@jbrowse/react-app2 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 (74) hide show
  1. package/esm/JBrowseApp/JBrowseApp.d.ts +2 -2
  2. package/esm/JBrowseApp/JBrowseApp.js +3 -3
  3. package/esm/JBrowseApp/index.d.ts +1 -1
  4. package/esm/JBrowseApp/index.js +1 -1
  5. package/esm/components/PreferencesDialog.d.ts +2 -0
  6. package/esm/components/PreferencesDialog.js +7 -5
  7. package/esm/corePlugins.d.ts +2 -2
  8. package/esm/corePlugins.js +2 -2
  9. package/esm/createModel.d.ts +56 -41
  10. package/esm/createModel.js +3 -3
  11. package/esm/createViewState.d.ts +160 -112
  12. package/esm/createViewState.js +2 -2
  13. package/esm/index.d.ts +4 -4
  14. package/esm/index.js +4 -4
  15. package/esm/jbrowseModel.d.ts +53 -35
  16. package/esm/jbrowseModel.js +2 -2
  17. package/esm/rootModel/rootModel.d.ts +53 -38
  18. package/esm/rootModel/rootModel.js +23 -12
  19. package/esm/rpcWorker.d.ts +1 -1
  20. package/esm/rpcWorker.js +2 -2
  21. package/esm/sessionModel/index.d.ts +1645 -1866
  22. package/esm/types.d.ts +1 -1
  23. package/esm/util.d.ts +2 -2
  24. package/esm/util.js +5 -5
  25. package/esm/version.d.ts +1 -1
  26. package/esm/version.js +1 -1
  27. package/esm/webpack.d.ts +4 -4
  28. package/esm/webpack.js +4 -4
  29. package/package.json +65 -74
  30. package/dist/JBrowseApp/AppReExport.d.ts +0 -1
  31. package/dist/JBrowseApp/AppReExport.js +0 -5
  32. package/dist/JBrowseApp/JBrowseApp.d.ts +0 -5
  33. package/dist/JBrowseApp/JBrowseApp.js +0 -55
  34. package/dist/JBrowseApp/index.d.ts +0 -1
  35. package/dist/JBrowseApp/index.js +0 -8
  36. package/dist/components/AboutDialog.d.ts +0 -1
  37. package/dist/components/AboutDialog.js +0 -5
  38. package/dist/components/PreferencesDialog.d.ts +0 -14
  39. package/dist/components/PreferencesDialog.js +0 -21
  40. package/dist/corePlugins.d.ts +0 -3
  41. package/dist/corePlugins.js +0 -64
  42. package/dist/createModel.d.ts +0 -565
  43. package/dist/createModel.js +0 -26
  44. package/dist/createViewState.d.ts +0 -1684
  45. package/dist/createViewState.js +0 -26
  46. package/dist/index.d.ts +0 -4
  47. package/dist/index.js +0 -14
  48. package/dist/jbrowseModel.d.ts +0 -139
  49. package/dist/jbrowseModel.js +0 -7
  50. package/dist/loadPlugins.d.ts +0 -12
  51. package/dist/loadPlugins.js +0 -12
  52. package/dist/react-app.umd.production.min.js +0 -229
  53. package/dist/react-app.umd.production.min.js.LICENSE.txt +0 -195
  54. package/dist/react-app.umd.production.min.js.map +0 -1
  55. package/dist/rootModel/rootModel.d.ts +0 -577
  56. package/dist/rootModel/rootModel.js +0 -166
  57. package/dist/rootModel/rootModel.test.d.ts +0 -1
  58. package/dist/rootModel/rootModel.test.js +0 -140
  59. package/dist/rpcWorker.d.ts +0 -2
  60. package/dist/rpcWorker.js +0 -57
  61. package/dist/sessionModel/index.d.ts +0 -10028
  62. package/dist/sessionModel/index.js +0 -10
  63. package/dist/types.d.ts +0 -27
  64. package/dist/types.js +0 -2
  65. package/dist/util.d.ts +0 -5
  66. package/dist/util.js +0 -119
  67. package/dist/version.d.ts +0 -1
  68. package/dist/version.js +0 -4
  69. package/dist/webpack.d.ts +0 -7
  70. package/dist/webpack.js +0 -53
  71. package/dist/workerPolyfill.d.ts +0 -0
  72. package/dist/workerPolyfill.js +0 -34
  73. package/esm/workerPolyfill.d.ts +0 -0
  74. package/esm/workerPolyfill.js +0 -34
@@ -1,577 +0,0 @@
1
- import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
2
- import assemblyConfigSchemaFactory from '@jbrowse/core/assemblyManager/assemblyConfigSchema';
3
- import RpcManager from '@jbrowse/core/rpc/RpcManager';
4
- import type PluginManager from '@jbrowse/core/PluginManager';
5
- import type { MenuItem } from '@jbrowse/core/ui';
6
- import type { BaseSessionType } from '@jbrowse/product-core';
7
- import type { IAnyType, Instance, SnapshotIn } from 'mobx-state-tree';
8
- export interface Menu {
9
- label: string;
10
- menuItems: MenuItem[];
11
- }
12
- type AssemblyConfig = ReturnType<typeof assemblyConfigSchemaFactory>;
13
- type SessionModelFactory = (args: {
14
- pluginManager: PluginManager;
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- assemblyConfigSchema: AssemblyConfig;
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- }) => IAnyType;
17
- export default function RootModel({ pluginManager, sessionModelFactory, makeWorkerInstance, }: {
