
4501
- defaultValue: {};
4502
- };
4503
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4504
- assembly: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
4505
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
4506
- internetAccounts: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
4507
- connections: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
4508
- aggregateTextSearchAdapters: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
4509
- plugins: import("mobx-state-tree").IType<any, any, any>;
4510
- }, {
4511
- readonly assemblies: ({
4512
- [x: string]: any;
4513
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4514
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4515
- [x: string]: any;
4516
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4517
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4518
- [x: string]: any;
4519
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4520
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4521
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
4522
- readonly assemblyName: string;
4523
- readonly rpcManager: any;
4524
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
4525
- readonly pluginManager: PluginManager;
4526
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
4527
- pluginManager: PluginManager;
4528
- };
4529
- export type ViewStateModel = ReturnType<typeof createModel>['model'];
4530
- export type ViewModel = Instance<ViewStateModel>;