@jbrowse/react-circular-genome-view2 3.7.0 → 4.0.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (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 +517 -680
  9. package/esm/createModel/createModel.js +5 -5
  10. package/esm/createModel/createSessionModel.d.ts +247 -327
  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 +1305 -1757
  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 -4588
  36. package/dist/createModel/createModel.js +0 -117
  37. package/dist/createModel/createSessionModel.d.ts +0 -1870
  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 -11770
  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 -145
  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
@@ -1,4588 +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;
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- 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: {
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- type: string;
26
- description: string;
27
- defaultValue: {};
28
- contextVariable: string[];
29
- };
30
- subfeatures: {
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- 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;
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- };
65
- categories: {
66
- type: string;
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- 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;
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- 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
- getCanonicalRefName2(asmName: string): string;
210
- getRefNameColor(refName: string): string | undefined;
211
- isValidRefName(refName: string): boolean;
212
- } & {
213
- setLoaded({ regions, refNameAliases, cytobands, }: {
214
- regions: import("@jbrowse/core/util").Region[];
215
- refNameAliases: {
216
- [x: string]: string;
217
- };
218
- cytobands: import("@jbrowse/core/util").Feature[];
219
- }): void;
220
- setError(e: unknown): void;
221
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
222
- setRefNameAliases(aliases: {
223
- [x: string]: string;
224
- }): void;
225
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
226
- setLoadingP(p?: Promise<void>): void;
227
- load(): Promise<void>;
228
- loadPre(): Promise<void>;
229
- } & {
230
- getAdapterMapEntry(adapterConf: {
231
- [x: string]: unknown;
232
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
233
- getRefNameMapForAdapter(adapterConf: {
234
- [x: string]: unknown;
235
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
236
- [x: string]: string;
237
- }>;
238
- getReverseRefNameMapForAdapter(adapterConf: {
239
- [x: string]: unknown;
240
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
241
- [x: string]: string;
242
- }>;
243
- afterCreate(): void;
244
- }, 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<{
245
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
246
- }, {
247
- error: unknown;
248
- loadingP: Promise<void> | undefined;
249
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
250
- refNameAliases: {
251
- [x: string]: string;
252
- } | undefined;
253
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
254
- } & {
255
- getConf(arg: string): any;
256
- readonly lowerCaseRefNameAliases: {
257
- [k: string]: string;
258
- } | undefined;
259
- } & {
260
- readonly initialized: boolean;
261
- readonly name: string;
262
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
263
- readonly aliases: string[];
264
- readonly displayName: string;
265
- hasName(name: string): boolean;
266
- readonly allAliases: string[];
267
- readonly allRefNames: string[] | undefined;
268
- readonly lowerCaseRefNames: string[] | undefined;
269
- readonly allRefNamesWithLowerCase: string[] | undefined;
270
- readonly rpcManager: RpcManager;
271
- readonly refNameColors: string[];
272
- } & {
273
- readonly refNames: string[] | undefined;
274
- } & {
275
- getCanonicalRefName(refName: string): string | undefined;
276
- getCanonicalRefName2(asmName: string): string;
277
- getRefNameColor(refName: string): string | undefined;
278
- isValidRefName(refName: string): boolean;
279
- } & {
280
- setLoaded({ regions, refNameAliases, cytobands, }: {
281
- regions: import("@jbrowse/core/util").Region[];
282
- refNameAliases: {
283
- [x: string]: string;
284
- };
285
- cytobands: import("@jbrowse/core/util").Feature[];
286
- }): void;
287
- setError(e: unknown): void;
288
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
289
- setRefNameAliases(aliases: {
290
- [x: string]: string;
291
- }): void;
292
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
293
- setLoadingP(p?: Promise<void>): void;
294
- load(): Promise<void>;
295
- loadPre(): Promise<void>;
296
- } & {
297
- getAdapterMapEntry(adapterConf: {
298
- [x: string]: unknown;
299
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
300
- getRefNameMapForAdapter(adapterConf: {
301
- [x: string]: unknown;
302
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
303
- [x: string]: string;
304
- }>;
305
- getReverseRefNameMapForAdapter(adapterConf: {
306
- [x: string]: unknown;
307
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
308
- [x: string]: string;
309
- }>;
310
- afterCreate(): void;
311
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
312
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
313
- readonly assemblyNameMap: Record<string, {
314
- configuration: any;
315
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
316
- error: unknown;
317
- loadingP: Promise<void> | undefined;
318
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
319
- refNameAliases: {
320
- [x: string]: string;
321
- } | undefined;
322
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
323
- } & {
324
- getConf(arg: string): any;
325
- readonly lowerCaseRefNameAliases: {
326
- [k: string]: string;
327
- } | undefined;
328
- } & {
329
- readonly initialized: boolean;
330
- readonly name: string;
331
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
332
- readonly aliases: string[];
333
- readonly displayName: string;
334
- hasName(name: string): boolean;
335
- readonly allAliases: string[];
336
- readonly allRefNames: string[] | undefined;
337
- readonly lowerCaseRefNames: string[] | undefined;
338
- readonly allRefNamesWithLowerCase: string[] | undefined;
339
- readonly rpcManager: RpcManager;
340
- readonly refNameColors: string[];
341
- } & {
342
- readonly refNames: string[] | undefined;
343
- } & {
344
- getCanonicalRefName(refName: string): string | undefined;
345
- getCanonicalRefName2(asmName: string): string;
346
- getRefNameColor(refName: string): string | undefined;
347
- isValidRefName(refName: string): boolean;
348
- } & {
349
- setLoaded({ regions, refNameAliases, cytobands, }: {
350
- regions: import("@jbrowse/core/util").Region[];
351
- refNameAliases: {
352
- [x: string]: string;
353
- };
354
- cytobands: import("@jbrowse/core/util").Feature[];
355
- }): void;
356
- setError(e: unknown): void;
357
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
358
- setRefNameAliases(aliases: {
359
- [x: string]: string;
360
- }): void;
361
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
362
- setLoadingP(p?: Promise<void>): void;
363
- load(): Promise<void>;
364
- loadPre(): Promise<void>;
365
- } & {
366
- getAdapterMapEntry(adapterConf: {
367
- [x: string]: unknown;
368
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
369
- getRefNameMapForAdapter(adapterConf: {
370
- [x: string]: unknown;
371
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
372
- [x: string]: string;
373
- }>;
374
- getReverseRefNameMapForAdapter(adapterConf: {
375
- [x: string]: unknown;
376
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
377
- [x: string]: string;
378
- }>;
379
- afterCreate(): void;
380
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
381
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
382
- }, {
383
- error: unknown;
384
- loadingP: Promise<void> | undefined;
385
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
386
- refNameAliases: {
387
- [x: string]: string;
388
- } | undefined;
389
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
390
- } & {
391
- getConf(arg: string): any;
392
- readonly lowerCaseRefNameAliases: {
393
- [k: string]: string;
394
- } | undefined;
395
- } & {
396
- readonly initialized: boolean;
397
- readonly name: string;
398
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
399
- readonly aliases: string[];
400
- readonly displayName: string;
401
- hasName(name: string): boolean;
402
- readonly allAliases: string[];
403
- readonly allRefNames: string[] | undefined;
404
- readonly lowerCaseRefNames: string[] | undefined;
405
- readonly allRefNamesWithLowerCase: string[] | undefined;
406
- readonly rpcManager: RpcManager;
407
- readonly refNameColors: string[];
408
- } & {
409
- readonly refNames: string[] | undefined;
410
- } & {
411
- getCanonicalRefName(refName: string): string | undefined;
412
- getCanonicalRefName2(asmName: string): string;
413
- getRefNameColor(refName: string): string | undefined;
414
- isValidRefName(refName: string): boolean;
415
- } & {
416
- setLoaded({ regions, refNameAliases, cytobands, }: {
417
- regions: import("@jbrowse/core/util").Region[];
418
- refNameAliases: {
419
- [x: string]: string;
420
- };
421
- cytobands: import("@jbrowse/core/util").Feature[];
422
- }): void;
423
- setError(e: unknown): void;
424
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
425
- setRefNameAliases(aliases: {
426
- [x: string]: string;
427
- }): void;
428
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
429
- setLoadingP(p?: Promise<void>): void;
430
- load(): Promise<void>;
431
- loadPre(): Promise<void>;
432
- } & {
433
- getAdapterMapEntry(adapterConf: {
434
- [x: string]: unknown;
435
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
436
- getRefNameMapForAdapter(adapterConf: {
437
- [x: string]: unknown;
438
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
439
- [x: string]: string;
440
- }>;
441
- getReverseRefNameMapForAdapter(adapterConf: {
442
- [x: string]: unknown;
443
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
444
- [x: string]: string;
445
- }>;
446
- afterCreate(): void;
447
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
448
- } & {
449
- getCanonicalAssemblyName(asmName: string): string | undefined;
450
- getCanonicalAssemblyName2(asmName: string): string;
451
- get(asmName: string): ({
452
- configuration: any;
453
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
454
- error: unknown;
455
- loadingP: Promise<void> | undefined;
456
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
457
- refNameAliases: {
458
- [x: string]: string;
459
- } | undefined;
460
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
461
- } & {
462
- getConf(arg: string): any;
463
- readonly lowerCaseRefNameAliases: {
464
- [k: string]: string;
465
- } | undefined;
466
- } & {
467
- readonly initialized: boolean;
468
- readonly name: string;
469
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
470
- readonly aliases: string[];
471
- readonly displayName: string;
472
- hasName(name: string): boolean;
473
- readonly allAliases: string[];
474
- readonly allRefNames: string[] | undefined;
475
- readonly lowerCaseRefNames: string[] | undefined;
476
- readonly allRefNamesWithLowerCase: string[] | undefined;
477
- readonly rpcManager: RpcManager;
478
- readonly refNameColors: string[];
479
- } & {
480
- readonly refNames: string[] | undefined;
481
- } & {
482
- getCanonicalRefName(refName: string): string | undefined;
483
- getCanonicalRefName2(asmName: string): string;
484
- getRefNameColor(refName: string): string | undefined;
485
- isValidRefName(refName: string): boolean;
486
- } & {
487
- setLoaded({ regions, refNameAliases, cytobands, }: {
488
- regions: import("@jbrowse/core/util").Region[];
489
- refNameAliases: {
490
- [x: string]: string;
491
- };
492
- cytobands: import("@jbrowse/core/util").Feature[];
493
- }): void;
494
- setError(e: unknown): void;
495
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
496
- setRefNameAliases(aliases: {
497
- [x: string]: string;
498
- }): void;
499
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
500
- setLoadingP(p?: Promise<void>): void;
501
- load(): Promise<void>;
502
- loadPre(): Promise<void>;
503
- } & {
504
- getAdapterMapEntry(adapterConf: {
505
- [x: string]: unknown;
506
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
507
- getRefNameMapForAdapter(adapterConf: {
508
- [x: string]: unknown;
509
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
510
- [x: string]: string;
511
- }>;
512
- getReverseRefNameMapForAdapter(adapterConf: {
513
- [x: string]: unknown;
514
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
515
- [x: string]: string;
516
- }>;
517
- afterCreate(): void;
518
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
519
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
520
- }, {
521
- error: unknown;
522
- loadingP: Promise<void> | undefined;
523
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
524
- refNameAliases: {
525
- [x: string]: string;
526
- } | undefined;
527
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
528
- } & {
529
- getConf(arg: string): any;
530
- readonly lowerCaseRefNameAliases: {
531
- [k: string]: string;
532
- } | undefined;
533
- } & {
534
- readonly initialized: boolean;
535
- readonly name: string;
536
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
537
- readonly aliases: string[];
538
- readonly displayName: string;
539
- hasName(name: string): boolean;
540
- readonly allAliases: string[];
541
- readonly allRefNames: string[] | undefined;
542
- readonly lowerCaseRefNames: string[] | undefined;
543
- readonly allRefNamesWithLowerCase: string[] | undefined;
544
- readonly rpcManager: RpcManager;
545
- readonly refNameColors: string[];
546
- } & {
547
- readonly refNames: string[] | undefined;
548
- } & {
549
- getCanonicalRefName(refName: string): string | undefined;
550
- getCanonicalRefName2(asmName: string): string;
551
- getRefNameColor(refName: string): string | undefined;
552
- isValidRefName(refName: string): boolean;
553
- } & {
554
- setLoaded({ regions, refNameAliases, cytobands, }: {
555
- regions: import("@jbrowse/core/util").Region[];
556
- refNameAliases: {
557
- [x: string]: string;
558
- };
559
- cytobands: import("@jbrowse/core/util").Feature[];
560
- }): void;
561
- setError(e: unknown): void;
562
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
563
- setRefNameAliases(aliases: {
564
- [x: string]: string;
565
- }): void;
566
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
567
- setLoadingP(p?: Promise<void>): void;
568
- load(): Promise<void>;
569
- loadPre(): Promise<void>;
570
- } & {
571
- getAdapterMapEntry(adapterConf: {
572
- [x: string]: unknown;
573
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
574
- getRefNameMapForAdapter(adapterConf: {
575
- [x: string]: unknown;
576
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
577
- [x: string]: string;
578
- }>;
579
- getReverseRefNameMapForAdapter(adapterConf: {
580
- [x: string]: unknown;
581
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
582
- [x: string]: string;
583
- }>;
584
- afterCreate(): void;
585
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
586
- readonly assemblyNamesList: any[];
587
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
588
- readonly rpcManager: RpcManager;
589
- } & {
590
- waitForAssembly(assemblyName: string): Promise<({
591
- configuration: any;
592
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
593
- error: unknown;
594
- loadingP: Promise<void> | undefined;
595
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
596
- refNameAliases: {
597
- [x: string]: string;
598
- } | undefined;
599
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
600
- } & {
601
- getConf(arg: string): any;
602
- readonly lowerCaseRefNameAliases: {
603
- [k: string]: string;
604
- } | undefined;
605
- } & {
606
- readonly initialized: boolean;
607
- readonly name: string;
608
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
609
- readonly aliases: string[];
610
- readonly displayName: string;
611
- hasName(name: string): boolean;
612
- readonly allAliases: string[];
613
- readonly allRefNames: string[] | undefined;
614
- readonly lowerCaseRefNames: string[] | undefined;
615
- readonly allRefNamesWithLowerCase: string[] | undefined;
616
- readonly rpcManager: RpcManager;
617
- readonly refNameColors: string[];
618
- } & {
619
- readonly refNames: string[] | undefined;
620
- } & {
621
- getCanonicalRefName(refName: string): string | undefined;
622
- getCanonicalRefName2(asmName: string): string;
623
- getRefNameColor(refName: string): string | undefined;
624
- isValidRefName(refName: string): boolean;
625
- } & {
626
- setLoaded({ regions, refNameAliases, cytobands, }: {
627
- regions: import("@jbrowse/core/util").Region[];
628
- refNameAliases: {
629
- [x: string]: string;
630
- };
631
- cytobands: import("@jbrowse/core/util").Feature[];
632
- }): void;
633
- setError(e: unknown): void;
634
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
635
- setRefNameAliases(aliases: {
636
- [x: string]: string;
637
- }): void;
638
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
639
- setLoadingP(p?: Promise<void>): void;
640
- load(): Promise<void>;
641
- loadPre(): Promise<void>;
642
- } & {
643
- getAdapterMapEntry(adapterConf: {
644
- [x: string]: unknown;
645
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
646
- getRefNameMapForAdapter(adapterConf: {
647
- [x: string]: unknown;
648
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
649
- [x: string]: string;
650
- }>;
651
- getReverseRefNameMapForAdapter(adapterConf: {
652
- [x: string]: unknown;
653
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
654
- [x: string]: string;
655
- }>;
656
- afterCreate(): void;
657
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
658
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
659
- }, {
660
- error: unknown;
661
- loadingP: Promise<void> | undefined;
662
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
663
- refNameAliases: {
664
- [x: string]: string;
665
- } | undefined;
666
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
667
- } & {
668
- getConf(arg: string): any;
669
- readonly lowerCaseRefNameAliases: {
670
- [k: string]: string;
671
- } | undefined;
672
- } & {
673
- readonly initialized: boolean;
674
- readonly name: string;
675
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
676
- readonly aliases: string[];
677
- readonly displayName: string;
678
- hasName(name: string): boolean;
679
- readonly allAliases: string[];
680
- readonly allRefNames: string[] | undefined;
681
- readonly lowerCaseRefNames: string[] | undefined;
682
- readonly allRefNamesWithLowerCase: string[] | undefined;
683
- readonly rpcManager: RpcManager;
684
- readonly refNameColors: string[];
685
- } & {
686
- readonly refNames: string[] | undefined;
687
- } & {
688
- getCanonicalRefName(refName: string): string | undefined;
689
- getCanonicalRefName2(asmName: string): string;
690
- getRefNameColor(refName: string): string | undefined;
691
- isValidRefName(refName: string): boolean;
692
- } & {
693
- setLoaded({ regions, refNameAliases, cytobands, }: {
694
- regions: import("@jbrowse/core/util").Region[];
695
- refNameAliases: {
696
- [x: string]: string;
697
- };
698
- cytobands: import("@jbrowse/core/util").Feature[];
699
- }): void;
700
- setError(e: unknown): void;
701
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
702
- setRefNameAliases(aliases: {
703
- [x: string]: string;
704
- }): void;
705
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
706
- setLoadingP(p?: Promise<void>): void;
707
- load(): Promise<void>;
708
- loadPre(): Promise<void>;
709
- } & {
710
- getAdapterMapEntry(adapterConf: {
711
- [x: string]: unknown;
712
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
713
- getRefNameMapForAdapter(adapterConf: {
714
- [x: string]: unknown;
715
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
716
- [x: string]: string;
717
- }>;
718
- getReverseRefNameMapForAdapter(adapterConf: {
719
- [x: string]: unknown;
720
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
721
- [x: string]: string;
722
- }>;
723
- afterCreate(): void;
724
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
725
- getRefNameMapForAdapter(adapterConf: {
726
- [x: string]: unknown;
727
- }, assemblyName: string | undefined, opts: {
728
- stopToken?: string;
729
- sessionId: string;
730
- }): Promise<{
731
- [x: string]: string;
732
- } | undefined>;
733
- getReverseRefNameMapForAdapter(adapterConf: {
734
- [x: string]: unknown;
735
- }, assemblyName: string | undefined, opts: {
736
- stopToken?: string;
737
- sessionId: string;
738
- }): Promise<{
739
- [x: string]: string;