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- pluginManager: PluginManager;
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- sessionModelFactory: SessionModelFactory;
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- makeWorkerInstance?: () => Worker;
21
- }): import("mobx-state-tree").IModelType<{
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- jbrowse: IAnyType;
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- session: import("mobx-state-tree").IMaybe<IAnyType>;
24
- sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
25
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
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- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
27
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
28
- }, {
29
- error: unknown;
30
- loadingP: Promise<void> | undefined;
31
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
32
- refNameAliases: {
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- [x: string]: string;
34
- } | undefined;
35
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
36
- } & {
37
- getConf(arg: string): any;
38
- readonly lowerCaseRefNameAliases: {
39
- [k: string]: string;
40
- } | undefined;
41
- } & {
42
- readonly initialized: boolean;
43
- readonly name: string;
44
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
45
- readonly aliases: string[];
46
- readonly displayName: string;
47
- hasName(name: string): boolean;
48
- readonly allAliases: string[];
49
- readonly allRefNames: string[] | undefined;
50
- readonly lowerCaseRefNames: string[] | undefined;
51
- readonly allRefNamesWithLowerCase: string[] | undefined;
52
- readonly rpcManager: RpcManager;
53
- readonly refNameColors: string[];
54
- } & {
55
- readonly refNames: string[] | undefined;
56
- } & {
57
- getCanonicalRefName(refName: string): string | undefined;
58
- getCanonicalRefName2(asmName: string): string;
59
- getRefNameColor(refName: string): string | undefined;
60
- isValidRefName(refName: string): boolean;
61
- } & {
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- setLoaded({ regions, refNameAliases, cytobands, }: {
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- regions: import("@jbrowse/core/util").Region[];
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- refNameAliases: {
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- [x: string]: string;
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- };
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- cytobands: import("@jbrowse/core/util").Feature[];
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- }): void;
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- setError(e: unknown): void;
70
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
71
- setRefNameAliases(aliases: {
72
- [x: string]: string;
73
- }): void;
74
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
75
- setLoadingP(p?: Promise<void>): void;
76
- load(): Promise<void>;
77
- loadPre(): Promise<void>;
78
- } & {
79
- getAdapterMapEntry(adapterConf: {
80
- [x: string]: unknown;
81
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
82
- getRefNameMapForAdapter(adapterConf: {
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- [x: string]: unknown;
84
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
85
- [x: string]: string;
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- }>;
87
- getReverseRefNameMapForAdapter(adapterConf: {
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- [x: string]: unknown;
89
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
90
- [x: string]: string;
91
- }>;
92
- afterCreate(): void;
93
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
94
- }, {
95
- readonly assemblyNameMap: Record<string, {
96
- configuration: any;
97
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
98
- error: unknown;
99
- loadingP: Promise<void> | undefined;
100
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
101
- refNameAliases: {
102
- [x: string]: string;
103
- } | undefined;
104
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
105
- } & {
106
- getConf(arg: string): any;
107
- readonly lowerCaseRefNameAliases: {
108
- [k: string]: string;
109
- } | undefined;
110
- } & {
111
- readonly initialized: boolean;
112
- readonly name: string;
113
