@jbrowse/react-app2 3.7.0 → 4.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (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
@@ -1,565 +0,0 @@
1
- import PluginManager from '@jbrowse/core/PluginManager';
2
- import type { PluginConstructor } from '@jbrowse/core/Plugin';
3
- import type { Instance } from 'mobx-state-tree';
4
- export default function createModel({ runtimePlugins, makeWorkerInstance, }: {
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- runtimePlugins: PluginConstructor[];
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- makeWorkerInstance?: () => Worker;
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- }): {
8
- model: import("mobx-state-tree").IModelType<{
9
- jbrowse: import("mobx-state-tree").IAnyType;
10
- session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
11
- sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
12
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
13
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
14
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
15
- }, {
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- error: unknown;
17
- loadingP: Promise<void> | undefined;
18
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
19
- refNameAliases: {
20
- [x: string]: string;
21
- } | undefined;
22
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
23
- } & {
24
- getConf(arg: string): any;
25
- readonly lowerCaseRefNameAliases: {
26
- [k: string]: string;
27
- } | undefined;
28
- } & {
29
- readonly initialized: boolean;
30
- readonly name: string;
31
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
32
- readonly aliases: string[];
33
- readonly displayName: string;
34
- hasName(name: string): boolean;
35
- readonly allAliases: string[];
36
- readonly allRefNames: string[] | undefined;
37
- readonly lowerCaseRefNames: string[] | undefined;
38
- readonly allRefNamesWithLowerCase: string[] | undefined;
39
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
40
- readonly refNameColors: string[];
41
- } & {
42
- readonly refNames: string[] | undefined;
43
- } & {
44
- getCanonicalRefName(refName: string): string | undefined;
45
- getCanonicalRefName2(asmName: string): string;
46
- getRefNameColor(refName: string): string | undefined;
47
- isValidRefName(refName: string): boolean;
48
- } & {
49
- setLoaded({ regions, refNameAliases, cytobands, }: {
50
- regions: import("@jbrowse/core/util").Region[];
51
- refNameAliases: {
52
- [x: string]: string;
53
- };
54
- cytobands: import("@jbrowse/core/util").Feature[];
55
- }): void;
56
- setError(e: unknown): void;
57
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
58
- setRefNameAliases(aliases: {
59
- [x: string]: string;
60
- }): void;
61
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
62
- setLoadingP(p?: Promise<void>): void;
63
- load(): Promise<void>;
64
- loadPre(): Promise<void>;
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- } & {
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- getAdapterMapEntry(adapterConf: {
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- [x: string]: unknown;
68
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
69
- getRefNameMapForAdapter(adapterConf: {
70
- [x: string]: unknown;
71
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
72
- [x: string]: string;
73
- }>;
74
- getReverseRefNameMapForAdapter(adapterConf: {
75
- [x: string]: unknown;
76
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
77
- [x: string]: string;
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- }>;
79
- afterCreate(): void;
80
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
81
- }, {
82
- readonly assemblyNameMap: Record<string, {
83
- configuration: any;
84
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
85
- error: unknown;
86
- loadingP: Promise<void> | undefined;
87
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
88
- refNameAliases: {
89
- [x: string]: string;
90
- } | undefined;
91
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
92
- } & {
93
- getConf(arg: string): any;
94
- readonly lowerCaseRefNameAliases: {
95
- [k: string]: string;
96
- } | undefined;
97
- } & {
98
- readonly initialized: boolean;
99
- readonly name: string;
100
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
101
- readonly aliases: string[];
102
- readonly displayName: string;
103
- hasName(name: string): boolean;
104
- readonly allAliases: string[];
105
- readonly allRefNames: string[] | undefined;
106
- readonly lowerCaseRefNames: string[] | undefined;
107
- readonly allRefNamesWithLowerCase: string[] | undefined;
108
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
109
- readonly refNameColors: string[];
110
- } & {
111
- readonly refNames: string[] | undefined;
112
- } & {
113
- getCanonicalRefName(refName: string): string | undefined;
114
- getCanonicalRefName2(asmName: string): string;
115
- getRefNameColor(refName: string): string | undefined;
116
- isValidRefName(refName: string): boolean;
117
- } & {
118
- setLoaded({ regions, refNameAliases, cytobands, }: {
119
- regions: import("@jbrowse/core/util").Region[];
120
- refNameAliases: {
121
- [x: string]: string;
122
- };
123
- cytobands: import("@jbrowse/core/util").Feature[];
124
- }): void;
125
- setError(e: unknown): void;
126
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
127
- setRefNameAliases(aliases: {
128
- [x: string]: string;
129
- }): void;
130
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
131
- setLoadingP(p?: Promise<void>): void;
132
- load(): Promise<void>;
133
- loadPre(): Promise<void>;