740
- } | undefined>;
741
- isValidRefName(refName: string, assemblyName: string): boolean;
742
- } & {
743
- afterAttach(): void;
744
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
745
- addAssembly(configuration: any): void;
746
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
747
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
748
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
749
- }, {
750
- error: unknown;
751
- loadingP: Promise<void> | undefined;
752
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
753
- refNameAliases: {
754
- [x: string]: string;
755
- } | undefined;
756
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
757
- } & {
758
- getConf(arg: string): any;
759
- readonly lowerCaseRefNameAliases: {
760
- [k: string]: string;
761
- } | undefined;
762
- } & {
763
- readonly initialized: boolean;
764
- readonly name: string;
765
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
766
- readonly aliases: string[];
767
- readonly displayName: string;
768
- hasName(name: string): boolean;
769
- readonly allAliases: string[];
770
- readonly allRefNames: string[] | undefined;
771
- readonly lowerCaseRefNames: string[] | undefined;
772
- readonly allRefNamesWithLowerCase: string[] | undefined;
773
- readonly rpcManager: RpcManager;
774
- readonly refNameColors: string[];
775
- } & {
776
- readonly refNames: string[] | undefined;
777
- } & {
778
- getCanonicalRefName(refName: string): string | undefined;
779
- getCanonicalRefName2(asmName: string): string;
780
- getRefNameColor(refName: string): string | undefined;
781
- isValidRefName(refName: string): boolean;
782
- } & {
783
- setLoaded({ regions, refNameAliases, cytobands, }: {
784
- regions: import("@jbrowse/core/util").Region[];
785
- refNameAliases: {
786
- [x: string]: string;
787
- };
788
- cytobands: import("@jbrowse/core/util").Feature[];
789
- }): void;
790
- setError(e: unknown): void;
791
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
792
- setRefNameAliases(aliases: {
793
- [x: string]: string;
794
- }): void;
795
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
796
- setLoadingP(p?: Promise<void>): void;
797
- load(): Promise<void>;
798
- loadPre(): Promise<void>;
799
- } & {
800
- getAdapterMapEntry(adapterConf: {
801
- [x: string]: unknown;
802
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
803
- getRefNameMapForAdapter(adapterConf: {
804
- [x: string]: unknown;
805
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
806
- [x: string]: string;
807
- }>;
808
- getReverseRefNameMapForAdapter(adapterConf: {
809
- [x: string]: unknown;
810
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
811
- [x: string]: string;
812
- }>;
813
- afterCreate(): void;
814
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
815
- }, {
816
- readonly assemblyNameMap: Record<string, {
817
- configuration: any;
818
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
819
- error: unknown;
820
- loadingP: Promise<void> | undefined;
821
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
822
- refNameAliases: {
823
- [x: string]: string;
824
- } | undefined;
825
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
826
- } & {
827
- getConf(arg: string): any;
828
- readonly lowerCaseRefNameAliases: {
829
- [k: string]: string;
830
- } | undefined;
831
- } & {
832
- readonly initialized: boolean;
833
- readonly name: string;
834
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
835
- readonly aliases: string[];
836
- readonly displayName: string;
837
- hasName(name: string): boolean;
838
- readonly allAliases: string[];
839
- readonly allRefNames: string[] | undefined;
840
- readonly lowerCaseRefNames: string[] | undefined;
841
- readonly allRefNamesWithLowerCase: string[] | undefined;
842
- readonly rpcManager: RpcManager;
843
- readonly refNameColors: string[];
844
- } & {
845
- readonly refNames: string[] | undefined;
846
- } & {
847
- getCanonicalRefName(refName: string): string | undefined;
848
- getCanonicalRefName2(asmName: string): string;
849
- getRefNameColor(refName: string): string | undefined;
850
- isValidRefName(refName: string): boolean;
851
- } & {
852
- setLoaded({ regions, refNameAliases, cytobands, }: {
853
- regions: import("@jbrowse/core/util").Region[];
854
- refNameAliases: {
855
- [x: string]: string;
856
- };
857
- cytobands: import("@jbrowse/core/util").Feature[];
858
- }): void;
859
- setError(e: unknown): void;
860
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
861
- setRefNameAliases(aliases: {
862
- [x: string]: string;
863
- }): void;
864
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
865
- setLoadingP(p?: Promise<void>): void;
866
- load(): Promise<void>;
867
- loadPre(): Promise<void>;
868
- } & {
869
- getAdapterMapEntry(adapterConf: {
870
- [x: string]: unknown;
871
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
872
- getRefNameMapForAdapter(adapterConf: {
873
- [x: string]: unknown;
874
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
875
- [x: string]: string;
876
- }>;
877
- getReverseRefNameMapForAdapter(adapterConf: {
878
- [x: string]: unknown;
879
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
880
- [x: string]: string;
881
- }>;
882
- afterCreate(): void;
883
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
884
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
885
- }, {
886
- error: unknown;
887
- loadingP: Promise<void> | undefined;
888
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
889
- refNameAliases: {
890
- [x: string]: string;
891
- } | undefined;
892
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
893
- } & {
894
- getConf(arg: string): any;
895
- readonly lowerCaseRefNameAliases: {
896
- [k: string]: string;
897
- } | undefined;
898
- } & {
899
- readonly initialized: boolean;
900
- readonly name: string;
901
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
902
- readonly aliases: string[];
903
- readonly displayName: string;
904
- hasName(name: string): boolean;
905
- readonly allAliases: string[];
906
- readonly allRefNames: string[] | undefined;
907
- readonly lowerCaseRefNames: string[] | undefined;
908
- readonly allRefNamesWithLowerCase: string[] | undefined;
909
- readonly rpcManager: RpcManager;
910
- readonly refNameColors: string[];
911
- } & {
912
- readonly refNames: string[] | undefined;
913
- } & {
914
- getCanonicalRefName(refName: string): string | undefined;
915
- getCanonicalRefName2(asmName: string): string;
916
- getRefNameColor(refName: string): string | undefined;
917
- isValidRefName(refName: string): boolean;
918
- } & {
919
- setLoaded({ regions, refNameAliases, cytobands, }: {
920
- regions: import("@jbrowse/core/util").Region[];
921
- refNameAliases: {
922
- [x: string]: string;
923
- };
924
- cytobands: import("@jbrowse/core/util").Feature[];
925
- }): void;
926
- setError(e: unknown): void;
927
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
928
- setRefNameAliases(aliases: {
929
- [x: string]: string;
930
- }): void;
931
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
932
- setLoadingP(p?: Promise<void>): void;
933
- load(): Promise<void>;
934
- loadPre(): Promise<void>;
935
- } & {
936
- getAdapterMapEntry(adapterConf: {
937
- [x: string]: unknown;
938
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
939
- getRefNameMapForAdapter(adapterConf: {
940
- [x: string]: unknown;
941
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
942
- [x: string]: string;
943
- }>;
944
- getReverseRefNameMapForAdapter(adapterConf: {
945
- [x: string]: unknown;
946
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
947
- [x: string]: string;
948
- }>;
949
- afterCreate(): void;
950
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
951
- } & {
952
- getCanonicalAssemblyName(asmName: string): string | undefined;
953
- getCanonicalAssemblyName2(asmName: string): string;
954
- get(asmName: string): ({
955
- configuration: any;
956
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
957
- error: unknown;
958
- loadingP: Promise<void> | undefined;
959
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
960
- refNameAliases: {
961
- [x: string]: string;
962
- } | undefined;
963
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
964
- } & {
965
- getConf(arg: string): any;
966
- readonly lowerCaseRefNameAliases: {
967
- [k: string]: string;
968
- } | undefined;
969
- } & {
970
- readonly initialized: boolean;
971
- readonly name: string;
972
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
973
- readonly aliases: string[];
974
- readonly displayName: string;
975
- hasName(name: string): boolean;
976
- readonly allAliases: string[];
977
- readonly allRefNames: string[] | undefined;
978
- readonly lowerCaseRefNames: string[] | undefined;
979
- readonly allRefNamesWithLowerCase: string[] | undefined;
980
- readonly rpcManager: RpcManager;
981
- readonly refNameColors: string[];
982
- } & {
983
- readonly refNames: string[] | undefined;
984
- } & {
985
- getCanonicalRefName(refName: string): string | undefined;
986
- getCanonicalRefName2(asmName: string): string;
987
- getRefNameColor(refName: string): string | undefined;
988
- isValidRefName(refName: string): boolean;
989
- } & {
990
- setLoaded({ regions, refNameAliases, cytobands, }: {
991
- regions: import("@jbrowse/core/util").Region[];
992
- refNameAliases: {
993
- [x: string]: string;
994
- };
995
- cytobands: import("@jbrowse/core/util").Feature[];
996
- }): void;
997
- setError(e: unknown): void;
998
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
999
- setRefNameAliases(aliases: {
1000
- [x: string]: string;
1001
- }): void;
1002
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1003
- setLoadingP(p?: Promise<void>): void;
1004
- load(): Promise<void>;
1005
- loadPre(): Promise<void>;
1006
- } & {
1007
- getAdapterMapEntry(adapterConf: {
1008
- [x: string]: unknown;
1009
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1010
- getRefNameMapForAdapter(adapterConf: {
1011
- [x: string]: unknown;
1012
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1013
- [x: string]: string;
1014
- }>;
1015
- getReverseRefNameMapForAdapter(adapterConf: {
1016
- [x: string]: unknown;
1017
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1018
- [x: string]: string;
1019
- }>;
1020
- afterCreate(): void;
1021
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1022
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1023
- }, {
1024
- error: unknown;
1025
- loadingP: Promise<void> | undefined;
1026
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1027
- refNameAliases: {
1028
- [x: string]: string;
1029
- } | undefined;
1030
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1031
- } & {
1032
- getConf(arg: string): any;
1033
- readonly lowerCaseRefNameAliases: {
1034
- [k: string]: string;
1035
- } | undefined;
1036
- } & {
1037
- readonly initialized: boolean;
1038
- readonly name: string;
1039
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1040
- readonly aliases: string[];
1041
- readonly displayName: string;
1042
- hasName(name: string): boolean;
1043
- readonly allAliases: string[];
1044
- readonly allRefNames: string[] | undefined;
1045
- readonly lowerCaseRefNames: string[] | undefined;
1046
- readonly allRefNamesWithLowerCase: string[] | undefined;
1047
- readonly rpcManager: RpcManager;
1048
- readonly refNameColors: string[];
1049
- } & {
1050
- readonly refNames: string[] | undefined;
1051
- } & {
1052
- getCanonicalRefName(refName: string): string | undefined;
1053
- getCanonicalRefName2(asmName: string): string;
1054
- getRefNameColor(refName: string): string | undefined;
1055
- isValidRefName(refName: string): boolean;
1056
- } & {
1057
- setLoaded({ regions, refNameAliases, cytobands, }: {
1058
- regions: import("@jbrowse/core/util").Region[];
1059
- refNameAliases: {
1060
- [x: string]: string;
1061
- };
1062
- cytobands: import("@jbrowse/core/util").Feature[];
1063
- }): void;
1064
- setError(e: unknown): void;
1065
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1066
- setRefNameAliases(aliases: {
1067
- [x: string]: string;
1068
- }): void;
1069
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1070
- setLoadingP(p?: Promise<void>): void;
1071
- load(): Promise<void>;
1072
- loadPre(): Promise<void>;
1073
- } & {
1074
- getAdapterMapEntry(adapterConf: {
1075
- [x: string]: unknown;
1076
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1077
- getRefNameMapForAdapter(adapterConf: {
1078
- [x: string]: unknown;
1079
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1080
- [x: string]: string;
1081
- }>;
1082
- getReverseRefNameMapForAdapter(adapterConf: {
1083
- [x: string]: unknown;
1084
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1085
- [x: string]: string;
1086
- }>;
1087
- afterCreate(): void;
1088
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1089
- readonly assemblyNamesList: any[];
1090
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1091
- readonly rpcManager: RpcManager;
1092
- } & {
1093
- waitForAssembly(assemblyName: string): Promise<({
1094
- configuration: any;
1095
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1096
- error: unknown;
1097
- loadingP: Promise<void> | undefined;
1098
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1099
- refNameAliases: {
1100
- [x: string]: string;
1101
- } | undefined;
1102
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1103
- } & {
1104
- getConf(arg: string): any;
1105
- readonly lowerCaseRefNameAliases: {
1106
- [k: string]: string;
1107
- } | undefined;
1108
- } & {
1109
- readonly initialized: boolean;
1110
- readonly name: string;
1111
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1112
- readonly aliases: string[];
1113
- readonly displayName: string;
1114
- hasName(name: string): boolean;
1115
- readonly allAliases: string[];
1116
- readonly allRefNames: string[] | undefined;
1117
- readonly lowerCaseRefNames: string[] | undefined;
1118
- readonly allRefNamesWithLowerCase: string[] | undefined;
1119
- readonly rpcManager: RpcManager;
1120
- readonly refNameColors: string[];
1121
- } & {
1122
- readonly refNames: string[] | undefined;
1123
- } & {
1124
- getCanonicalRefName(refName: string): string | undefined;
1125
- getCanonicalRefName2(asmName: string): string;
1126
- getRefNameColor(refName: string): string | undefined;
1127
- isValidRefName(refName: string): boolean;
1128
- } & {
1129
- setLoaded({ regions, refNameAliases, cytobands, }: {
1130
- regions: import("@jbrowse/core/util").Region[];
1131
- refNameAliases: {
1132
- [x: string]: string;
1133
- };
1134
- cytobands: import("@jbrowse/core/util").Feature[];
1135
- }): void;
1136
- setError(e: unknown): void;
1137
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1138
- setRefNameAliases(aliases: {
1139
- [x: string]: string;
1140
- }): void;
1141
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1142
- setLoadingP(p?: Promise<void>): void;
1143
- load(): Promise<void>;
1144
- loadPre(): Promise<void>;
1145
- } & {
1146
- getAdapterMapEntry(adapterConf: {
1147
- [x: string]: unknown;
1148
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1149
- getRefNameMapForAdapter(adapterConf: {
1150
- [x: string]: unknown;
1151
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1152
- [x: string]: string;
1153
- }>;
1154
- getReverseRefNameMapForAdapter(adapterConf: {
1155
- [x: string]: unknown;
1156
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1157
- [x: string]: string;
1158
- }>;
1159
- afterCreate(): void;
1160
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1161
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1162
- }, {
1163
- error: unknown;
1164
- loadingP: Promise<void> | undefined;
1165
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1166
- refNameAliases: {
1167
- [x: string]: string;
1168
- } | undefined;
1169
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1170
- } & {
1171
- getConf(arg: string): any;
1172
- readonly lowerCaseRefNameAliases: {
1173
- [k: string]: string;
1174
- } | undefined;
1175
- } & {
1176
- readonly initialized: boolean;
1177
- readonly name: string;
1178
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1179
- readonly aliases: string[];
1180
- readonly displayName: string;
1181
- hasName(name: string): boolean;
1182
- readonly allAliases: string[];
1183
- readonly allRefNames: string[] | undefined;
1184
- readonly lowerCaseRefNames: string[] | undefined;
1185
- readonly allRefNamesWithLowerCase: string[] | undefined;
1186
- readonly rpcManager: RpcManager;
1187
- readonly refNameColors: string[];
1188
- } & {
1189
- readonly refNames: string[] | undefined;
1190
- } & {
1191
- getCanonicalRefName(refName: string): string | undefined;
1192
- getCanonicalRefName2(asmName: string): string;
1193
- getRefNameColor(refName: string): string | undefined;
1194
- isValidRefName(refName: string): boolean;
1195
- } & {
1196
- setLoaded({ regions, refNameAliases, cytobands, }: {
1197
- regions: import("@jbrowse/core/util").Region[];
1198
- refNameAliases: {
1199
- [x: string]: string;
1200
- };
1201
- cytobands: import("@jbrowse/core/util").Feature[];
1202
- }): void;
1203
- setError(e: unknown): void;
1204
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1205
- setRefNameAliases(aliases: {
1206
- [x: string]: string;
1207
- }): void;
1208
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1209
- setLoadingP(p?: Promise<void>): void;
1210
- load(): Promise<void>;
1211
- loadPre(): Promise<void>;
1212
- } & {
1213
- getAdapterMapEntry(adapterConf: {
1214
- [x: string]: unknown;
1215
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1216
- getRefNameMapForAdapter(adapterConf: {
1217
- [x: string]: unknown;
1218
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1219
- [x: string]: string;
1220
- }>;
1221
- getReverseRefNameMapForAdapter(adapterConf: {
1222
- [x: string]: unknown;
1223
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1224
- [x: string]: string;
1225
- }>;
1226
- afterCreate(): void;
1227
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1228
- getRefNameMapForAdapter(adapterConf: {
1229
- [x: string]: unknown;
1230
- }, assemblyName: string | undefined, opts: {
1231
- stopToken?: string;
1232
- sessionId: string;
1233
- }): Promise<{
1234
- [x: string]: string;
1235
- } | undefined>;
1236
- getReverseRefNameMapForAdapter(adapterConf: {
1237
- [x: string]: unknown;
1238
- }, assemblyName: string | undefined, opts: {
1239
- stopToken?: string;
1240
- sessionId: string;
1241
- }): Promise<{
1242
- [x: string]: string;
1243
- } | undefined>;
1244
- isValidRefName(refName: string, assemblyName: string): boolean;
1245
- } & {
1246
- afterAttach(): void;
1247
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1248
- addAssembly(configuration: any): void;
1249
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
1250
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1251
- rpcManager: RpcManager;
1252
- adminMode: boolean;
1253
- error: unknown;
1254
- textSearchManager: TextSearchManager;
1255
- pluginManager: PluginManager;
1256
- } & {
1257
- setError(error: unknown): void;
1258
- setSession(sessionSnapshot?: SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1259
- setDefaultSession(): void;
1260
- setSessionPath(path: string): void;
1261
- renameCurrentSession(newName: string): void;
1262
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1263
- jbrowse: import("mobx-state-tree").IAnyType;
1264
- session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
1265
- sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1266
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1267
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1268
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1269
- }, {
1270
- error: unknown;
1271
- loadingP: Promise<void> | undefined;
1272
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1273
- refNameAliases: {
1274
- [x: string]: string;
1275
- } | undefined;
1276
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1277
- } & {
1278
- getConf(arg: string): any;
1279
- readonly lowerCaseRefNameAliases: {
1280
- [k: string]: string;
1281
- } | undefined;
1282
- } & {
1283
- readonly initialized: boolean;
1284
- readonly name: string;
1285
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1286
- readonly aliases: string[];
1287
- readonly displayName: string;
1288
- hasName(name: string): boolean;
1289
- readonly allAliases: string[];
1290
- readonly allRefNames: string[] | undefined;
1291
- readonly lowerCaseRefNames: string[] | undefined;
1292
- readonly allRefNamesWithLowerCase: string[] | undefined;
1293
- readonly rpcManager: RpcManager;
1294
- readonly refNameColors: string[];
1295
- } & {
1296
- readonly refNames: string[] | undefined;
1297
- } & {
1298
- getCanonicalRefName(refName: string): string | undefined;
1299