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
114
- readonly aliases: string[];
115
- readonly displayName: string;
116
- hasName(name: string): boolean;
117
- readonly allAliases: string[];
118
- readonly allRefNames: string[] | undefined;
119
- readonly lowerCaseRefNames: string[] | undefined;
120
- readonly allRefNamesWithLowerCase: string[] | undefined;
121
- readonly rpcManager: RpcManager;
122
- readonly refNameColors: string[];
123
- } & {
124
- readonly refNames: string[] | undefined;
125
- } & {
126
- getCanonicalRefName(refName: string): string | undefined;
127
- getCanonicalRefName2(asmName: string): string;
128
- getRefNameColor(refName: string): string | undefined;
129
- isValidRefName(refName: string): boolean;
130
- } & {
131
- setLoaded({ regions, refNameAliases, cytobands, }: {
132
- regions: import("@jbrowse/core/util").Region[];
133
- refNameAliases: {
134
- [x: string]: string;
135
- };
136
- cytobands: import("@jbrowse/core/util").Feature[];
137
- }): void;
138
- setError(e: unknown): void;
139
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
140
- setRefNameAliases(aliases: {
141
- [x: string]: string;
142
- }): void;
143
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
144
- setLoadingP(p?: Promise<void>): void;
145
- load(): Promise<void>;
146
- loadPre(): Promise<void>;
147
- } & {
148
- getAdapterMapEntry(adapterConf: {
149
- [x: string]: unknown;
150
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
151
- getRefNameMapForAdapter(adapterConf: {
152
- [x: string]: unknown;
153
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
154
- [x: string]: string;
155
- }>;
156
- getReverseRefNameMapForAdapter(adapterConf: {
157
- [x: string]: unknown;
158
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
159
- [x: string]: string;
160
- }>;
161
- afterCreate(): void;
162
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
163
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
164
- }, {
165
- error: unknown;
166
- loadingP: Promise<void> | undefined;
167
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
168
- refNameAliases: {
169
- [x: string]: string;
170
- } | undefined;
171
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
172
- } & {
173
- getConf(arg: string): any;
174
- readonly lowerCaseRefNameAliases: {
175
- [k: string]: string;
176
- } | undefined;
177
- } & {
178
- readonly initialized: boolean;
179
- readonly name: string;
180
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
181
- readonly aliases: string[];
182
- readonly displayName: string;
183
- hasName(name: string): boolean;
184
- readonly allAliases: string[];
185
- readonly allRefNames: string[] | undefined;
186
- readonly lowerCaseRefNames: string[] | undefined;
187
- readonly allRefNamesWithLowerCase: string[] | undefined;
188
- readonly rpcManager: RpcManager;
189
- readonly refNameColors: string[];
190
- } & {
191
- readonly refNames: string[] | undefined;
192
- } & {
193
- getCanonicalRefName(refName: string): string | undefined;
194
- getCanonicalRefName2(asmName: string): string;
195
- getRefNameColor(refName: string): string | undefined;
196
- isValidRefName(refName: string): boolean;
197
- } & {
198
- setLoaded({ regions, refNameAliases, cytobands, }: {
199
- regions: import("@jbrowse/core/util").Region[];
200
- refNameAliases: {
201
- [x: string]: string;
202
- };
203
- cytobands: import("@jbrowse/core/util").Feature[];
204
- }): void;
205
- setError(e: unknown): void;
206
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
207
- setRefNameAliases(aliases: {
208
- [x: string]: string;
209
- }): void;
210
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
211
- setLoadingP(p?: Promise<void>): void;
212
- load(): Promise<void>;
213
- loadPre(): Promise<void>;
214
- } & {
215
- getAdapterMapEntry(adapterConf: {
216
- [x: string]: unknown;
217
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
218
- getRefNameMapForAdapter(adapterConf: {
219
- [x: string]: unknown;
220
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
221
- [x: string]: string;
222
- }>;
223
- getReverseRefNameMapForAdapter(adapterConf: {
224
- [x: string]: unknown;
225
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
226
- [x: string]: string;
227
- }>;
228
- afterCreate(): void;
229
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
230
- } & {
231