- getCanonicalRefName2(asmName: string): string;
1300
- getRefNameColor(refName: string): string | undefined;
1301
- isValidRefName(refName: string): boolean;
1302
- } & {
1303
- setLoaded({ regions, refNameAliases, cytobands, }: {
1304
- regions: import("@jbrowse/core/util").Region[];
1305
- refNameAliases: {
1306
- [x: string]: string;
1307
- };
1308
- cytobands: import("@jbrowse/core/util").Feature[];
1309
- }): void;
1310
- setError(e: unknown): void;
1311
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1312
- setRefNameAliases(aliases: {
1313
- [x: string]: string;
1314
- }): void;
1315
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1316
- setLoadingP(p?: Promise<void>): void;
1317
- load(): Promise<void>;
1318
- loadPre(): Promise<void>;
1319
- } & {
1320
- getAdapterMapEntry(adapterConf: {
1321
- [x: string]: unknown;
1322
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1323
- getRefNameMapForAdapter(adapterConf: {
1324
- [x: string]: unknown;
1325
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1326
- [x: string]: string;
1327
- }>;
1328
- getReverseRefNameMapForAdapter(adapterConf: {
1329
- [x: string]: unknown;
1330
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1331
- [x: string]: string;
1332
- }>;
1333
- afterCreate(): void;
1334
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1335
- }, {
1336
- readonly assemblyNameMap: Record<string, {
1337
- configuration: any;
1338
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1339
- error: unknown;
1340
- loadingP: Promise<void> | undefined;
1341
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1342
- refNameAliases: {
1343
- [x: string]: string;
1344
- } | undefined;
1345
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1346
- } & {
1347
- getConf(arg: string): any;
1348
- readonly lowerCaseRefNameAliases: {
1349
- [k: string]: string;
1350
- } | undefined;
1351
- } & {
1352
- readonly initialized: boolean;
1353
- readonly name: string;
1354
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1355
- readonly aliases: string[];
1356
- readonly displayName: string;
1357
- hasName(name: string): boolean;
1358
- readonly allAliases: string[];
1359
- readonly allRefNames: string[] | undefined;
1360
- readonly lowerCaseRefNames: string[] | undefined;
1361
- readonly allRefNamesWithLowerCase: string[] | undefined;
1362
- readonly rpcManager: RpcManager;
1363
- readonly refNameColors: string[];
1364
- } & {
1365
- readonly refNames: string[] | undefined;
1366
- } & {
1367
- getCanonicalRefName(refName: string): string | undefined;
1368
- getCanonicalRefName2(asmName: string): string;
1369
- getRefNameColor(refName: string): string | undefined;
1370
- isValidRefName(refName: string): boolean;
1371
- } & {
1372
- setLoaded({ regions, refNameAliases, cytobands, }: {
1373
- regions: import("@jbrowse/core/util").Region[];
1374
- refNameAliases: {
1375
- [x: string]: string;
1376
- };
1377
- cytobands: import("@jbrowse/core/util").Feature[];
1378
- }): void;
1379
- setError(e: unknown): void;
1380
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1381
- setRefNameAliases(aliases: {
1382
- [x: string]: string;
1383
- }): void;
1384
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1385
- setLoadingP(p?: Promise<void>): void;
1386
- load(): Promise<void>;
1387
- loadPre(): Promise<void>;
1388
- } & {
1389
- getAdapterMapEntry(adapterConf: {
1390
- [x: string]: unknown;
1391
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1392
- getRefNameMapForAdapter(adapterConf: {
1393
- [x: string]: unknown;
1394
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1395
- [x: string]: string;
1396
- }>;
1397
- getReverseRefNameMapForAdapter(adapterConf: {
1398
- [x: string]: unknown;
1399
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1400
- [x: string]: string;
1401
- }>;
1402
- afterCreate(): void;
1403
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1404
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1405
- }, {
1406
- error: unknown;
1407
- loadingP: Promise<void> | undefined;
1408
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1409
- refNameAliases: {
1410
- [x: string]: string;
1411
- } | undefined;
1412
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1413
- } & {
1414
- getConf(arg: string): any;
1415
- readonly lowerCaseRefNameAliases: {
1416
- [k: string]: string;
1417
- } | undefined;
1418
- } & {
1419
- readonly initialized: boolean;
1420
- readonly name: string;
1421
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1422
- readonly aliases: string[];
1423
- readonly displayName: string;
1424
- hasName(name: string): boolean;
1425
- readonly allAliases: string[];
1426
- readonly allRefNames: string[] | undefined;
1427
- readonly lowerCaseRefNames: string[] | undefined;
1428
- readonly allRefNamesWithLowerCase: string[] | undefined;
1429
- readonly rpcManager: RpcManager;
1430
- readonly refNameColors: string[];
1431
- } & {
1432
- readonly refNames: string[] | undefined;
1433
- } & {
1434
- getCanonicalRefName(refName: string): string | undefined;
1435
- getCanonicalRefName2(asmName: string): string;
1436
- getRefNameColor(refName: string): string | undefined;
1437
- isValidRefName(refName: string): boolean;
1438
- } & {
1439
- setLoaded({ regions, refNameAliases, cytobands, }: {
1440
- regions: import("@jbrowse/core/util").Region[];
1441
- refNameAliases: {
1442
- [x: string]: string;
1443
- };
1444
- cytobands: import("@jbrowse/core/util").Feature[];
1445
- }): void;
1446
- setError(e: unknown): void;
1447
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1448
- setRefNameAliases(aliases: {
1449
- [x: string]: string;
1450
- }): void;
1451
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1452
- setLoadingP(p?: Promise<void>): void;
1453
- load(): Promise<void>;
1454
- loadPre(): Promise<void>;
1455
- } & {
1456
- getAdapterMapEntry(adapterConf: {
1457
- [x: string]: unknown;
1458
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1459
- getRefNameMapForAdapter(adapterConf: {
1460
- [x: string]: unknown;
1461
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1462
- [x: string]: string;
1463
- }>;
1464
- getReverseRefNameMapForAdapter(adapterConf: {
1465
- [x: string]: unknown;
1466
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1467
- [x: string]: string;
1468
- }>;
1469
- afterCreate(): void;
1470
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
1471
- } & {
1472
- getCanonicalAssemblyName(asmName: string): string | undefined;
1473
- getCanonicalAssemblyName2(asmName: string): string;
1474
- get(asmName: string): ({
1475
- configuration: any;
1476
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1477
- error: unknown;
1478
- loadingP: Promise<void> | undefined;
1479
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1480
- refNameAliases: {
1481
- [x: string]: string;
1482
- } | undefined;
1483
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1484
- } & {
1485
- getConf(arg: string): any;
1486
- readonly lowerCaseRefNameAliases: {
1487
- [k: string]: string;
1488
- } | undefined;
1489
- } & {
1490
- readonly initialized: boolean;
1491
- readonly name: string;
1492
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1493
- readonly aliases: string[];
1494
- readonly displayName: string;
1495
- hasName(name: string): boolean;
1496
- readonly allAliases: string[];
1497
- readonly allRefNames: string[] | undefined;
1498
- readonly lowerCaseRefNames: string[] | undefined;
1499
- readonly allRefNamesWithLowerCase: string[] | undefined;
1500
- readonly rpcManager: RpcManager;
1501
- readonly refNameColors: string[];
1502
- } & {
1503
- readonly refNames: string[] | undefined;
1504
- } & {
1505
- getCanonicalRefName(refName: string): string | undefined;
1506
- getCanonicalRefName2(asmName: string): string;
1507
- getRefNameColor(refName: string): string | undefined;
1508
- isValidRefName(refName: string): boolean;
1509
- } & {
1510
- setLoaded({ regions, refNameAliases, cytobands, }: {
1511
- regions: import("@jbrowse/core/util").Region[];
1512
- refNameAliases: {
1513
- [x: string]: string;
1514
- };
1515
- cytobands: import("@jbrowse/core/util").Feature[];
1516
- }): void;
1517
- setError(e: unknown): void;
1518
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1519
- setRefNameAliases(aliases: {
1520
- [x: string]: string;
1521
- }): void;
1522
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1523
- setLoadingP(p?: Promise<void>): void;
1524
- load(): Promise<void>;
1525
- loadPre(): Promise<void>;
1526
- } & {
1527
- getAdapterMapEntry(adapterConf: {
1528
- [x: string]: unknown;
1529
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1530
- getRefNameMapForAdapter(adapterConf: {
1531
- [x: string]: unknown;
1532
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1533
- [x: string]: string;
1534
- }>;
1535
- getReverseRefNameMapForAdapter(adapterConf: {
1536
- [x: string]: unknown;
1537
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1538
- [x: string]: string;
1539
- }>;
1540
- afterCreate(): void;
1541
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1542
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1543
- }, {
1544
- error: unknown;
1545
- loadingP: Promise<void> | undefined;
1546
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1547
- refNameAliases: {
1548
- [x: string]: string;
1549
- } | undefined;
1550
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1551
- } & {
1552
- getConf(arg: string): any;
1553
- readonly lowerCaseRefNameAliases: {
1554
- [k: string]: string;
1555
- } | undefined;
1556
- } & {
1557
- readonly initialized: boolean;
1558
- readonly name: string;
1559
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1560
- readonly aliases: string[];
1561
- readonly displayName: string;
1562
- hasName(name: string): boolean;
1563
- readonly allAliases: string[];
1564
- readonly allRefNames: string[] | undefined;
1565
- readonly lowerCaseRefNames: string[] | undefined;
1566
- readonly allRefNamesWithLowerCase: string[] | undefined;
1567
- readonly rpcManager: RpcManager;
1568
- readonly refNameColors: string[];
1569
- } & {
1570
- readonly refNames: string[] | undefined;
1571
- } & {
1572
- getCanonicalRefName(refName: string): string | undefined;
1573
- getCanonicalRefName2(asmName: string): string;
1574
- getRefNameColor(refName: string): string | undefined;
1575
- isValidRefName(refName: string): boolean;
1576
- } & {
1577
- setLoaded({ regions, refNameAliases, cytobands, }: {
1578
- regions: import("@jbrowse/core/util").Region[];
1579
- refNameAliases: {
1580
- [x: string]: string;
1581
- };
1582
- cytobands: import("@jbrowse/core/util").Feature[];
1583
- }): void;
1584
- setError(e: unknown): void;
1585
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1586
- setRefNameAliases(aliases: {
1587
- [x: string]: string;
1588
- }): void;
1589
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1590
- setLoadingP(p?: Promise<void>): void;
1591
- load(): Promise<void>;
1592
- loadPre(): Promise<void>;
1593
- } & {
1594
- getAdapterMapEntry(adapterConf: {
1595
- [x: string]: unknown;
1596
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1597
- getRefNameMapForAdapter(adapterConf: {
1598
- [x: string]: unknown;
1599
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1600
- [x: string]: string;
1601
- }>;
1602
- getReverseRefNameMapForAdapter(adapterConf: {
1603
- [x: string]: unknown;
1604
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1605
- [x: string]: string;
1606
- }>;
1607
- afterCreate(): void;
1608
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1609
- readonly assemblyNamesList: any[];
1610
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1611
- readonly rpcManager: RpcManager;
1612
- } & {
1613
- waitForAssembly(assemblyName: string): Promise<({
1614
- configuration: any;
1615
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1616
- error: unknown;
1617
- loadingP: Promise<void> | undefined;
1618
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1619
- refNameAliases: {
1620
- [x: string]: string;
1621
- } | undefined;
1622
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1623
- } & {
1624
- getConf(arg: string): any;
1625
- readonly lowerCaseRefNameAliases: {
1626
- [k: string]: string;
1627
- } | undefined;
1628
- } & {
1629
- readonly initialized: boolean;
1630
- readonly name: string;
1631
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1632
- readonly aliases: string[];
1633
- readonly displayName: string;
1634
- hasName(name: string): boolean;
1635
- readonly allAliases: string[];
1636
- readonly allRefNames: string[] | undefined;
1637
- readonly lowerCaseRefNames: string[] | undefined;
1638
- readonly allRefNamesWithLowerCase: string[] | undefined;
1639
- readonly rpcManager: RpcManager;
1640
- readonly refNameColors: string[];
1641
- } & {
1642
- readonly refNames: string[] | undefined;
1643
- } & {
1644
- getCanonicalRefName(refName: string): string | undefined;
1645
- getCanonicalRefName2(asmName: string): string;
1646
- getRefNameColor(refName: string): string | undefined;
1647
- isValidRefName(refName: string): boolean;
1648
- } & {
1649
- setLoaded({ regions, refNameAliases, cytobands, }: {
1650
- regions: import("@jbrowse/core/util").Region[];
1651
- refNameAliases: {
1652
- [x: string]: string;
1653
- };
1654
- cytobands: import("@jbrowse/core/util").Feature[];
1655
- }): void;
1656
- setError(e: unknown): void;
1657
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1658
- setRefNameAliases(aliases: {
1659
- [x: string]: string;
1660
- }): void;
1661
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1662
- setLoadingP(p?: Promise<void>): void;
1663
- load(): Promise<void>;
1664
- loadPre(): Promise<void>;
1665
- } & {
1666
- getAdapterMapEntry(adapterConf: {
1667
- [x: string]: unknown;
1668
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1669
- getRefNameMapForAdapter(adapterConf: {
1670
- [x: string]: unknown;
1671
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1672
- [x: string]: string;
1673
- }>;
1674
- getReverseRefNameMapForAdapter(adapterConf: {
1675
- [x: string]: unknown;
1676
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1677
- [x: string]: string;
1678
- }>;
1679
- afterCreate(): void;
1680
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1681
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1682
- }, {
1683
- error: unknown;
1684
- loadingP: Promise<void> | undefined;
1685
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1686
- refNameAliases: {
1687
- [x: string]: string;
1688
- } | undefined;
1689
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1690
- } & {
1691
- getConf(arg: string): any;
1692
- readonly lowerCaseRefNameAliases: {
1693
- [k: string]: string;
1694
- } | undefined;
1695
- } & {
1696
- readonly initialized: boolean;
1697
- readonly name: string;
1698
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1699
- readonly aliases: string[];
1700
- readonly displayName: string;
1701
- hasName(name: string): boolean;
1702
- readonly allAliases: string[];
1703
- readonly allRefNames: string[] | undefined;
1704
- readonly lowerCaseRefNames: string[] | undefined;
1705
- readonly allRefNamesWithLowerCase: string[] | undefined;
1706
- readonly rpcManager: RpcManager;
1707
- readonly refNameColors: string[];
1708
- } & {
1709
- readonly refNames: string[] | undefined;
1710
- } & {
1711
- getCanonicalRefName(refName: string): string | undefined;
1712
- getCanonicalRefName2(asmName: string): string;
1713
- getRefNameColor(refName: string): string | undefined;
1714
- isValidRefName(refName: string): boolean;
1715
- } & {
1716
- setLoaded({ regions, refNameAliases, cytobands, }: {
1717
- regions: import("@jbrowse/core/util").Region[];
1718
- refNameAliases: {
1719
- [x: string]: string;
1720
- };
1721
- cytobands: import("@jbrowse/core/util").Feature[];
1722
- }): void;
1723
- setError(e: unknown): void;
1724
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1725
- setRefNameAliases(aliases: {
1726
- [x: string]: string;
1727
- }): void;
1728
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1729
- setLoadingP(p?: Promise<void>): void;
1730
- load(): Promise<void>;
1731
- loadPre(): Promise<void>;
1732
- } & {
1733
- getAdapterMapEntry(adapterConf: {
1734
- [x: string]: unknown;
1735
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1736
- getRefNameMapForAdapter(adapterConf: {
1737
- [x: string]: unknown;
1738
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1739
- [x: string]: string;
1740
- }>;
1741
- getReverseRefNameMapForAdapter(adapterConf: {
1742
- [x: string]: unknown;
1743
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1744
- [x: string]: string;
1745
- }>;
1746
- afterCreate(): void;
1747
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1748
- getRefNameMapForAdapter(adapterConf: {
1749
- [x: string]: unknown;
1750
- }, assemblyName: string | undefined, opts: {
1751
- stopToken?: string;
1752
- sessionId: string;
1753
- }): Promise<{
1754
- [x: string]: string;
1755
- } | undefined>;
1756
- getReverseRefNameMapForAdapter(adapterConf: {
1757
- [x: string]: unknown;
1758
- }, assemblyName: string | undefined, opts: {
1759
- stopToken?: string;
1760
- sessionId: string;
1761
- }): Promise<{
1762
- [x: string]: string;
1763
- } | undefined>;
1764
- isValidRefName(refName: string, assemblyName: string): boolean;
1765
- } & {
1766
- afterAttach(): void;
1767
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1768
- addAssembly(configuration: any): void;
1769
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
1770
- }, {
1771
- rpcManager: RpcManager;
1772
- adminMode: boolean;
1773
- error: unknown;
1774
- textSearchManager: TextSearchManager;
1775
- pluginManager: PluginManager;
1776
- } & {
1777
- setError(error: unknown): void;
1778
- setSession(sessionSnapshot?: SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1779
- setDefaultSession(): void;
1780
- setSessionPath(path: string): void;
1781
- renameCurrentSession(newName: string): void;
1782
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1783
- } & {
1784
- readonly jbrowse: any;
1785
- readonly rpcManager: RpcManager;
1786
- readonly configuration: {
1787
- [x: string]: any;
1788
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1789
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1790
- [x: string]: any;
1791
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1792
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1793
- [x: string]: any;
1794
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1795
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1796
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1797
- readonly adminMode: boolean;
1798
- readonly textSearchManager: TextSearchManager;
1799
- } & {
1800
- readonly assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
1801
- } & {
1802
- setSelection(thing: unknown): void;
1803
- clearSelection(): void;
1804
- setHovered(thing: unknown): void;
1805
- } & {
1806
- readonly visibleWidget: any;
1807
- } & {
1808
- setDrawerPosition(arg: string): void;
1809
- updateDrawerWidth(drawerWidth: number): number;
1810
- resizeDrawer(distance: number): number;
1811
- addWidget(typeName: string, id: string, initialState?: {}, conf?: unknown): any;
1812
- showWidget(widget: any): void;
1813
- hasWidget(widget: any): boolean;
1814
- hideWidget(widget: any): void;
1815
- minimizeWidgetDrawer(): void;
1816
- showWidgetDrawer(): void;
1817
- hideAllWidgets(): void;
1818
- editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1819
- afterAttach(): void;
1820
- } & {
1821
- readonly connections: import("@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig").BaseConnectionConfigModel[];
1822
- } & {
1823
- makeConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: {}): ({
1824
- name: string;
1825
- 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>>;
1826
- configuration: {
1827
- [x: string]: any;
1828
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1829
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1830
- [x: string]: any;
1831
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1832
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1833
- [x: string]: any;
1834
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1835
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1836
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1837
- name: {
1838
- type: string;
1839
- defaultValue: string;
1840
- description: string;
1841
- };
1842
- assemblyNames: {
1843
- type: string;
1844
- defaultValue: never[];
1845
- description: string;
1846
- };
1847
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>;
1848
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1849
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1850
- } & {
1851
- afterAttach(): void;
1852
- addTrackConf(trackConf: Record<string, unknown> | ({
1853
- [x: string]: any;
1854
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1855
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1856
- [x: string]: any;
1857
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1858
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1859
- [x: string]: any;
1860
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1861
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1862
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
1863
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
1864
- [x: string]: any;
1865
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1866
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1867
- [x: string]: any;
1868
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1869
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1870
- [x: string]: any;
1871
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1872
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1873
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
1874
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
1875
- clear(): void;
1876
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1877
- name: import("mobx-state-tree").ISimpleType<string>;
1878
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
1879
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1880
- name: {
1881
- type: string;
1882
- defaultValue: string;
1883
- description: string;
1884
- };
1885
- assemblyNames: {
1886
- type: string;
1887
- defaultValue: never[];
1888
- description: string;
1889
- };
1890
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
1891
- }, {
1892
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1893
- } & {
1894
- afterAttach(): void;
1895
- addTrackConf(trackConf: Record<string, unknown> | ({
1896
- [x: string]: any;
1897
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1898
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1899
- [x: string]: any;
1900
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1901
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1902
- [x: string]: any;
1903
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1904
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1905
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
1906
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
1907
- [x: string]: any;
1908
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1909
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1910
- [x: string]: any;
1911
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1912
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1913
- [x: string]: any;
1914
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1915
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1916
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
1917
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
1918
- clear(): void;
1919
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1920
- prepareToBreakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): (Record<string, number> | (() => void))[] | undefined;
1921
- breakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1922
- deleteConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1923
- addConnectionConf(connectionConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1924
- clearConnections(): void;
1925
- } & {
1926
- queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, unknown][];
1927
- } & {
1928
- readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType | undefined;
1929
- readonly DialogProps: unknown;
1930
- } & {
1931
- removeActiveDialog(): void;
1932
- queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, unknown]): void;
1933
- } & {
1934
- getReferring(object: import("mobx-state-tree").IAnyStateTreeNode): import("@jbrowse/product-core").ReferringNode[];
1935
- } & {
1936
- removeReferring(referring: import("@jbrowse/product-core").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
1937
- } & {
1938
- readonly tracks: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1939
- } & {
1940
- addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfiguration): any;
1941
- deleteTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1942
- } & {
1943
- snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1944
- } & {
1945
- readonly snackbarMessageSet: Map<string, import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1946
- } & {
1947
- notify(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction): void;
1948
- notifyError(errorMessage: string, error?: unknown, extra?: unknown): void;
1949
- pushSnackbarMessage(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction): void;
1950
- popSnackbarMessage(): import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage | undefined;
1951
- removeSnackbarMessage(message: string): void;
1952
- } & {
1953
- task: undefined;
1954
- } & {
1955
- readonly version: any;
1956
- readonly assemblies: any[];
1957
- readonly assemblyNames: any[];
1958
- readonly connections: any;
1959
- readonly assemblyManager: any;
1960
- readonly views: any[];
1961
- renderProps(): {
1962
- theme: any;
1963
- highResolutionScaling: any;
1964
- };
1965
- } & {
1966
- addView(typeName: string, initialState?: {}): any;
1967
- removeView(): void;
1968
- } & {
1969
- getTrackActionMenuItems(config: any): {
1970
- label: string;
1971
- onClick: () => void;
1972
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
1973
- muiName: string;
1974
- };
1975
- }[];
1976
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
1977
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1978
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1979
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1980
- }, {
1981
- error: unknown;
1982
- loadingP: Promise<void> | undefined;
1983
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1984
- refNameAliases: {
1985
- [x: string]: string;
1986
- } | undefined;
1987
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1988
- } & {
1989
- getConf(arg: string): any;
1990
- readonly lowerCaseRefNameAliases: {
1991
- [k: string]: string;
1992
- } | undefined;
1993
- } & {
1994
- readonly initialized: boolean;
1995
- readonly name: string;
1996
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1997
- readonly aliases: string[];
1998
- readonly displayName: string;
1999
- hasName(name: string): boolean;
2000
- readonly allAliases: string[];
2001
- readonly allRefNames: string[] | undefined;
2002
- readonly lowerCaseRefNames: string[] | undefined;
2003
- readonly allRefNamesWithLowerCase: string[] | undefined;
2004
- readonly rpcManager: RpcManager;
2005
- readonly refNameColors: string[];
2006
- } & {
2007
- readonly refNames: string[] | undefined;
2008
- } & {
2009
- getCanonicalRefName(refName: string): string | undefined;
2010
- getCanonicalRefName2(asmName: string): string;
2011
- getRefNameColor(refName: string): string | undefined;
2012
- isValidRefName(refName: string): boolean;
2013
- } & {
2014
- setLoaded({ regions, refNameAliases, cytobands, }: {
2015
- regions: import("@jbrowse/core/util").Region[];
2016
- refNameAliases: {
2017
- [x: string]: string;
2018
- };
2019
- cytobands: import("@jbrowse/core/util").Feature[];
2020
- }): void;
2021
- setError(e: unknown): void;
2022
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2023
- setRefNameAliases(aliases: {
2024
- [x: string]: string;
2025
- }): void;
2026
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2027
- setLoadingP(p?: Promise<void>): void;
2028
- load(): Promise<void>;
2029
- loadPre(): Promise<void>;
2030
- } & {
2031
- getAdapterMapEntry(adapterConf: {
2032
- [x: string]: unknown;
2033
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2034
- getRefNameMapForAdapter(adapterConf: {
2035
- [x: string]: unknown;
2036
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2037
- [x: string]: string;
2038
- }>;
2039
- getReverseRefNameMapForAdapter(adapterConf: {
2040
- [x: string]: unknown;
2041
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2042
- [x: string]: string;
2043
- }>;
2044
- afterCreate(): void;
2045
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
2046
- }, {
2047
- readonly assemblyNameMap: Record<string, {
2048
- configuration: any;
2049
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2050
- error: unknown;
2051
- loadingP: Promise<void> | undefined;
2052
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2053
- refNameAliases: {
2054
- [x: string]: string;
2055
- } | undefined;
2056
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2057
- } & {
2058
- getConf(arg: string): any;
2059
- readonly lowerCaseRefNameAliases: {
2060
- [k: string]: string;
2061
- } | undefined;
2062
- } & {
2063
- readonly initialized: boolean;
2064
- readonly name: string;
2065
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2066
- readonly aliases: string[];
2067
- readonly displayName: string;
2068
- hasName(name: string): boolean;
2069
- readonly allAliases: string[];
2070
- readonly allRefNames: string[] | undefined;
2071
- readonly lowerCaseRefNames: string[] | undefined;
2072
- readonly allRefNamesWithLowerCase: string[] | undefined;
2073
- readonly rpcManager: RpcManager;
2074
- readonly refNameColors: string[];
2075
- } & {
2076
- readonly refNames: string[] | undefined;
2077
- } & {
2078
- getCanonicalRefName(refName: string): string | undefined;
2079
- getCanonicalRefName2(asmName: string): string;
2080
- getRefNameColor(refName: string): string | undefined;
2081
- isValidRefName(refName: string): boolean;
2082
- } & {
2083
- setLoaded({ regions, refNameAliases, cytobands, }: {
2084
- regions: import("@jbrowse/core/util").Region[];
2085
- refNameAliases: {
2086
- [x: string]: string;
2087
- };
2088
- cytobands: import("@jbrowse/core/util").Feature[];
2089
- }): void;
2090
- setError(e: unknown): void;
2091
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2092
- setRefNameAliases(aliases: {
2093
- [x: string]: string;
2094
- }): void;
2095
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2096
- setLoadingP(p?: Promise<void>): void;
2097
- load(): Promise<void>;
2098
- loadPre(): Promise<void>;
2099
- } & {
2100
- getAdapterMapEntry(adapterConf: {
2101
- [x: string]: unknown;
2102
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2103
- getRefNameMapForAdapter(adapterConf: {
2104
- [x: string]: unknown;
2105
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2106
- [x: string]: string;
2107
- }>;
2108
- getReverseRefNameMapForAdapter(adapterConf: {
2109
- [x: string]: unknown;
2110
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2111
- [x: string]: string;
2112
- }>;
2113
- afterCreate(): void;
2114
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2115
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2116
- }, {
2117
- error: unknown;
2118
- loadingP: Promise<void> | undefined;
2119
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2120
- refNameAliases: {
2121
- [x: string]: string;
2122
- } | undefined;
2123
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2124
- } & {
2125
- getConf(arg: string): any;
2126
- readonly lowerCaseRefNameAliases: {
2127
- [k: string]: string;
2128
- } | undefined;
2129
- } & {
2130
- readonly initialized: boolean;
2131
- readonly name: string;
2132
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2133
- readonly aliases: string[];
2134
- readonly displayName: string;
2135
- hasName(name: string): boolean;
2136
- readonly allAliases: string[];
2137
- readonly allRefNames: string[] | undefined;
2138
- readonly lowerCaseRefNames: string[] | undefined;
2139
- readonly allRefNamesWithLowerCase: string[] | undefined;
2140
- readonly rpcManager: RpcManager;
2141
- readonly refNameColors: string[];
2142
- } & {
2143
- readonly refNames: string[] | undefined;
2144
- } & {
2145
- getCanonicalRefName(refName: string): string | undefined;
2146
- getCanonicalRefName2(asmName: string): string;
2147
- getRefNameColor(refName: string): string | undefined;
2148
- isValidRefName(refName: string): boolean;
2149
- } & {
2150
- setLoaded({ regions, refNameAliases, cytobands, }: {
2151
- regions: import("@jbrowse/core/util").Region[];
2152
- refNameAliases: {
2153
- [x: string]: string;
2154
- };
2155
- cytobands: import("@jbrowse/core/util").Feature[];
2156
- }): void;
2157
- setError(e: unknown): void;
2158
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2159
- setRefNameAliases(aliases: {
2160
- [x: string]: string;
2161
- }): void;
2162
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2163
- setLoadingP(p?: Promise<void>): void;
2164
- load(): Promise<void>;
2165
- loadPre(): Promise<void>;
2166
- } & {
2167
- getAdapterMapEntry(adapterConf: {
2168
- [x: string]: unknown;
2169
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2170
- getRefNameMapForAdapter(adapterConf: {
2171
- [x: string]: unknown;
2172
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2173
- [x: string]: string;
2174
- }>;
2175
- getReverseRefNameMapForAdapter(adapterConf: {
2176
- [x: string]: unknown;
2177
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2178
- [x: string]: string;
2179
- }>;
2180
- afterCreate(): void;
2181
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
2182
- } & {
2183
- getCanonicalAssemblyName(asmName: string): string | undefined;
2184
- getCanonicalAssemblyName2(asmName: string): string;
2185
- get(asmName: string): ({
2186
- configuration: any;
2187
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2188
- error: unknown;
2189
- loadingP: Promise<void> | undefined;
2190
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2191
- refNameAliases: {
2192
- [x: string]: string;
2193
- } | undefined;
2194
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2195
- } & {
2196
- getConf(arg: string): any;
2197
- readonly lowerCaseRefNameAliases: {
2198
- [k: string]: string;
2199
- } | undefined;
2200
- } & {
2201
- readonly initialized: boolean;
2202
- readonly name: string;
2203
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2204
- readonly aliases: string[];
2205
- readonly displayName: string;
2206
- hasName(name: string): boolean;
2207
- readonly allAliases: string[];
2208
- readonly allRefNames: string[] | undefined;
2209
- readonly lowerCaseRefNames: string[] | undefined;
2210
- readonly allRefNamesWithLowerCase: string[] | undefined;
2211
- readonly rpcManager: RpcManager;
2212
- readonly refNameColors: string[];
2213
- } & {
2214
- readonly refNames: string[] | undefined;
2215
- } & {
2216
- getCanonicalRefName(refName: string): string | undefined;
2217
- getCanonicalRefName2(asmName: string): string;
2218
- getRefNameColor(refName: string): string | undefined;
2219
- isValidRefName(refName: string): boolean;
2220
- } & {
2221
- setLoaded({ regions, refNameAliases, cytobands, }: {
2222
- regions: import("@jbrowse/core/util").Region[];
2223
- refNameAliases: {
2224
- [x: string]: string;
2225
- };
2226
- cytobands: import("@jbrowse/core/util").Feature[];
2227
- }): void;
2228
- setError(e: unknown): void;
2229
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2230
- setRefNameAliases(aliases: {
2231
- [x: string]: string;
2232
- }): void;
2233
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2234
- setLoadingP(p?: Promise<void>): void;
2235
- load(): Promise<void>;
2236
- loadPre(): Promise<void>;
2237
- } & {
2238
- getAdapterMapEntry(adapterConf: {
2239
- [x: string]: unknown;
2240
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2241
- getRefNameMapForAdapter(adapterConf: {
2242
- [x: string]: unknown;
2243
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2244
- [x: string]: string;
2245
- }>;
2246
- getReverseRefNameMapForAdapter(adapterConf: {
2247
- [x: string]: unknown;
2248
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2249
- [x: string]: string;
2250
- }>;
2251
- afterCreate(): void;
2252
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2253
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2254
- }, {
2255
- error: unknown;
2256
- loadingP: Promise<void> | undefined;
2257
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2258
- refNameAliases: {
2259
- [x: string]: string;
2260
- } | undefined;
2261
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2262
- } & {
2263
- getConf(arg: string): any;
2264
- readonly lowerCaseRefNameAliases: {
2265
- [k: string]: string;
2266
- } | undefined;
2267
- } & {
2268
- readonly initialized: boolean;
2269
- readonly name: string;
2270
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2271
- readonly aliases: string[];
2272
- readonly displayName: string;
2273
- hasName(name: string): boolean;
2274
- readonly allAliases: string[];
2275
- readonly allRefNames: string[] | undefined;
2276
- readonly lowerCaseRefNames: string[] | undefined;
2277
- readonly allRefNamesWithLowerCase: string[] | undefined;
2278
- readonly rpcManager: RpcManager;
2279
- readonly refNameColors: string[];
2280
- } & {
2281
- readonly refNames: string[] | undefined;
2282
- } & {
2283
- getCanonicalRefName(refName: string): string | undefined;
2284
- getCanonicalRefName2(asmName: string): string;
2285
- getRefNameColor(refName: string): string | undefined;
2286
- isValidRefName(refName: string): boolean;
2287
- } & {
2288
- setLoaded({ regions, refNameAliases, cytobands, }: {
2289
- regions: import("@jbrowse/core/util").Region[];
2290
- refNameAliases: {
2291
- [x: string]: string;
2292
- };
2293
- cytobands: import("@jbrowse/core/util").Feature[];
2294
- }): void;
2295
- setError(e: unknown): void;
2296
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2297
- setRefNameAliases(aliases: {
2298
- [x: string]: string;
2299
- }): void;
2300
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2301
- setLoadingP(p?: Promise<void>): void;
2302
- load(): Promise<void>;
2303
- loadPre(): Promise<void>;
2304
- } & {
2305
- getAdapterMapEntry(adapterConf: {
2306
- [x: string]: unknown;
2307
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2308
- getRefNameMapForAdapter(adapterConf: {
2309
- [x: string]: unknown;
2310
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2311
- [x: string]: string;
2312
- }>;
2313
- getReverseRefNameMapForAdapter(adapterConf: {
2314
- [x: string]: unknown;
2315
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2316
- [x: string]: string;
2317
- }>;
2318
- afterCreate(): void;
2319
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
2320
- readonly assemblyNamesList: any[];
2321
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
2322
- readonly rpcManager: RpcManager;
2323
- } & {
2324
- waitForAssembly(assemblyName: string): Promise<({
2325
- configuration: any;
2326
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2327
- error: unknown;
2328
- loadingP: Promise<void> | undefined;
2329
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2330
- refNameAliases: {
2331
- [x: string]: string;
2332
- } | undefined;
2333
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2334
- } & {
2335
- getConf(arg: string): any;
2336
- readonly lowerCaseRefNameAliases: {
2337
- [k: string]: string;
2338
- } | undefined;
2339
- } & {
2340
- readonly initialized: boolean;
2341
- readonly name: string;
2342
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2343
- readonly aliases: string[];
2344
- readonly displayName: string;
2345
- hasName(name: string): boolean;
2346
- readonly allAliases: string[];
2347
- readonly allRefNames: string[] | undefined;
2348
- readonly lowerCaseRefNames: string[] | undefined;
2349
- readonly allRefNamesWithLowerCase: string[] | undefined;
2350
- readonly rpcManager: RpcManager;
2351
- readonly refNameColors: string[];
2352
- } & {
2353
- readonly refNames: string[] | undefined;
2354
- } & {
2355
- getCanonicalRefName(refName: string): string | undefined;
2356
- getCanonicalRefName2(asmName: string): string;
2357
- getRefNameColor(refName: string): string | undefined;
2358
- isValidRefName(refName: string): boolean;
2359
- } & {
2360
- setLoaded({ regions, refNameAliases, cytobands, }: {
2361
- regions: import("@jbrowse/core/util").Region[];
2362
- refNameAliases: {
2363
- [x: string]: string;
2364
- };
2365
- cytobands: import("@jbrowse/core/util").Feature[];
2366
- }): void;
2367
- setError(e: unknown): void;
2368
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2369
- setRefNameAliases(aliases: {
2370
- [x: string]: string;
2371
- }): void;
2372
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2373
- setLoadingP(p?: Promise<void>): void;
2374
- load(): Promise<void>;
2375
- loadPre(): Promise<void>;
2376
- } & {
2377
- getAdapterMapEntry(adapterConf: {
2378
- [x: string]: unknown;
2379
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2380
- getRefNameMapForAdapter(adapterConf: {
2381
- [x: string]: unknown;
2382
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2383
- [x: string]: string;