- getCanonicalAssemblyName(asmName: string): string | undefined;
232
- getCanonicalAssemblyName2(asmName: string): string;
233
- get(asmName: string): ({
234
- configuration: any;
235
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
236
- error: unknown;
237
- loadingP: Promise<void> | undefined;
238
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
239
- refNameAliases: {
240
- [x: string]: string;
241
- } | undefined;
242
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
243
- } & {
244
- getConf(arg: string): any;
245
- readonly lowerCaseRefNameAliases: {
246
- [k: string]: string;
247
- } | undefined;
248
- } & {
249
- readonly initialized: boolean;
250
- readonly name: string;
251
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
252
- readonly aliases: string[];
253
- readonly displayName: string;
254
- hasName(name: string): boolean;
255
- readonly allAliases: string[];
256
- readonly allRefNames: string[] | undefined;
257
- readonly lowerCaseRefNames: string[] | undefined;
258
- readonly allRefNamesWithLowerCase: string[] | undefined;
259
- readonly rpcManager: RpcManager;
260
- readonly refNameColors: string[];
261
- } & {
262
- readonly refNames: string[] | undefined;
263
- } & {
264
- getCanonicalRefName(refName: string): string | undefined;
265
- getCanonicalRefName2(asmName: string): string;
266
- getRefNameColor(refName: string): string | undefined;
267
- isValidRefName(refName: string): boolean;
268
- } & {
269
- setLoaded({ regions, refNameAliases, cytobands, }: {
270
- regions: import("@jbrowse/core/util").Region[];
271
- refNameAliases: {
272
- [x: string]: string;
273
- };
274
- cytobands: import("@jbrowse/core/util").Feature[];
275
- }): void;
276
- setError(e: unknown): void;
277
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
278
- setRefNameAliases(aliases: {
279
- [x: string]: string;
280
- }): void;
281
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
282
- setLoadingP(p?: Promise<void>): void;
283
- load(): Promise<void>;
284
- loadPre(): Promise<void>;
285
- } & {
286
- getAdapterMapEntry(adapterConf: {
287
- [x: string]: unknown;
288
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
289
- getRefNameMapForAdapter(adapterConf: {
290
- [x: string]: unknown;
291
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
292
- [x: string]: string;
293
- }>;
294
- getReverseRefNameMapForAdapter(adapterConf: {
295
- [x: string]: unknown;
296
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
297
- [x: string]: string;
298
- }>;
299
- afterCreate(): void;
300
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
301
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
302
- }, {
303
- error: unknown;
304
- loadingP: Promise<void> | undefined;
305
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
306
- refNameAliases: {
307
- [x: string]: string;
308
- } | undefined;
309
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
310
- } & {
311
- getConf(arg: string): any;
312
- readonly lowerCaseRefNameAliases: {
313
- [k: string]: string;
314
- } | undefined;
315
- } & {
316
- readonly initialized: boolean;
317
- readonly name: string;
318
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
319
- readonly aliases: string[];
320
- readonly displayName: string;
321
- hasName(name: string): boolean;
322
- readonly allAliases: string[];
323
- readonly allRefNames: string[] | undefined;
324
- readonly lowerCaseRefNames: string[] | undefined;
325
- readonly allRefNamesWithLowerCase: string[] | undefined;
326
- readonly rpcManager: RpcManager;
327
- readonly refNameColors: string[];
328
- } & {
329
- readonly refNames: string[] | undefined;
330
- } & {
331
- getCanonicalRefName(refName: string): string | undefined;
332
- getCanonicalRefName2(asmName: string): string;
333
- getRefNameColor(refName: string): string | undefined;
334
- isValidRefName(refName: string): boolean;
335
- } & {
336
- setLoaded({ regions, refNameAliases, cytobands, }: {
337
- regions: import("@jbrowse/core/util").Region[];
338
- refNameAliases: {
339
- [x: string]: string;
340
- };
341
- cytobands: import("@jbrowse/core/util").Feature[];
342
- }): void;
343
- setError(e: unknown): void;
344
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
345
- setRefNameAliases(aliases: {
346
- [x: string]: string;
347
- }): void;
348
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