2384
- }>;
2385
- getReverseRefNameMapForAdapter(adapterConf: {
2386
- [x: string]: unknown;
2387
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2388
- [x: string]: string;
2389
- }>;
2390
- afterCreate(): void;
2391
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2392
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2393
- }, {
2394
- error: unknown;
2395
- loadingP: Promise<void> | undefined;
2396
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2397
- refNameAliases: {
2398
- [x: string]: string;
2399
- } | undefined;
2400
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2401
- } & {
2402
- getConf(arg: string): any;
2403
- readonly lowerCaseRefNameAliases: {
2404
- [k: string]: string;
2405
- } | undefined;
2406
- } & {
2407
- readonly initialized: boolean;
2408
- readonly name: string;
2409
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2410
- readonly aliases: string[];
2411
- readonly displayName: string;
2412
- hasName(name: string): boolean;
2413
- readonly allAliases: string[];
2414
- readonly allRefNames: string[] | undefined;
2415
- readonly lowerCaseRefNames: string[] | undefined;
2416
- readonly allRefNamesWithLowerCase: string[] | undefined;
2417
- readonly rpcManager: RpcManager;
2418
- readonly refNameColors: string[];
2419
- } & {
2420
- readonly refNames: string[] | undefined;
2421
- } & {
2422
- getCanonicalRefName(refName: string): string | undefined;
2423
- getCanonicalRefName2(asmName: string): string;
2424
- getRefNameColor(refName: string): string | undefined;
2425
- isValidRefName(refName: string): boolean;
2426
- } & {
2427
- setLoaded({ regions, refNameAliases, cytobands, }: {
2428
- regions: import("@jbrowse/core/util").Region[];
2429
- refNameAliases: {
2430
- [x: string]: string;
2431
- };
2432
- cytobands: import("@jbrowse/core/util").Feature[];
2433
- }): void;
2434
- setError(e: unknown): void;
2435
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2436
- setRefNameAliases(aliases: {
2437
- [x: string]: string;
2438
- }): void;
2439
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2440
- setLoadingP(p?: Promise<void>): void;
2441
- load(): Promise<void>;
2442
- loadPre(): Promise<void>;
2443
- } & {
2444
- getAdapterMapEntry(adapterConf: {
2445
- [x: string]: unknown;
2446
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2447
- getRefNameMapForAdapter(adapterConf: {
2448
- [x: string]: unknown;
2449
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2450
- [x: string]: string;
2451
- }>;
2452
- getReverseRefNameMapForAdapter(adapterConf: {
2453
- [x: string]: unknown;
2454
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2455
- [x: string]: string;
2456
- }>;
2457
- afterCreate(): void;
2458
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
2459
- getRefNameMapForAdapter(adapterConf: {
2460
- [x: string]: unknown;
2461
- }, assemblyName: string | undefined, opts: {
2462
- stopToken?: string;
2463
- sessionId: string;
2464
- }): Promise<{
2465
- [x: string]: string;
2466
- } | undefined>;
2467
- getReverseRefNameMapForAdapter(adapterConf: {
2468
- [x: string]: unknown;
2469
- }, assemblyName: string | undefined, opts: {
2470
- stopToken?: string;
2471
- sessionId: string;
2472
- }): Promise<{
2473
- [x: string]: string;
2474
- } | undefined>;
2475
- isValidRefName(refName: string, assemblyName: string): boolean;
2476
- } & {
2477
- afterAttach(): void;
2478
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
2479
- addAssembly(configuration: any): void;
2480
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
2481
- internetAccounts: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
2482
- }, {
2483
- error: unknown;
2484
- adminMode: boolean;
2485
- version: string;
2486
- rpcManager: RpcManager;
2487
- textSearchManager: TextSearchManager;
2488
- } & {
2489
- setSession(sessionSnapshot: SnapshotIn<import("mobx-state-tree").IModelType<{
2490
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2491
- name: import("mobx-state-tree").ISimpleType<string>;
2492
- margin: import("mobx-state-tree").IType<number | undefined, number, number>;
2493
- } & {
2494
- drawerPosition: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2495
- drawerWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
2496
- widgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyType>;
2497
- activeWidgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>>;
2498
- minimized: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2499
- } & {
2500
- connectionInstances: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
2501
- name: import("mobx-state-tree").ISimpleType<string>;
2502
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
2503
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2504
- name: {
2505
- type: string;
2506
- defaultValue: string;
2507
- description: string;
2508
- };
2509
- assemblyNames: {
2510
- type: string;
2511
- defaultValue: never[];
2512
- description: string;
2513
- };
2514
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
2515
- }, {
2516
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
2517
- } & {
2518
- afterAttach(): void;
2519
- addTrackConf(trackConf: Record<string, unknown> | ({
2520
- [x: string]: any;
2521
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2522
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
2523
- [x: string]: any;
2524
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2525
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
2526
- [x: string]: any;
2527
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
2528
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
2529
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
2530
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
2531
- [x: string]: any;
2532
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2533
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
2534
- [x: string]: any;
2535
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2536
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
2537
- [x: string]: any;
2538
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
2539
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
2540
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
2541
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
2542
- clear(): void;
2543
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
2544
- } & {
2545
- view: import("mobx-state-tree").IAnyModelType;
2546
- }, {
2547
- selection: unknown;
2548
- hovered: unknown;
2549
- } & {
2550
- readonly root: {
2551
- jbrowse: any;
2552
- session: any;
2553
- sessionPath: string;
2554
- assemblyManager: {
2555
- assemblies: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
2556
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2557
- }, {
2558
- error: unknown;
2559
- loadingP: Promise<void> | undefined;
2560
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2561
- refNameAliases: {
2562
- [x: string]: string;
2563
- } | undefined;
2564
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2565
- } & {
2566
- getConf(arg: string): any;
2567
- readonly lowerCaseRefNameAliases: {
2568
- [k: string]: string;
2569
- } | undefined;
2570
- } & {
2571
- readonly initialized: boolean;
2572
- readonly name: string;
2573
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2574
- readonly aliases: string[];
2575
- readonly displayName: string;
2576
- hasName(name: string): boolean;
2577
- readonly allAliases: string[];
2578
- readonly allRefNames: string[] | undefined;
2579
- readonly lowerCaseRefNames: string[] | undefined;
2580
- readonly allRefNamesWithLowerCase: string[] | undefined;
2581
- readonly rpcManager: RpcManager;
2582
- readonly refNameColors: string[];
2583
- } & {
2584
- readonly refNames: string[] | undefined;
2585
- } & {
2586
- getCanonicalRefName(refName: string): string | undefined;
2587
- getCanonicalRefName2(asmName: string): string;
2588
- getRefNameColor(refName: string): string | undefined;
2589
- isValidRefName(refName: string): boolean;
2590
- } & {
2591
- setLoaded({ regions, refNameAliases, cytobands, }: {
2592
- regions: import("@jbrowse/core/util").Region[];
2593
- refNameAliases: {
2594
- [x: string]: string;
2595
- };
2596
- cytobands: import("@jbrowse/core/util").Feature[];
2597
- }): void;
2598
- setError(e: unknown): void;
2599
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2600
- setRefNameAliases(aliases: {
2601
- [x: string]: string;
2602
- }): void;
2603
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2604
- setLoadingP(p?: Promise<void>): void;
2605
- load(): Promise<void>;
2606
- loadPre(): Promise<void>;
2607
- } & {
2608
- getAdapterMapEntry(adapterConf: {
2609
- [x: string]: unknown;
2610
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2611
- getRefNameMapForAdapter(adapterConf: {
2612
- [x: string]: unknown;
2613
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2614
- [x: string]: string;
2615
- }>;
2616
- getReverseRefNameMapForAdapter(adapterConf: {
2617
- [x: string]: unknown;
2618
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2619
- [x: string]: string;
2620
- }>;
2621
- afterCreate(): void;
2622
- }, 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<{
2623
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2624
- }, {
2625
- error: unknown;
2626
- loadingP: Promise<void> | undefined;
2627
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2628
- refNameAliases: {
2629
- [x: string]: string;
2630
- } | undefined;
2631
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2632
- } & {
2633
- getConf(arg: string): any;
2634
- readonly lowerCaseRefNameAliases: {
2635
- [k: string]: string;
2636
- } | undefined;
2637
- } & {
2638
- readonly initialized: boolean;
2639
- readonly name: string;
2640
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2641
- readonly aliases: string[];
2642
- readonly displayName: string;
2643
- hasName(name: string): boolean;
2644
- readonly allAliases: string[];
2645
- readonly allRefNames: string[] | undefined;
2646
- readonly lowerCaseRefNames: string[] | undefined;
2647
- readonly allRefNamesWithLowerCase: string[] | undefined;
2648
- readonly rpcManager: RpcManager;
2649
- readonly refNameColors: string[];
2650
- } & {
2651
- readonly refNames: string[] | undefined;
2652
- } & {
2653
- getCanonicalRefName(refName: string): string | undefined;
2654
- getCanonicalRefName2(asmName: string): string;
2655
- getRefNameColor(refName: string): string | undefined;
2656
- isValidRefName(refName: string): boolean;
2657
- } & {
2658
- setLoaded({ regions, refNameAliases, cytobands, }: {
2659
- regions: import("@jbrowse/core/util").Region[];
2660
- refNameAliases: {
2661
- [x: string]: string;
2662
- };
2663
- cytobands: import("@jbrowse/core/util").Feature[];
2664
- }): void;
2665
- setError(e: unknown): void;
2666
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2667
- setRefNameAliases(aliases: {
2668
- [x: string]: string;
2669
- }): void;
2670
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2671
- setLoadingP(p?: Promise<void>): void;
2672
- load(): Promise<void>;
2673
- loadPre(): Promise<void>;
2674
- } & {
2675
- getAdapterMapEntry(adapterConf: {
2676
- [x: string]: unknown;
2677
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2678
- getRefNameMapForAdapter(adapterConf: {
2679
- [x: string]: unknown;
2680
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2681
- [x: string]: string;
2682
- }>;
2683
- getReverseRefNameMapForAdapter(adapterConf: {
2684
- [x: string]: unknown;
2685
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2686
- [x: string]: string;
2687
- }>;
2688
- afterCreate(): void;
2689
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
2690
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2691
- readonly assemblyNameMap: Record<string, {
2692
- configuration: any;
2693
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2694
- error: unknown;
2695
- loadingP: Promise<void> | undefined;
2696
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2697
- refNameAliases: {
2698
- [x: string]: string;
2699
- } | undefined;
2700
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2701
- } & {
2702
- getConf(arg: string): any;
2703
- readonly lowerCaseRefNameAliases: {
2704
- [k: string]: string;
2705
- } | undefined;
2706
- } & {
2707
- readonly initialized: boolean;
2708
- readonly name: string;
2709
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2710
- readonly aliases: string[];
2711
- readonly displayName: string;
2712
- hasName(name: string): boolean;
2713
- readonly allAliases: string[];
2714
- readonly allRefNames: string[] | undefined;
2715
- readonly lowerCaseRefNames: string[] | undefined;
2716
- readonly allRefNamesWithLowerCase: string[] | undefined;
2717
- readonly rpcManager: RpcManager;
2718
- readonly refNameColors: string[];
2719
- } & {
2720
- readonly refNames: string[] | undefined;
2721
- } & {
2722
- getCanonicalRefName(refName: string): string | undefined;
2723
- getCanonicalRefName2(asmName: string): string;
2724
- getRefNameColor(refName: string): string | undefined;
2725
- isValidRefName(refName: string): boolean;
2726
- } & {
2727
- setLoaded({ regions, refNameAliases, cytobands, }: {
2728
- regions: import("@jbrowse/core/util").Region[];
2729
- refNameAliases: {
2730
- [x: string]: string;
2731
- };
2732
- cytobands: import("@jbrowse/core/util").Feature[];
2733
- }): void;
2734
- setError(e: unknown): void;
2735
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2736
- setRefNameAliases(aliases: {
2737
- [x: string]: string;
2738
- }): void;
2739
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2740
- setLoadingP(p?: Promise<void>): void;
2741
- load(): Promise<void>;
2742
- loadPre(): Promise<void>;
2743
- } & {
2744
- getAdapterMapEntry(adapterConf: {
2745
- [x: string]: unknown;
2746
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2747
- getRefNameMapForAdapter(adapterConf: {
2748
- [x: string]: unknown;
2749
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2750
- [x: string]: string;
2751
- }>;
2752
- getReverseRefNameMapForAdapter(adapterConf: {
2753
- [x: string]: unknown;
2754
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2755
- [x: string]: string;
2756
- }>;
2757
- afterCreate(): void;
2758
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2759
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2760
- }, {
2761
- error: unknown;
2762
- loadingP: Promise<void> | undefined;
2763
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2764
- refNameAliases: {
2765
- [x: string]: string;
2766
- } | undefined;
2767
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2768
- } & {
2769
- getConf(arg: string): any;
2770
- readonly lowerCaseRefNameAliases: {
2771
- [k: string]: string;
2772
- } | undefined;
2773
- } & {
2774
- readonly initialized: boolean;
2775
- readonly name: string;
2776
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2777
- readonly aliases: string[];
2778
- readonly displayName: string;
2779
- hasName(name: string): boolean;
2780
- readonly allAliases: string[];
2781
- readonly allRefNames: string[] | undefined;
2782
- readonly lowerCaseRefNames: string[] | undefined;
2783
- readonly allRefNamesWithLowerCase: string[] | undefined;
2784
- readonly rpcManager: RpcManager;
2785
- readonly refNameColors: string[];
2786
- } & {
2787
- readonly refNames: string[] | undefined;
2788
- } & {
2789
- getCanonicalRefName(refName: string): string | undefined;
2790
- getCanonicalRefName2(asmName: string): string;
2791
- getRefNameColor(refName: string): string | undefined;
2792
- isValidRefName(refName: string): boolean;
2793
- } & {
2794
- setLoaded({ regions, refNameAliases, cytobands, }: {
2795
- regions: import("@jbrowse/core/util").Region[];
2796
- refNameAliases: {
2797
- [x: string]: string;
2798
- };
2799
- cytobands: import("@jbrowse/core/util").Feature[];
2800
- }): void;
2801
- setError(e: unknown): void;
2802
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2803
- setRefNameAliases(aliases: {
2804
- [x: string]: string;
2805
- }): void;
2806
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2807
- setLoadingP(p?: Promise<void>): void;
2808
- load(): Promise<void>;
2809
- loadPre(): Promise<void>;
2810
- } & {
2811
- getAdapterMapEntry(adapterConf: {
2812
- [x: string]: unknown;
2813
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2814
- getRefNameMapForAdapter(adapterConf: {
2815
- [x: string]: unknown;
2816
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2817
- [x: string]: string;
2818
- }>;
2819
- getReverseRefNameMapForAdapter(adapterConf: {
2820
- [x: string]: unknown;
2821
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2822
- [x: string]: string;
2823
- }>;
2824
- afterCreate(): void;
2825
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
2826
- } & {
2827
- getCanonicalAssemblyName(asmName: string): string | undefined;
2828
- getCanonicalAssemblyName2(asmName: string): string;
2829
- get(asmName: string): ({
2830
- configuration: any;
2831
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2832
- error: unknown;
2833
- loadingP: Promise<void> | undefined;
2834
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2835
- refNameAliases: {
2836
- [x: string]: string;
2837
- } | undefined;
2838
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2839
- } & {
2840
- getConf(arg: string): any;
2841
- readonly lowerCaseRefNameAliases: {
2842
- [k: string]: string;
2843
- } | undefined;
2844
- } & {
2845
- readonly initialized: boolean;
2846
- readonly name: string;
2847
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2848
- readonly aliases: string[];
2849
- readonly displayName: string;
2850
- hasName(name: string): boolean;
2851
- readonly allAliases: string[];
2852
- readonly allRefNames: string[] | undefined;
2853
- readonly lowerCaseRefNames: string[] | undefined;
2854
- readonly allRefNamesWithLowerCase: string[] | undefined;
2855
- readonly rpcManager: RpcManager;
2856
- readonly refNameColors: string[];
2857
- } & {
2858
- readonly refNames: string[] | undefined;
2859
- } & {
2860
- getCanonicalRefName(refName: string): string | undefined;
2861
- getCanonicalRefName2(asmName: string): string;
2862
- getRefNameColor(refName: string): string | undefined;
2863
- isValidRefName(refName: string): boolean;
2864
- } & {
2865
- setLoaded({ regions, refNameAliases, cytobands, }: {
2866
- regions: import("@jbrowse/core/util").Region[];
2867
- refNameAliases: {
2868
- [x: string]: string;
2869
- };
2870
- cytobands: import("@jbrowse/core/util").Feature[];
2871
- }): void;
2872
- setError(e: unknown): void;
2873
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2874
- setRefNameAliases(aliases: {
2875
- [x: string]: string;
2876
- }): void;
2877
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2878
- setLoadingP(p?: Promise<void>): void;
2879
- load(): Promise<void>;
2880
- loadPre(): Promise<void>;
2881
- } & {
2882
- getAdapterMapEntry(adapterConf: {
2883
- [x: string]: unknown;
2884
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2885
- getRefNameMapForAdapter(adapterConf: {
2886
- [x: string]: unknown;
2887
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2888
- [x: string]: string;
2889
- }>;
2890
- getReverseRefNameMapForAdapter(adapterConf: {
2891
- [x: string]: unknown;
2892
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2893
- [x: string]: string;
2894
- }>;
2895
- afterCreate(): void;
2896
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2897
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
2898
- }, {
2899
- error: unknown;
2900
- loadingP: Promise<void> | undefined;
2901
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2902
- refNameAliases: {
2903
- [x: string]: string;
2904
- } | undefined;
2905
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2906
- } & {
2907
- getConf(arg: string): any;
2908
- readonly lowerCaseRefNameAliases: {
2909
- [k: string]: string;
2910
- } | undefined;
2911
- } & {
2912
- readonly initialized: boolean;
2913
- readonly name: string;
2914
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2915
- readonly aliases: string[];
2916
- readonly displayName: string;
2917
- hasName(name: string): boolean;
2918
- readonly allAliases: string[];
2919
- readonly allRefNames: string[] | undefined;
2920
- readonly lowerCaseRefNames: string[] | undefined;
2921
- readonly allRefNamesWithLowerCase: string[] | undefined;
2922
- readonly rpcManager: RpcManager;
2923
- readonly refNameColors: string[];
2924
- } & {
2925
- readonly refNames: string[] | undefined;
2926
- } & {
2927
- getCanonicalRefName(refName: string): string | undefined;
2928
- getCanonicalRefName2(asmName: string): string;
2929
- getRefNameColor(refName: string): string | undefined;
2930
- isValidRefName(refName: string): boolean;
2931
- } & {
2932
- setLoaded({ regions, refNameAliases, cytobands, }: {
2933
- regions: import("@jbrowse/core/util").Region[];
2934
- refNameAliases: {
2935
- [x: string]: string;
2936
- };
2937
- cytobands: import("@jbrowse/core/util").Feature[];
2938
- }): void;
2939
- setError(e: unknown): void;
2940
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
2941
- setRefNameAliases(aliases: {
2942
- [x: string]: string;
2943
- }): void;
2944
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
2945
- setLoadingP(p?: Promise<void>): void;
2946
- load(): Promise<void>;
2947
- loadPre(): Promise<void>;
2948
- } & {
2949
- getAdapterMapEntry(adapterConf: {
2950
- [x: string]: unknown;
2951
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
2952
- getRefNameMapForAdapter(adapterConf: {
2953
- [x: string]: unknown;
2954
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2955
- [x: string]: string;
2956
- }>;
2957
- getReverseRefNameMapForAdapter(adapterConf: {
2958
- [x: string]: unknown;
2959
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
2960
- [x: string]: string;
2961
- }>;
2962
- afterCreate(): void;
2963
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
2964
- readonly assemblyNamesList: any[];
2965
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
2966
- readonly rpcManager: RpcManager;
2967
- } & {
2968
- waitForAssembly(assemblyName: string): Promise<({
2969
- configuration: any;
2970
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2971
- error: unknown;
2972
- loadingP: Promise<void> | undefined;
2973
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2974
- refNameAliases: {
2975
- [x: string]: string;
2976
- } | undefined;
2977
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
2978
- } & {
2979
- getConf(arg: string): any;
2980
- readonly lowerCaseRefNameAliases: {
2981
- [k: string]: string;
2982
- } | undefined;
2983
- } & {
2984
- readonly initialized: boolean;
2985
- readonly name: string;
2986
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
2987
- readonly aliases: string[];
2988
- readonly displayName: string;
2989
- hasName(name: string): boolean;
2990
- readonly allAliases: string[];
2991
- readonly allRefNames: string[] | undefined;
2992
- readonly lowerCaseRefNames: string[] | undefined;
2993
- readonly allRefNamesWithLowerCase: string[] | undefined;
2994
- readonly rpcManager: RpcManager;
2995
- readonly refNameColors: string[];
2996
- } & {
2997
- readonly refNames: string[] | undefined;
2998
- } & {
2999
- getCanonicalRefName(refName: string): string | undefined;
3000
- getCanonicalRefName2(asmName: string): string;
3001
- getRefNameColor(refName: string): string | undefined;
3002
- isValidRefName(refName: string): boolean;
3003
- } & {
3004
- setLoaded({ regions, refNameAliases, cytobands, }: {
3005
- regions: import("@jbrowse/core/util").Region[];
3006
- refNameAliases: {
3007
- [x: string]: string;
3008
- };
3009
- cytobands: import("@jbrowse/core/util").Feature[];
3010
- }): void;
3011
- setError(e: unknown): void;
3012
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3013
- setRefNameAliases(aliases: {
3014
- [x: string]: string;
3015
- }): void;
3016
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3017
- setLoadingP(p?: Promise<void>): void;
3018
- load(): Promise<void>;
3019
- loadPre(): Promise<void>;
3020
- } & {
3021
- getAdapterMapEntry(adapterConf: {
3022
- [x: string]: unknown;
3023
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3024
- getRefNameMapForAdapter(adapterConf: {
3025
- [x: string]: unknown;
3026
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3027
- [x: string]: string;
3028
- }>;
3029
- getReverseRefNameMapForAdapter(adapterConf: {
3030
- [x: string]: unknown;
3031
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3032
- [x: string]: string;
3033
- }>;
3034
- afterCreate(): void;
3035
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
3036
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3037
- }, {
3038
- error: unknown;
3039
- loadingP: Promise<void> | undefined;
3040
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3041
- refNameAliases: {
3042
- [x: string]: string;
3043
- } | undefined;
3044
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3045
- } & {
3046
- getConf(arg: string): any;
3047
- readonly lowerCaseRefNameAliases: {
3048
- [k: string]: string;
3049
- } | undefined;
3050
- } & {
3051
- readonly initialized: boolean;
3052
- readonly name: string;
3053
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3054
- readonly aliases: string[];
3055
- readonly displayName: string;
3056
- hasName(name: string): boolean;
3057
- readonly allAliases: string[];
3058
- readonly allRefNames: string[] | undefined;
3059
- readonly lowerCaseRefNames: string[] | undefined;
3060
- readonly allRefNamesWithLowerCase: string[] | undefined;
3061
- readonly rpcManager: RpcManager;
3062
- readonly refNameColors: string[];
3063
- } & {
3064
- readonly refNames: string[] | undefined;
3065
- } & {
3066
- getCanonicalRefName(refName: string): string | undefined;
3067
- getCanonicalRefName2(asmName: string): string;
3068
- getRefNameColor(refName: string): string | undefined;
3069
- isValidRefName(refName: string): boolean;
3070
- } & {
3071
- setLoaded({ regions, refNameAliases, cytobands, }: {
3072
- regions: import("@jbrowse/core/util").Region[];
3073
- refNameAliases: {
3074
- [x: string]: string;
3075
- };
3076
- cytobands: import("@jbrowse/core/util").Feature[];
3077
- }): void;
3078
- setError(e: unknown): void;
3079
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3080
- setRefNameAliases(aliases: {
3081
- [x: string]: string;
3082
- }): void;
3083
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3084
- setLoadingP(p?: Promise<void>): void;
3085
- load(): Promise<void>;
3086
- loadPre(): Promise<void>;
3087
- } & {
3088
- getAdapterMapEntry(adapterConf: {
3089
- [x: string]: unknown;
3090
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3091
- getRefNameMapForAdapter(adapterConf: {
3092
- [x: string]: unknown;
3093
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3094
- [x: string]: string;
3095
- }>;
3096
- getReverseRefNameMapForAdapter(adapterConf: {
3097
- [x: string]: unknown;
3098
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3099
- [x: string]: string;
3100
- }>;
3101
- afterCreate(): void;
3102
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
3103
- getRefNameMapForAdapter(adapterConf: {
3104
- [x: string]: unknown;
3105
- }, assemblyName: string | undefined, opts: {
3106
- stopToken?: string;
3107
- sessionId: string;
3108
- }): Promise<{
3109
- [x: string]: string;
3110
- } | undefined>;
3111
- getReverseRefNameMapForAdapter(adapterConf: {
3112
- [x: string]: unknown;
3113
- }, assemblyName: string | undefined, opts: {
3114
- stopToken?: string;
3115
- sessionId: string;
3116
- }): Promise<{
3117
- [x: string]: string;
3118
- } | undefined>;
3119
- isValidRefName(refName: string, assemblyName: string): boolean;
3120
- } & {
3121
- afterAttach(): void;
3122
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
3123
- addAssembly(configuration: any): void;
3124
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
3125
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
3126
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3127
- }, {
3128
- error: unknown;
3129
- loadingP: Promise<void> | undefined;
3130
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3131
- refNameAliases: {
3132
- [x: string]: string;
3133
- } | undefined;
3134
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3135
- } & {
3136
- getConf(arg: string): any;
3137
- readonly lowerCaseRefNameAliases: {
3138
- [k: string]: string;
3139
- } | undefined;
3140
- } & {
3141
- readonly initialized: boolean;
3142
- readonly name: string;
3143
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3144
- readonly aliases: string[];
3145
- readonly displayName: string;
3146
- hasName(name: string): boolean;
3147
- readonly allAliases: string[];
3148
- readonly allRefNames: string[] | undefined;
3149
- readonly lowerCaseRefNames: string[] | undefined;
3150
- readonly allRefNamesWithLowerCase: string[] | undefined;
3151
- readonly rpcManager: RpcManager;
3152
- readonly refNameColors: string[];
3153
- } & {
3154
- readonly refNames: string[] | undefined;
3155
- } & {
3156
- getCanonicalRefName(refName: string): string | undefined;
3157
- getCanonicalRefName2(asmName: string): string;
3158
- getRefNameColor(refName: string): string | undefined;
3159
- isValidRefName(refName: string): boolean;
3160
- } & {
3161
- setLoaded({ regions, refNameAliases, cytobands, }: {
3162
- regions: import("@jbrowse/core/util").Region[];
3163
- refNameAliases: {
3164
- [x: string]: string;
3165
- };
3166
- cytobands: import("@jbrowse/core/util").Feature[];
3167
- }): void;
3168
- setError(e: unknown): void;
3169
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3170
- setRefNameAliases(aliases: {
3171
- [x: string]: string;
3172
- }): void;
3173
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3174
- setLoadingP(p?: Promise<void>): void;
3175
- load(): Promise<void>;
3176
- loadPre(): Promise<void>;
3177
- } & {
3178
- getAdapterMapEntry(adapterConf: {
3179
- [x: string]: unknown;
3180
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3181
- getRefNameMapForAdapter(adapterConf: {
3182
- [x: string]: unknown;
3183
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3184
- [x: string]: string;
3185
- }>;
3186
- getReverseRefNameMapForAdapter(adapterConf: {
3187
- [x: string]: unknown;
3188
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3189
- [x: string]: string;
3190
- }>;
3191
- afterCreate(): void;
3192
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
3193
- }, {
3194
- readonly assemblyNameMap: Record<string, {
3195
- configuration: any;
3196
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3197
- error: unknown;
3198
- loadingP: Promise<void> | undefined;
3199
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3200
- refNameAliases: {
3201
- [x: string]: string;
3202
- } | undefined;
3203
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3204
- } & {
3205
- getConf(arg: string): any;
3206
- readonly lowerCaseRefNameAliases: {
3207
- [k: string]: string;
3208
- } | undefined;
3209
- } & {
3210
- readonly initialized: boolean;
3211
- readonly name: string;
3212
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3213
- readonly aliases: string[];
3214
- readonly displayName: string;
3215
- hasName(name: string): boolean;
3216
- readonly allAliases: string[];
3217
- readonly allRefNames: string[] | undefined;
3218
- readonly lowerCaseRefNames: string[] | undefined;
3219
- readonly allRefNamesWithLowerCase: string[] | undefined;
3220
- readonly rpcManager: RpcManager;
3221
- readonly refNameColors: string[];
3222
- } & {
3223
- readonly refNames: string[] | undefined;
3224
- } & {
3225
- getCanonicalRefName(refName: string): string | undefined;
3226
- getCanonicalRefName2(asmName: string): string;
3227
- getRefNameColor(refName: string): string | undefined;
3228
- isValidRefName(refName: string): boolean;
3229
- } & {
3230
- setLoaded({ regions, refNameAliases, cytobands, }: {
3231
- regions: import("@jbrowse/core/util").Region[];
3232
- refNameAliases: {
3233
- [x: string]: string;
3234
- };
3235
- cytobands: import("@jbrowse/core/util").Feature[];
3236
- }): void;
3237
- setError(e: unknown): void;
3238
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3239
- setRefNameAliases(aliases: {
3240
- [x: string]: string;
3241
- }): void;
3242
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3243
- setLoadingP(p?: Promise<void>): void;
3244
- load(): Promise<void>;
3245
- loadPre(): Promise<void>;
3246
- } & {
3247
- getAdapterMapEntry(adapterConf: {
3248
- [x: string]: unknown;
3249
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3250
- getRefNameMapForAdapter(adapterConf: {
3251
- [x: string]: unknown;
3252
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3253
- [x: string]: string;
3254
- }>;
3255
- getReverseRefNameMapForAdapter(adapterConf: {
3256
- [x: string]: unknown;
3257
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3258
- [x: string]: string;
3259
- }>;
3260
- afterCreate(): void;
3261
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
3262
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3263
- }, {
3264
- error: unknown;
3265
- loadingP: Promise<void> | undefined;
3266
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3267
- refNameAliases: {
3268
- [x: string]: string;
3269
- } | undefined;
3270
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3271
- } & {
3272
- getConf(arg: string): any;
3273
- readonly lowerCaseRefNameAliases: {
3274
- [k: string]: string;
3275
- } | undefined;
3276
- } & {
3277
- readonly initialized: boolean;
3278
- readonly name: string;
3279
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3280
- readonly aliases: string[];
3281
- readonly displayName: string;
3282
- hasName(name: string): boolean;
3283
- readonly allAliases: string[];
3284
- readonly allRefNames: string[] | undefined;
3285
- readonly lowerCaseRefNames: string[] | undefined;
3286
- readonly allRefNamesWithLowerCase: string[] | undefined;
3287
- readonly rpcManager: RpcManager;
3288
- readonly refNameColors: string[];
3289
- } & {
3290
- readonly refNames: string[] | undefined;
3291
- } & {
3292
- getCanonicalRefName(refName: string): string | undefined;
3293
- getCanonicalRefName2(asmName: string): string;
3294
- getRefNameColor(refName: string): string | undefined;
3295
- isValidRefName(refName: string): boolean;
3296
- } & {
3297
- setLoaded({ regions, refNameAliases, cytobands, }: {
3298
- regions: import("@jbrowse/core/util").Region[];
3299
- refNameAliases: {
3300
- [x: string]: string;
3301
- };
3302
- cytobands: import("@jbrowse/core/util").Feature[];
3303
- }): void;
3304
- setError(e: unknown): void;
3305
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3306
- setRefNameAliases(aliases: {
3307
- [x: string]: string;
3308
- }): void;
3309
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3310
- setLoadingP(p?: Promise<void>): void;
3311
- load(): Promise<void>;
3312
- loadPre(): Promise<void>;
3313
- } & {
3314
- getAdapterMapEntry(adapterConf: {
3315
- [x: string]: unknown;
3316
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3317
- getRefNameMapForAdapter(adapterConf: {
3318
- [x: string]: unknown;
3319
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3320
- [x: string]: string;
3321
- }>;
3322
- getReverseRefNameMapForAdapter(adapterConf: {
3323
- [x: string]: unknown;
3324
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3325
- [x: string]: string;
3326
- }>;
3327
- afterCreate(): void;
3328
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
3329
- } & {
3330
- getCanonicalAssemblyName(asmName: string): string | undefined;
3331
- getCanonicalAssemblyName2(asmName: string): string;
3332
- get(asmName: string): ({
3333
- configuration: any;
3334
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3335
- error: unknown;
3336
- loadingP: Promise<void> | undefined;
3337
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3338
- refNameAliases: {
3339
- [x: string]: string;
3340
- } | undefined;
3341
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3342
- } & {
3343
- getConf(arg: string): any;
3344
- readonly lowerCaseRefNameAliases: {
3345
- [k: string]: string;
3346
- } | undefined;
3347
- } & {
3348
- readonly initialized: boolean;
3349
- readonly name: string;
3350
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3351
- readonly aliases: string[];
3352
- readonly displayName: string;
3353
- hasName(name: string): boolean;
3354
- readonly allAliases: string[];
3355
- readonly allRefNames: string[] | undefined;
3356
- readonly lowerCaseRefNames: string[] | undefined;
3357
- readonly allRefNamesWithLowerCase: string[] | undefined;
3358
- readonly rpcManager: RpcManager;
3359
- readonly refNameColors: string[];
3360
- } & {
3361
- readonly refNames: string[] | undefined;
3362
- } & {
3363
- getCanonicalRefName(refName: string): string | undefined;
3364
- getCanonicalRefName2(asmName: string): string;
3365
- getRefNameColor(refName: string): string | undefined;
3366
- isValidRefName(refName: string): boolean;
3367
- } & {
3368
- setLoaded({ regions, refNameAliases, cytobands, }: {
3369
- regions: import("@jbrowse/core/util").Region[];
3370
- refNameAliases: {
3371
- [x: string]: string;
3372
- };
3373
- cytobands: import("@jbrowse/core/util").Feature[];
3374
- }): void;
3375
- setError(e: unknown): void;
3376
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3377
- setRefNameAliases(aliases: {
3378
- [x: string]: string;
3379
- }): void;
3380
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3381
- setLoadingP(p?: Promise<void>): void;
3382
- load(): Promise<void>;
3383
- loadPre(): Promise<void>;
3384
- } & {
3385
- getAdapterMapEntry(adapterConf: {
3386
- [x: string]: unknown;
3387
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3388
- getRefNameMapForAdapter(adapterConf: {
3389
- [x: string]: unknown;
3390
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3391
- [x: string]: string;
3392
- }>;
3393
- getReverseRefNameMapForAdapter(adapterConf: {
3394
- [x: string]: unknown;
3395
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3396
- [x: string]: string;
3397
- }>;
3398
- afterCreate(): void;
3399
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
3400
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3401
- }, {
3402
- error: unknown;
3403
- loadingP: Promise<void> | undefined;
3404
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3405
- refNameAliases: {
3406
- [x: string]: string;
3407
- } | undefined;
3408
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3409
- } & {
3410
- getConf(arg: string): any;
3411
- readonly lowerCaseRefNameAliases: {
3412
- [k: string]: string;
3413
- } | undefined;
3414
- } & {
3415
- readonly initialized: boolean;
3416
- readonly name: string;
3417
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3418
- readonly aliases: string[];
3419
- readonly displayName: string;
3420
- hasName(name: string): boolean;
3421
- readonly allAliases: string[];
3422
- readonly allRefNames: string[] | undefined;
3423
- readonly lowerCaseRefNames: string[] | undefined;
3424
- readonly allRefNamesWithLowerCase: string[] | undefined;
3425
- readonly rpcManager: RpcManager;
3426
- readonly refNameColors: string[];
3427
- } & {
3428
- readonly refNames: string[] | undefined;
3429
- } & {
3430
- getCanonicalRefName(refName: string): string | undefined;
3431
- getCanonicalRefName2(asmName: string): string;
3432
- getRefNameColor(refName: string): string | undefined;
3433
- isValidRefName(refName: string): boolean;
3434
- } & {
3435
- setLoaded({ regions, refNameAliases, cytobands, }: {
3436
- regions: import("@jbrowse/core/util").Region[];
3437
- refNameAliases: {
3438
- [x: string]: string;
3439
- };
3440
- cytobands: import("@jbrowse/core/util").Feature[];
3441
- }): void;
3442
- setError(e: unknown): void;
3443
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3444
- setRefNameAliases(aliases: {
3445
- [x: string]: string;
3446
- }): void;
3447
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3448
- setLoadingP(p?: Promise<void>): void;
3449
- load(): Promise<void>;
3450
- loadPre(): Promise<void>;
3451
- } & {
3452
- getAdapterMapEntry(adapterConf: {
3453
- [x: string]: unknown;
3454
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3455
- getRefNameMapForAdapter(adapterConf: {
3456
- [x: string]: unknown;
3457
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3458
- [x: string]: string;
3459
- }>;
3460
- getReverseRefNameMapForAdapter(adapterConf: {
3461
- [x: string]: unknown;
3462
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3463
- [x: string]: string;
3464
- }>;
3465
- afterCreate(): void;
3466
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
3467
- readonly assemblyNamesList: any[];
3468
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
3469
- readonly rpcManager: RpcManager;
3470
- } & {
3471
- waitForAssembly(assemblyName: string): Promise<({
3472
- configuration: any;
3473
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3474
- error: unknown;
3475
- loadingP: Promise<void> | undefined;
3476
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3477
- refNameAliases: {
3478
- [x: string]: string;
3479
- } | undefined;
3480
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3481
- } & {
3482
- getConf(arg: string): any;
3483
- readonly lowerCaseRefNameAliases: {
3484
- [k: string]: string;
3485
- } | undefined;
3486
- } & {
3487
- readonly initialized: boolean;
3488
- readonly name: string;
3489
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3490
- readonly aliases: string[];
3491
- readonly displayName: string;
3492
- hasName(name: string): boolean;
3493