349
- setLoadingP(p?: Promise<void>): void;
350
- load(): Promise<void>;
351
- loadPre(): Promise<void>;
352
- } & {
353
- getAdapterMapEntry(adapterConf: {
354
- [x: string]: unknown;
355
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
356
- getRefNameMapForAdapter(adapterConf: {
357
- [x: string]: unknown;
358
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
359
- [x: string]: string;
360
- }>;
361
- getReverseRefNameMapForAdapter(adapterConf: {
362
- [x: string]: unknown;
363
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
364
- [x: string]: string;
365
- }>;
366
- afterCreate(): void;
367
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
368
- readonly assemblyNamesList: any[];
369
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
370
- readonly rpcManager: RpcManager;
371
- } & {
372
- waitForAssembly(assemblyName: string): Promise<({
373
- configuration: any;
374
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
375
- error: unknown;
376
- loadingP: Promise<void> | undefined;
377
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
378
- refNameAliases: {
379
- [x: string]: string;
380
- } | undefined;
381
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
382
- } & {
383
- getConf(arg: string): any;
384
- readonly lowerCaseRefNameAliases: {
385
- [k: string]: string;
386
- } | undefined;
387
- } & {
388
- readonly initialized: boolean;
389
- readonly name: string;
390
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
391
- readonly aliases: string[];
392
- readonly displayName: string;
393
- hasName(name: string): boolean;
394
- readonly allAliases: string[];
395
- readonly allRefNames: string[] | undefined;
396
- readonly lowerCaseRefNames: string[] | undefined;
397
- readonly allRefNamesWithLowerCase: string[] | undefined;
398
- readonly rpcManager: RpcManager;
399
- readonly refNameColors: string[];
400
- } & {
401
- readonly refNames: string[] | undefined;
402
- } & {
403
- getCanonicalRefName(refName: string): string | undefined;
404
- getCanonicalRefName2(asmName: string): string;
405
- getRefNameColor(refName: string): string | undefined;
406
- isValidRefName(refName: string): boolean;
407
- } & {
408
- setLoaded({ regions, refNameAliases, cytobands, }: {
409
- regions: import("@jbrowse/core/util").Region[];
410
- refNameAliases: {
411
- [x: string]: string;
412
- };
413
- cytobands: import("@jbrowse/core/util").Feature[];
414
- }): void;
415
- setError(e: unknown): void;
416
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
417
- setRefNameAliases(aliases: {
418
- [x: string]: string;
419
- }): void;
420
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
421
- setLoadingP(p?: Promise<void>): void;
422
- load(): Promise<void>;
423
- loadPre(): Promise<void>;
424
- } & {
425
- getAdapterMapEntry(adapterConf: {
426
- [x: string]: unknown;
427
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
428
- getRefNameMapForAdapter(adapterConf: {
429
- [x: string]: unknown;
430
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
431
- [x: string]: string;
432
- }>;
433
- getReverseRefNameMapForAdapter(adapterConf: {
434
- [x: string]: unknown;
435
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
436
- [x: string]: string;
437
- }>;
438
- afterCreate(): void;
439
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
440
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
441
- }, {
442
- error: unknown;
443
- loadingP: Promise<void> | undefined;
444
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
445
- refNameAliases: {
446
- [x: string]: string;
447
- } | undefined;
448
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
449
- } & {
450
- getConf(arg: string): any;
451
- readonly lowerCaseRefNameAliases: {
452
- [k: string]: string;
453
- } | undefined;
454
- } & {
455
- readonly initialized: boolean;
456
- readonly name: string;
457
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
458
- readonly aliases: string[];
459
- readonly displayName: string;
460
- hasName(name: string): boolean;
461
- readonly allAliases: string[];
462
- readonly allRefNames: string[] | undefined;
463
- readonly lowerCaseRefNames: string[] | undefined;
464
- readonly allRefNamesWithLowerCase: string[] | undefined;
465
- readonly rpcManager: RpcManager;
466
- readonly refNameColors: string[];
467
- } & {
468