- readonly allAliases: string[];
3494
- readonly allRefNames: string[] | undefined;
3495
- readonly lowerCaseRefNames: string[] | undefined;
3496
- readonly allRefNamesWithLowerCase: string[] | undefined;
3497
- readonly rpcManager: RpcManager;
3498
- readonly refNameColors: string[];
3499
- } & {
3500
- readonly refNames: string[] | undefined;
3501
- } & {
3502
- getCanonicalRefName(refName: string): string | undefined;
3503
- getCanonicalRefName2(asmName: string): string;
3504
- getRefNameColor(refName: string): string | undefined;
3505
- isValidRefName(refName: string): boolean;
3506
- } & {
3507
- setLoaded({ regions, refNameAliases, cytobands, }: {
3508
- regions: import("@jbrowse/core/util").Region[];
3509
- refNameAliases: {
3510
- [x: string]: string;
3511
- };
3512
- cytobands: import("@jbrowse/core/util").Feature[];
3513
- }): void;
3514
- setError(e: unknown): void;
3515
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3516
- setRefNameAliases(aliases: {
3517
- [x: string]: string;
3518
- }): void;
3519
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3520
- setLoadingP(p?: Promise<void>): void;
3521
- load(): Promise<void>;
3522
- loadPre(): Promise<void>;
3523
- } & {
3524
- getAdapterMapEntry(adapterConf: {
3525
- [x: string]: unknown;
3526
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3527
- getRefNameMapForAdapter(adapterConf: {
3528
- [x: string]: unknown;
3529
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3530
- [x: string]: string;
3531
- }>;
3532
- getReverseRefNameMapForAdapter(adapterConf: {
3533
- [x: string]: unknown;
3534
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3535
- [x: string]: string;
3536
- }>;
3537
- afterCreate(): void;
3538
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
3539
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3540
- }, {
3541
- error: unknown;
3542
- loadingP: Promise<void> | undefined;
3543
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3544
- refNameAliases: {
3545
- [x: string]: string;
3546
- } | undefined;
3547
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3548
- } & {
3549
- getConf(arg: string): any;
3550
- readonly lowerCaseRefNameAliases: {
3551
- [k: string]: string;
3552
- } | undefined;
3553
- } & {
3554
- readonly initialized: boolean;
3555
- readonly name: string;
3556
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3557
- readonly aliases: string[];
3558
- readonly displayName: string;
3559
- hasName(name: string): boolean;
3560
- readonly allAliases: string[];
3561
- readonly allRefNames: string[] | undefined;
3562
- readonly lowerCaseRefNames: string[] | undefined;
3563
- readonly allRefNamesWithLowerCase: string[] | undefined;
3564
- readonly rpcManager: RpcManager;
3565
- readonly refNameColors: string[];
3566
- } & {
3567
- readonly refNames: string[] | undefined;
3568
- } & {
3569
- getCanonicalRefName(refName: string): string | undefined;
3570
- getCanonicalRefName2(asmName: string): string;
3571
- getRefNameColor(refName: string): string | undefined;
3572
- isValidRefName(refName: string): boolean;
3573
- } & {
3574
- setLoaded({ regions, refNameAliases, cytobands, }: {
3575
- regions: import("@jbrowse/core/util").Region[];
3576
- refNameAliases: {
3577
- [x: string]: string;
3578
- };
3579
- cytobands: import("@jbrowse/core/util").Feature[];
3580
- }): void;
3581
- setError(e: unknown): void;
3582
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3583
- setRefNameAliases(aliases: {
3584
- [x: string]: string;
3585
- }): void;
3586
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3587
- setLoadingP(p?: Promise<void>): void;
3588
- load(): Promise<void>;
3589
- loadPre(): Promise<void>;
3590
- } & {
3591
- getAdapterMapEntry(adapterConf: {
3592
- [x: string]: unknown;
3593
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3594
- getRefNameMapForAdapter(adapterConf: {
3595
- [x: string]: unknown;
3596
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3597
- [x: string]: string;
3598
- }>;
3599
- getReverseRefNameMapForAdapter(adapterConf: {
3600
- [x: string]: unknown;
3601
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3602
- [x: string]: string;
3603
- }>;
3604
- afterCreate(): void;
3605
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
3606
- getRefNameMapForAdapter(adapterConf: {
3607
- [x: string]: unknown;
3608
- }, assemblyName: string | undefined, opts: {
3609
- stopToken?: string;
3610
- sessionId: string;
3611
- }): Promise<{
3612
- [x: string]: string;
3613
- } | undefined>;
3614
- getReverseRefNameMapForAdapter(adapterConf: {
3615
- [x: string]: unknown;
3616
- }, assemblyName: string | undefined, opts: {
3617
- stopToken?: string;
3618
- sessionId: string;
3619
- }): Promise<{
3620
- [x: string]: string;
3621
- } | undefined>;
3622
- isValidRefName(refName: string, assemblyName: string): boolean;
3623
- } & {
3624
- afterAttach(): void;
3625
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
3626
- addAssembly(configuration: any): void;
3627
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
3628
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3629
- rpcManager: RpcManager;
3630
- adminMode: boolean;
3631
- error: unknown;
3632
- textSearchManager: TextSearchManager;
3633
- pluginManager: PluginManager;
3634
- } & {
3635
- setError(error: unknown): void;
3636
- setSession(sessionSnapshot?: SnapshotIn<import("mobx-state-tree").IAnyType>): void;
3637
- setDefaultSession(): void;
3638
- setSessionPath(path: string): void;
3639
- renameCurrentSession(newName: string): void;
3640
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
3641
- jbrowse: import("mobx-state-tree").IAnyType;
3642
- session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
3643
- sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
3644
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
3645
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
3646
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3647
- }, {
3648
- error: unknown;
3649
- loadingP: Promise<void> | undefined;
3650
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3651
- refNameAliases: {
3652
- [x: string]: string;
3653
- } | undefined;
3654
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3655
- } & {
3656
- getConf(arg: string): any;
3657
- readonly lowerCaseRefNameAliases: {
3658
- [k: string]: string;
3659
- } | undefined;
3660
- } & {
3661
- readonly initialized: boolean;
3662
- readonly name: string;
3663
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3664
- readonly aliases: string[];
3665
- readonly displayName: string;
3666
- hasName(name: string): boolean;
3667
- readonly allAliases: string[];
3668
- readonly allRefNames: string[] | undefined;
3669
- readonly lowerCaseRefNames: string[] | undefined;
3670
- readonly allRefNamesWithLowerCase: string[] | undefined;
3671
- readonly rpcManager: RpcManager;
3672
- readonly refNameColors: string[];
3673
- } & {
3674
- readonly refNames: string[] | undefined;
3675
- } & {
3676
- getCanonicalRefName(refName: string): string | undefined;
3677
- getCanonicalRefName2(asmName: string): string;
3678
- getRefNameColor(refName: string): string | undefined;
3679
- isValidRefName(refName: string): boolean;
3680
- } & {
3681
- setLoaded({ regions, refNameAliases, cytobands, }: {
3682
- regions: import("@jbrowse/core/util").Region[];
3683
- refNameAliases: {
3684
- [x: string]: string;
3685
- };
3686
- cytobands: import("@jbrowse/core/util").Feature[];
3687
- }): void;
3688
- setError(e: unknown): void;
3689
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3690
- setRefNameAliases(aliases: {
3691
- [x: string]: string;
3692
- }): void;
3693
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3694
- setLoadingP(p?: Promise<void>): void;
3695
- load(): Promise<void>;
3696
- loadPre(): Promise<void>;
3697
- } & {
3698
- getAdapterMapEntry(adapterConf: {
3699
- [x: string]: unknown;
3700
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3701
- getRefNameMapForAdapter(adapterConf: {
3702
- [x: string]: unknown;
3703
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3704
- [x: string]: string;
3705
- }>;
3706
- getReverseRefNameMapForAdapter(adapterConf: {
3707
- [x: string]: unknown;
3708
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3709
- [x: string]: string;
3710
- }>;
3711
- afterCreate(): void;
3712
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
3713
- }, {
3714
- readonly assemblyNameMap: Record<string, {
3715
- configuration: any;
3716
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3717
- error: unknown;
3718
- loadingP: Promise<void> | undefined;
3719
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3720
- refNameAliases: {
3721
- [x: string]: string;
3722
- } | undefined;
3723
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3724
- } & {
3725
- getConf(arg: string): any;
3726
- readonly lowerCaseRefNameAliases: {
3727
- [k: string]: string;
3728
- } | undefined;
3729
- } & {
3730
- readonly initialized: boolean;
3731
- readonly name: string;
3732
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3733
- readonly aliases: string[];
3734
- readonly displayName: string;
3735
- hasName(name: string): boolean;
3736
- readonly allAliases: string[];
3737
- readonly allRefNames: string[] | undefined;
3738
- readonly lowerCaseRefNames: string[] | undefined;
3739
- readonly allRefNamesWithLowerCase: string[] | undefined;
3740
- readonly rpcManager: RpcManager;
3741
- readonly refNameColors: string[];
3742
- } & {
3743
- readonly refNames: string[] | undefined;
3744
- } & {
3745
- getCanonicalRefName(refName: string): string | undefined;
3746
- getCanonicalRefName2(asmName: string): string;
3747
- getRefNameColor(refName: string): string | undefined;
3748
- isValidRefName(refName: string): boolean;
3749
- } & {
3750
- setLoaded({ regions, refNameAliases, cytobands, }: {
3751
- regions: import("@jbrowse/core/util").Region[];
3752
- refNameAliases: {
3753
- [x: string]: string;
3754
- };
3755
- cytobands: import("@jbrowse/core/util").Feature[];
3756
- }): void;
3757
- setError(e: unknown): void;
3758
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3759
- setRefNameAliases(aliases: {
3760
- [x: string]: string;
3761
- }): void;
3762
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3763
- setLoadingP(p?: Promise<void>): void;
3764
- load(): Promise<void>;
3765
- loadPre(): Promise<void>;
3766
- } & {
3767
- getAdapterMapEntry(adapterConf: {
3768
- [x: string]: unknown;
3769
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3770
- getRefNameMapForAdapter(adapterConf: {
3771
- [x: string]: unknown;
3772
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3773
- [x: string]: string;
3774
- }>;
3775
- getReverseRefNameMapForAdapter(adapterConf: {
3776
- [x: string]: unknown;
3777
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3778
- [x: string]: string;
3779
- }>;
3780
- afterCreate(): void;
3781
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
3782
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3783
- }, {
3784
- error: unknown;
3785
- loadingP: Promise<void> | undefined;
3786
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3787
- refNameAliases: {
3788
- [x: string]: string;
3789
- } | undefined;
3790
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3791
- } & {
3792
- getConf(arg: string): any;
3793
- readonly lowerCaseRefNameAliases: {
3794
- [k: string]: string;
3795
- } | undefined;
3796
- } & {
3797
- readonly initialized: boolean;
3798
- readonly name: string;
3799
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3800
- readonly aliases: string[];
3801
- readonly displayName: string;
3802
- hasName(name: string): boolean;
3803
- readonly allAliases: string[];
3804
- readonly allRefNames: string[] | undefined;
3805
- readonly lowerCaseRefNames: string[] | undefined;
3806
- readonly allRefNamesWithLowerCase: string[] | undefined;
3807
- readonly rpcManager: RpcManager;
3808
- readonly refNameColors: string[];
3809
- } & {
3810
- readonly refNames: string[] | undefined;
3811
- } & {
3812
- getCanonicalRefName(refName: string): string | undefined;
3813
- getCanonicalRefName2(asmName: string): string;
3814
- getRefNameColor(refName: string): string | undefined;
3815
- isValidRefName(refName: string): boolean;
3816
- } & {
3817
- setLoaded({ regions, refNameAliases, cytobands, }: {
3818
- regions: import("@jbrowse/core/util").Region[];
3819
- refNameAliases: {
3820
- [x: string]: string;
3821
- };
3822
- cytobands: import("@jbrowse/core/util").Feature[];
3823
- }): void;
3824
- setError(e: unknown): void;
3825
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3826
- setRefNameAliases(aliases: {
3827
- [x: string]: string;
3828
- }): void;
3829
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3830
- setLoadingP(p?: Promise<void>): void;
3831
- load(): Promise<void>;
3832
- loadPre(): Promise<void>;
3833
- } & {
3834
- getAdapterMapEntry(adapterConf: {
3835
- [x: string]: unknown;
3836
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3837
- getRefNameMapForAdapter(adapterConf: {
3838
- [x: string]: unknown;
3839
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3840
- [x: string]: string;
3841
- }>;
3842
- getReverseRefNameMapForAdapter(adapterConf: {
3843
- [x: string]: unknown;
3844
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3845
- [x: string]: string;
3846
- }>;
3847
- afterCreate(): void;
3848
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
3849
- } & {
3850
- getCanonicalAssemblyName(asmName: string): string | undefined;
3851
- getCanonicalAssemblyName2(asmName: string): string;
3852
- get(asmName: string): ({
3853
- configuration: any;
3854
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3855
- error: unknown;
3856
- loadingP: Promise<void> | undefined;
3857
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3858
- refNameAliases: {
3859
- [x: string]: string;
3860
- } | undefined;
3861
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3862
- } & {
3863
- getConf(arg: string): any;
3864
- readonly lowerCaseRefNameAliases: {
3865
- [k: string]: string;
3866
- } | undefined;
3867
- } & {
3868
- readonly initialized: boolean;
3869
- readonly name: string;
3870
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3871
- readonly aliases: string[];
3872
- readonly displayName: string;
3873
- hasName(name: string): boolean;
3874
- readonly allAliases: string[];
3875
- readonly allRefNames: string[] | undefined;
3876
- readonly lowerCaseRefNames: string[] | undefined;
3877
- readonly allRefNamesWithLowerCase: string[] | undefined;
3878
- readonly rpcManager: RpcManager;
3879
- readonly refNameColors: string[];
3880
- } & {
3881
- readonly refNames: string[] | undefined;
3882
- } & {
3883
- getCanonicalRefName(refName: string): string | undefined;
3884
- getCanonicalRefName2(asmName: string): string;
3885
- getRefNameColor(refName: string): string | undefined;
3886
- isValidRefName(refName: string): boolean;
3887
- } & {
3888
- setLoaded({ regions, refNameAliases, cytobands, }: {
3889
- regions: import("@jbrowse/core/util").Region[];
3890
- refNameAliases: {
3891
- [x: string]: string;
3892
- };
3893
- cytobands: import("@jbrowse/core/util").Feature[];
3894
- }): void;
3895
- setError(e: unknown): void;
3896
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3897
- setRefNameAliases(aliases: {
3898
- [x: string]: string;
3899
- }): void;
3900
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3901
- setLoadingP(p?: Promise<void>): void;
3902
- load(): Promise<void>;
3903
- loadPre(): Promise<void>;
3904
- } & {
3905
- getAdapterMapEntry(adapterConf: {
3906
- [x: string]: unknown;
3907
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3908
- getRefNameMapForAdapter(adapterConf: {
3909
- [x: string]: unknown;
3910
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3911
- [x: string]: string;
3912
- }>;
3913
- getReverseRefNameMapForAdapter(adapterConf: {
3914
- [x: string]: unknown;
3915
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3916
- [x: string]: string;
3917
- }>;
3918
- afterCreate(): void;
3919
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
3920
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
3921
- }, {
3922
- error: unknown;
3923
- loadingP: Promise<void> | undefined;
3924
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3925
- refNameAliases: {
3926
- [x: string]: string;
3927
- } | undefined;
3928
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
3929
- } & {
3930
- getConf(arg: string): any;
3931
- readonly lowerCaseRefNameAliases: {
3932
- [k: string]: string;
3933
- } | undefined;
3934
- } & {
3935
- readonly initialized: boolean;
3936
- readonly name: string;
3937
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3938
- readonly aliases: string[];
3939
- readonly displayName: string;
3940
- hasName(name: string): boolean;
3941
- readonly allAliases: string[];
3942
- readonly allRefNames: string[] | undefined;
3943
- readonly lowerCaseRefNames: string[] | undefined;
3944
- readonly allRefNamesWithLowerCase: string[] | undefined;
3945
- readonly rpcManager: RpcManager;
3946
- readonly refNameColors: string[];
3947
- } & {
3948
- readonly refNames: string[] | undefined;
3949
- } & {
3950
- getCanonicalRefName(refName: string): string | undefined;
3951
- getCanonicalRefName2(asmName: string): string;
3952
- getRefNameColor(refName: string): string | undefined;
3953
- isValidRefName(refName: string): boolean;
3954
- } & {
3955
- setLoaded({ regions, refNameAliases, cytobands, }: {
3956
- regions: import("@jbrowse/core/util").Region[];
3957
- refNameAliases: {
3958
- [x: string]: string;
3959
- };
3960
- cytobands: import("@jbrowse/core/util").Feature[];
3961
- }): void;
3962
- setError(e: unknown): void;
3963
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
3964
- setRefNameAliases(aliases: {
3965
- [x: string]: string;
3966
- }): void;
3967
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
3968
- setLoadingP(p?: Promise<void>): void;
3969
- load(): Promise<void>;
3970
- loadPre(): Promise<void>;
3971
- } & {
3972
- getAdapterMapEntry(adapterConf: {
3973
- [x: string]: unknown;
3974
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
3975
- getRefNameMapForAdapter(adapterConf: {
3976
- [x: string]: unknown;
3977
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3978
- [x: string]: string;
3979
- }>;
3980
- getReverseRefNameMapForAdapter(adapterConf: {
3981
- [x: string]: unknown;
3982
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
3983
- [x: string]: string;
3984
- }>;
3985
- afterCreate(): void;
3986
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
3987
- readonly assemblyNamesList: any[];
3988
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
3989
- readonly rpcManager: RpcManager;
3990
- } & {
3991
- waitForAssembly(assemblyName: string): Promise<({
3992
- configuration: any;
3993
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3994
- error: unknown;
3995
- loadingP: Promise<void> | undefined;
3996
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
3997
- refNameAliases: {
3998
- [x: string]: string;
3999
- } | undefined;
4000
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
4001
- } & {
4002
- getConf(arg: string): any;
4003
- readonly lowerCaseRefNameAliases: {
4004
- [k: string]: string;
4005
- } | undefined;
4006
- } & {
4007
- readonly initialized: boolean;
4008
- readonly name: string;
4009
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
4010
- readonly aliases: string[];
4011
- readonly displayName: string;
4012
- hasName(name: string): boolean;
4013
- readonly allAliases: string[];
4014
- readonly allRefNames: string[] | undefined;
4015
- readonly lowerCaseRefNames: string[] | undefined;
4016
- readonly allRefNamesWithLowerCase: string[] | undefined;
4017
- readonly rpcManager: RpcManager;
4018
- readonly refNameColors: string[];
4019
- } & {
4020
- readonly refNames: string[] | undefined;
4021
- } & {
4022
- getCanonicalRefName(refName: string): string | undefined;
4023
- getCanonicalRefName2(asmName: string): string;
4024
- getRefNameColor(refName: string): string | undefined;
4025
- isValidRefName(refName: string): boolean;
4026
- } & {
4027
- setLoaded({ regions, refNameAliases, cytobands, }: {
4028
- regions: import("@jbrowse/core/util").Region[];
4029
- refNameAliases: {
4030
- [x: string]: string;
4031
- };
4032
- cytobands: import("@jbrowse/core/util").Feature[];
4033
- }): void;
4034
- setError(e: unknown): void;
4035
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
4036
- setRefNameAliases(aliases: {
4037
- [x: string]: string;
4038
- }): void;
4039
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
4040
- setLoadingP(p?: Promise<void>): void;
4041
- load(): Promise<void>;
4042
- loadPre(): Promise<void>;
4043
- } & {
4044
- getAdapterMapEntry(adapterConf: {
4045
- [x: string]: unknown;