- readonly refNames: string[] | undefined;
469
- } & {
470
- getCanonicalRefName(refName: string): string | undefined;
471
- getCanonicalRefName2(asmName: string): string;
472
- getRefNameColor(refName: string): string | undefined;
473
- isValidRefName(refName: string): boolean;
474
- } & {
475
- setLoaded({ regions, refNameAliases, cytobands, }: {
476
- regions: import("@jbrowse/core/util").Region[];
477
- refNameAliases: {
478
- [x: string]: string;
479
- };
480
- cytobands: import("@jbrowse/core/util").Feature[];
481
- }): void;
482
- setError(e: unknown): void;
483
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
484
- setRefNameAliases(aliases: {
485
- [x: string]: string;
486
- }): void;
487
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
488
- setLoadingP(p?: Promise<void>): void;
489
- load(): Promise<void>;
490
- loadPre(): Promise<void>;
491
- } & {
492
- getAdapterMapEntry(adapterConf: {
493
- [x: string]: unknown;
494
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
495
- getRefNameMapForAdapter(adapterConf: {
496
- [x: string]: unknown;
497
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
498
- [x: string]: string;
499
- }>;
500
- getReverseRefNameMapForAdapter(adapterConf: {
501
- [x: string]: unknown;
502
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
503
- [x: string]: string;
504
- }>;
505
- afterCreate(): void;
506
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
507
- getRefNameMapForAdapter(adapterConf: {
508
- [x: string]: unknown;
509
- }, assemblyName: string | undefined, opts: {
510
- stopToken?: string;
511
- sessionId: string;
512
- }): Promise<{
513
- [x: string]: string;
514
- } | undefined>;
515
- getReverseRefNameMapForAdapter(adapterConf: {
516
- [x: string]: unknown;
517
- }, assemblyName: string | undefined, opts: {
518
- stopToken?: string;
519
- sessionId: string;
520
- }): Promise<{
521
- [x: string]: string;
522
- } | undefined>;
523
- isValidRefName(refName: string, assemblyName: string): boolean;
524
- } & {
525
- afterAttach(): void;
526
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
527
- addAssembly(configuration: any): void;
528
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
529
- } & {
530
- internetAccounts: import("mobx-state-tree").IArrayType<IAnyType>;
531
- }, {
532
- rpcManager: RpcManager;
533
- adminMode: boolean;
534
- error: unknown;
535
- textSearchManager: TextSearchManager;
536
- pluginManager: PluginManager;
537
- } & {
538
- setError(error: unknown): void;
539
- setSession(sessionSnapshot?: SnapshotIn<IAnyType>): void;
540
- setDefaultSession(): void;
541
- setSessionPath(path: string): void;
542
- renameCurrentSession(newName: string): void;
543
- } & {
544
- initializeInternetAccount(internetAccountConfig: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: {}): any;
545
- createEphemeralInternetAccount(internetAccountId: string, initialSnapshot: Record<string, unknown>, url: string): any;
546
- findAppropriateInternetAccount(location: import("@jbrowse/core/util").UriLocation): any;
547
- } & {
548
- afterCreate(): void;
549
- } & {
550
- mutableMenuActions: import("@jbrowse/app-core").MenuAction[];
551
- } & {
552
- setMenus(newMenus: import("@jbrowse/app-core").Menu[]): void;
553
- appendMenu(menuName: string): void;
554
- insertMenu(menuName: string, position: number): void;
555
- appendToMenu(menuName: string, menuItem: MenuItem): void;
556
- insertInMenu(menuName: string, menuItem: MenuItem, position: number): void;
557
- appendToSubMenu(menuPath: string[], menuItem: MenuItem): void;
558
- insertInSubMenu(menuPath: string[], menuItem: MenuItem, position: number): void;
559
- } & {
560
- version: string;
561
- pluginsUpdated: boolean;
562
- rpcManager: RpcManager;
563
- textSearchManager: TextSearchManager;
564
- error: unknown;
565
- } & {
566
- afterCreate(): void;
567
- setSession(sessionSnapshot?: SnapshotIn<BaseSessionType>): void;
568
- setPluginsUpdated(flag: boolean): void;
569
- setDefaultSession(): void;
570
- renameCurrentSession(sessionName: string): void;
571
- setError(error?: unknown): void;
572
- } & {
573
- menus(): import("@jbrowse/app-core").Menu[];
574
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
575
- export type WebRootModelType = ReturnType<typeof RootModel>;
576
- export type WebRootModel = Instance<WebRootModelType>;
577
- export {};