4046
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
4047
- getRefNameMapForAdapter(adapterConf: {
4048
- [x: string]: unknown;
4049
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
4050
- [x: string]: string;
4051
- }>;
4052
- getReverseRefNameMapForAdapter(adapterConf: {
4053
- [x: string]: unknown;
4054
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
4055
- [x: string]: string;
4056
- }>;
4057
- afterCreate(): void;
4058
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
4059
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
4060
- }, {
4061
- error: unknown;
4062
- loadingP: Promise<void> | undefined;
4063
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
4064
- refNameAliases: {
4065
- [x: string]: string;
4066
- } | undefined;
4067
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
4068
- } & {
4069
- getConf(arg: string): any;
4070
- readonly lowerCaseRefNameAliases: {
4071
- [k: string]: string;
4072
- } | undefined;
4073
- } & {
4074
- readonly initialized: boolean;
4075
- readonly name: string;
4076
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
4077
- readonly aliases: string[];
4078
- readonly displayName: string;
4079
- hasName(name: string): boolean;
4080
- readonly allAliases: string[];
4081
- readonly allRefNames: string[] | undefined;
4082
- readonly lowerCaseRefNames: string[] | undefined;
4083
- readonly allRefNamesWithLowerCase: string[] | undefined;
4084
- readonly rpcManager: RpcManager;
4085
- readonly refNameColors: string[];
4086
- } & {
4087
- readonly refNames: string[] | undefined;
4088
- } & {
4089
- getCanonicalRefName(refName: string): string | undefined;
4090
- getCanonicalRefName2(asmName: string): string;
4091
- getRefNameColor(refName: string): string | undefined;
4092
- isValidRefName(refName: string): boolean;
4093
- } & {
4094
- setLoaded({ regions, refNameAliases, cytobands, }: {
4095
- regions: import("@jbrowse/core/util").Region[];
4096
- refNameAliases: {
4097
- [x: string]: string;
4098
- };
4099
- cytobands: import("@jbrowse/core/util").Feature[];
4100
- }): void;
4101
- setError(e: unknown): void;
4102
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
4103
- setRefNameAliases(aliases: {
4104
- [x: string]: string;
4105
- }): void;
4106
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
4107
- setLoadingP(p?: Promise<void>): void;
4108
- load(): Promise<void>;
4109
- loadPre(): Promise<void>;
4110
- } & {
4111
- getAdapterMapEntry(adapterConf: {
4112
- [x: string]: unknown;
4113
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
4114
- getRefNameMapForAdapter(adapterConf: {
4115
- [x: string]: unknown;
4116
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
4117
- [x: string]: string;
4118
- }>;
4119
- getReverseRefNameMapForAdapter(adapterConf: {
4120
- [x: string]: unknown;
4121
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
4122
- [x: string]: string;
4123
- }>;
4124
- afterCreate(): void;
4125
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
4126
- getRefNameMapForAdapter(adapterConf: {
4127
- [x: string]: unknown;
4128
- }, assemblyName: string | undefined, opts: {
4129
- stopToken?: string;
4130
- sessionId: string;
4131
- }): Promise<{
4132
- [x: string]: string;
4133
- } | undefined>;
4134
- getReverseRefNameMapForAdapter(adapterConf: {
4135
- [x: string]: unknown;
4136
- }, assemblyName: string | undefined, opts: {
4137
- stopToken?: string;
4138
- sessionId: string;
4139
- }): Promise<{
4140
- [x: string]: string;
4141
- } | undefined>;
4142
- isValidRefName(refName: string, assemblyName: string): boolean;
4143
- } & {
4144
- afterAttach(): void;
4145
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
4146
- addAssembly(configuration: any): void;
4147
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
4148
- }, {
4149
- rpcManager: RpcManager;
4150
- adminMode: boolean;
4151
- error: unknown;
4152
- textSearchManager: TextSearchManager;
4153
- pluginManager: PluginManager;
4154
- } & {
4155
- setError(error: unknown): void;
4156
- setSession(sessionSnapshot?: SnapshotIn<import("mobx-state-tree").IAnyType>): void;
4157
- setDefaultSession(): void;
4158
- setSessionPath(path: string): void;
4159
- renameCurrentSession(newName: string): void;
4160
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
4161
- } & {
4162
- readonly jbrowse: any;
4163
- readonly rpcManager: RpcManager;
4164
- readonly configuration: {
4165
- [x: string]: any;
4166
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4167
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4168
- [x: string]: any;
4169
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4170
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4171
- [x: string]: any;
4172
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4173
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4174
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
4175
- readonly adminMode: boolean;
4176
- readonly textSearchManager: TextSearchManager;
4177
- } & {
4178
- readonly assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
4179
- } & {
4180
- setSelection(thing: unknown): void;
4181
- clearSelection(): void;
4182
- setHovered(thing: unknown): void;
4183
- } & {
4184
- readonly visibleWidget: any;
4185
- } & {
4186
- setDrawerPosition(arg: string): void;
4187
- updateDrawerWidth(drawerWidth: number): number;
4188
- resizeDrawer(distance: number): number;
4189
- addWidget(typeName: string, id: string, initialState?: {}, conf?: unknown): any;
4190
- showWidget(widget: any): void;
4191
- hasWidget(widget: any): boolean;
4192
- hideWidget(widget: any): void;
4193
- minimizeWidgetDrawer(): void;
4194
- showWidgetDrawer(): void;
4195
- hideAllWidgets(): void;
4196
- editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
4197
- afterAttach(): void;
4198
- } & {
4199
- readonly connections: import("@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig").BaseConnectionConfigModel[];
4200
- } & {
4201
- makeConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: {}): ({
4202
- name: string;
4203
- 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>>;
4204
- configuration: {
4205
- [x: string]: any;
4206
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4207
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4208
- [x: string]: any;
4209
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4210
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4211
- [x: string]: any;
4212
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4213
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4214
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4215
- name: {
4216
- type: string;
4217
- defaultValue: string;
4218
- description: string;
4219
- };
4220
- assemblyNames: {
4221
- type: string;
4222
- defaultValue: never[];
4223
- description: string;
4224
- };
4225
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>;
4226
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4227
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
4228
- } & {
4229
- afterAttach(): void;
4230
- addTrackConf(trackConf: Record<string, unknown> | ({
4231
- [x: string]: any;
4232
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4233
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4234
- [x: string]: any;
4235
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4236
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4237
- [x: string]: any;
4238
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4239
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4240
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
4241
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
4242
- [x: string]: any;
4243
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4244
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4245
- [x: string]: any;
4246
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4247
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4248
- [x: string]: any;
4249
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4250
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4251
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
4252
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
4253
- clear(): void;
4254
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
4255
- name: import("mobx-state-tree").ISimpleType<string>;
4256
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
4257
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4258
- name: {
4259
- type: string;
4260
- defaultValue: string;
4261
- description: string;
4262
- };
4263
- assemblyNames: {
4264
- type: string;
4265
- defaultValue: never[];
4266
- description: string;
4267
- };
4268
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
4269
- }, {
4270
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
4271
- } & {
4272
- afterAttach(): void;
4273
- addTrackConf(trackConf: Record<string, unknown> | ({
4274
- [x: string]: any;
4275
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4276
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4277
- [x: string]: any;
4278
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4279
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4280
- [x: string]: any;
4281
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4282
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4283
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
4284
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
4285
- [x: string]: any;
4286
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4287
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4288
- [x: string]: any;
4289
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4290
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4291
- [x: string]: any;
4292
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4293
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4294
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
4295
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
4296
- clear(): void;
4297
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
4298
- prepareToBreakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): (Record<string, number> | (() => void))[] | undefined;
4299
- breakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
4300
- deleteConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
4301
- addConnectionConf(connectionConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
4302
- clearConnections(): void;
4303
- } & {
4304
- queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, unknown][];
4305
- } & {
4306
- readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType | undefined;
4307
- readonly DialogProps: unknown;
4308
- } & {
4309
- removeActiveDialog(): void;
4310
- queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, unknown]): void;
4311
- } & {
4312
- getReferring(object: import("mobx-state-tree").IAnyStateTreeNode): import("@jbrowse/product-core").ReferringNode[];
4313
- } & {
4314
- removeReferring(referring: import("@jbrowse/product-core").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
4315
- } & {
4316
- readonly tracks: import("@jbrowse/core/configuration").AnyConfigurationModel[];
4317
- } & {
4318
- addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfiguration): any;
4319
- deleteTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
4320
- } & {
4321
- snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
4322
- } & {
4323
- readonly snackbarMessageSet: Map<string, import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
4324
- } & {
4325
- notify(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction): void;
4326
- notifyError(errorMessage: string, error?: unknown, extra?: unknown): void;
4327
- pushSnackbarMessage(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction): void;
4328
- popSnackbarMessage(): import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage | undefined;
4329
- removeSnackbarMessage(message: string): void;
4330
- } & {
4331
- task: undefined;
4332
- } & {
4333
- readonly version: any;
4334
- readonly assemblies: any[];
4335
- readonly assemblyNames: any[];
4336
- readonly connections: any;
4337
- readonly assemblyManager: any;
4338
- readonly views: any[];
4339
- renderProps(): {
4340
- theme: any;
4341
- highResolutionScaling: any;
4342
- };
4343
- } & {
4344
- addView(typeName: string, initialState?: {}): any;
4345
- removeView(): void;
4346
- } & {
4347
- getTrackActionMenuItems(config: any): {
4348
- label: string;
4349
- onClick: () => void;
4350
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
4351
- muiName: string;
4352
- };
4353
- }[];
4354
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): void;
4355
- renameCurrentSession(sessionName: string): void;
4356
- setError(error: unknown): void;
4357
- addInternetAccount(internetAccount: SnapshotIn<any>): void;
4358
- findAppropriateInternetAccount(location: UriLocation): any;
4359
- } & {
4360
- readonly jbrowse: {
4361
- configuration: {
4362
- [x: string]: any;
4363
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4364
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4365
- [x: string]: any;
4366
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4367
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4368
- [x: string]: any;
4369
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4370
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4371
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4372
- rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4373
- defaultDriver: {
4374
- type: string;
4375
- description: string;
4376
- defaultValue: string;
4377
- };
4378
- 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]>;
4379
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4380
- highResolutionScaling: {
4381
- type: string;
4382
- defaultValue: number;
4383
- };
4384
- formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4385
- feature: {
4386
- type: string;
4387
- description: string;
4388
- defaultValue: {};
4389
- contextVariable: string[];
4390
- };
4391
- subfeatures: {
4392
- type: string;
4393
- description: string;
4394
- defaultValue: {};
4395
- contextVariable: string[];
4396
- };
4397
- depth: {
4398
- type: string;
4399
- defaultValue: number;
4400
- description: string;
4401
- };
4402
- maxDepth: {
4403
- type: string;
4404
- defaultValue: number;
4405
- description: string;
4406
- };
4407
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4408
- formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4409
- config: {
4410
- type: string;
4411
- description: string;
4412
- defaultValue: {};
4413
- contextVariable: string[];
4414
- };
4415
- hideUris: {
4416
- type: string;
4417
- defaultValue: boolean;
4418
- };
4419
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4420
- hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4421
- sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4422
- trackNames: {
4423
- type: string;
4424
- defaultValue: boolean;
4425
- };
4426
- categories: {
4427
- type: string;
4428
- defaultValue: boolean;
4429
- };
4430
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4431
- defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4432
- categoryNames: {
4433
- type: string;
4434
- defaultValue: never[];
4435
- };
4436
- topLevelCategories: {
4437
- type: string;
4438
- defaultValue: boolean;
4439
- };
4440
- subCategories: {
4441
- type: string;
4442
- defaultValue: boolean;
4443
- };
4444
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4445
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4446
- theme: {
4447
- type: string;
4448
- defaultValue: {};
4449
- };
4450
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>>;
4451
- assembly: {
4452
- [x: string]: any;
4453
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4454
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4455
- [x: string]: any;
4456
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4457
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4458
- [x: string]: any;
4459
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4460
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4461
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
4462
- 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>>;
4463
- 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>>;
4464
- 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>>;
4465
- 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>>;
4466
- plugins: any;
4467
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4468
- readonly assemblies: ({
4469
- [x: string]: any;
4470
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4471
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4472
- [x: string]: any;
4473
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4474
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4475
- [x: string]: any;
4476
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4477
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4478
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
4479
- readonly assemblyName: string;
4480
- readonly rpcManager: any;
4481
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
4482
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4483
- rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4484
- defaultDriver: {
4485
- type: string;
4486
- description: string;
4487
- defaultValue: string;
4488
- };
4489
- 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]>;
4490
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4491
- highResolutionScaling: {
4492
- type: string;
4493
- defaultValue: number;
4494
- };
4495
- formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4496
- feature: {
4497
- type: string;
4498
- description: string;
4499
- defaultValue: {};
4500
- contextVariable: string[];
4501
- };
4502
- subfeatures: {
4503
- type: string;
4504
- description: string;
4505
- defaultValue: {};
4506
- contextVariable: string[];
4507
- };
4508
- depth: {
4509
- type: string;
4510
- defaultValue: number;
4511
- description: string;
4512
- };
4513
- maxDepth: {
4514
- type: string;
4515
- defaultValue: number;
4516
- description: string;
4517
- };
4518
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4519
- formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4520
- config: {
4521
- type: string;
4522
- description: string;
4523
- defaultValue: {};
4524
- contextVariable: string[];
4525
- };
4526
- hideUris: {
4527
- type: string;
4528
- defaultValue: boolean;
4529
- };
4530
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4531
- hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4532
- sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4533
- trackNames: {
4534
- type: string;
4535
- defaultValue: boolean;
4536
- };
4537
- categories: {
4538
- type: string;
4539
- defaultValue: boolean;
4540
- };
4541
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4542
- defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
4543
- categoryNames: {
4544
- type: string;
4545
- defaultValue: never[];
4546
- };
4547
- topLevelCategories: {
4548
- type: string;
4549
- defaultValue: boolean;
4550
- };
4551
- subCategories: {
4552
- type: string;
4553
- defaultValue: boolean;
4554
- };
4555
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4556
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4557
- theme: {
4558
- type: string;
4559
- defaultValue: {};
4560
- };
4561
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4562
- assembly: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
4563
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
4564
- internetAccounts: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
4565
- connections: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
4566
- aggregateTextSearchAdapters: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
4567
- plugins: import("mobx-state-tree").IType<any, any, any>;
4568
- }, {
4569
- readonly assemblies: ({
4570
- [x: string]: any;
4571
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4572
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4573
- [x: string]: any;
4574
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
4575
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
4576
- [x: string]: any;
4577
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4578
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
4579
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
4580
- readonly assemblyName: string;
4581
- readonly rpcManager: any;
4582
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
4583
- readonly pluginManager: PluginManager;
4584
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
4585
- pluginManager: PluginManager;
4586
- };
4587
- export type ViewStateModel = ReturnType<typeof createModel>['model'];
4588
- export type ViewModel = Instance<ViewStateModel>;