134
- } & {
135
- getAdapterMapEntry(adapterConf: {
136
- [x: string]: unknown;
137
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
138
- getRefNameMapForAdapter(adapterConf: {
139
- [x: string]: unknown;
140
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
141
- [x: string]: string;
142
- }>;
143
- getReverseRefNameMapForAdapter(adapterConf: {
144
- [x: string]: unknown;
145
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
146
- [x: string]: string;
147
- }>;
148
- afterCreate(): void;
149
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
150
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
151
- }, {
152
- error: unknown;
153
- loadingP: Promise<void> | undefined;
154
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
155
- refNameAliases: {
156
- [x: string]: string;
157
- } | undefined;
158
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
159
- } & {
160
- getConf(arg: string): any;
161
- readonly lowerCaseRefNameAliases: {
162
- [k: string]: string;
163
- } | undefined;
164
- } & {
165
- readonly initialized: boolean;
166
- readonly name: string;
167
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
168
- readonly aliases: string[];
169
- readonly displayName: string;
170
- hasName(name: string): boolean;
171
- readonly allAliases: string[];
172
- readonly allRefNames: string[] | undefined;
173
- readonly lowerCaseRefNames: string[] | undefined;
174
- readonly allRefNamesWithLowerCase: string[] | undefined;
175
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
176
- readonly refNameColors: string[];
177
- } & {
178
- readonly refNames: string[] | undefined;
179
- } & {
180
- getCanonicalRefName(refName: string): string | undefined;
181
- getCanonicalRefName2(asmName: string): string;
182
- getRefNameColor(refName: string): string | undefined;
183
- isValidRefName(refName: string): boolean;
184
- } & {
185
- setLoaded({ regions, refNameAliases, cytobands, }: {
186
- regions: import("@jbrowse/core/util").Region[];
187
- refNameAliases: {
188
- [x: string]: string;
189
- };
190
- cytobands: import("@jbrowse/core/util").Feature[];
191
- }): void;
192
- setError(e: unknown): void;
193
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
194
- setRefNameAliases(aliases: {
195
- [x: string]: string;
196
- }): void;
197
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
198
- setLoadingP(p?: Promise<void>): void;
199
- load(): Promise<void>;
200
- loadPre(): Promise<void>;
201
- } & {
202
- getAdapterMapEntry(adapterConf: {
203
- [x: string]: unknown;
204
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
205
- getRefNameMapForAdapter(adapterConf: {
206
- [x: string]: unknown;
207
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
208
- [x: string]: string;
209
- }>;
210
- getReverseRefNameMapForAdapter(adapterConf: {
211
- [x: string]: unknown;
212
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
213
- [x: string]: string;
214
- }>;
215
- afterCreate(): void;
216
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
217
- } & {
218
- getCanonicalAssemblyName(asmName: string): string | undefined;
219
- getCanonicalAssemblyName2(asmName: string): string;
220
- get(asmName: string): ({
221
- configuration: any;
222
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
223
- error: unknown;
224
- loadingP: Promise<void> | undefined;
225
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
226
- refNameAliases: {
227
- [x: string]: string;
228
- } | undefined;
229
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
230
- } & {
231
- getConf(arg: string): any;
232
- readonly lowerCaseRefNameAliases: {
233
- [k: string]: string;
234
- } | undefined;
235
- } & {
236
- readonly initialized: boolean;
237
- readonly name: string;
238
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
239
- readonly aliases: string[];
240
- readonly displayName: string;
241
- hasName(name: string): boolean;
242
- readonly allAliases: string[];
243
- readonly allRefNames: string[] | undefined;
244
- readonly lowerCaseRefNames: string[] | undefined;
245
- readonly allRefNamesWithLowerCase: string[] | undefined;
246
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
247
- readonly refNameColors: string[];
248
- } & {
249
- readonly refNames: string[] | undefined;
250
- } & {
251
- getCanonicalRefName(refName: string): string | undefined;
252
- getCanonicalRefName2(asmName: string): string;
253
- getRefNameColor(refName: string): string | undefined;
254
- isValidRefName(refName: string): boolean;
255
- } & {
256
- setLoaded({ regions, refNameAliases, cytobands, }: {
257
- regions: import("@jbrowse/core/util").Region[];
258
- refNameAliases: {
259
- [x: string]: string;
260
- };
261
- cytobands: import("@jbrowse/core/util").Feature[];
262
- }): void;
263
- setError(e: unknown): void;
264
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
265
- setRefNameAliases(aliases: {
266
- [x: string]: string;
267
- }): void;
268
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
269
- setLoadingP(p?: Promise<void>): void;
270
- load(): Promise<void>;
271
- loadPre(): Promise<void>;
272
- } & {
273
- getAdapterMapEntry(adapterConf: {
274
- [x: string]: unknown;
275
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
276
- getRefNameMapForAdapter(adapterConf: {
277
- [x: string]: unknown;
278
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
279
- [x: string]: string;
280
- }>;
281
- getReverseRefNameMapForAdapter(adapterConf: {
282
- [x: string]: unknown;
283
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
284
- [x: string]: string;
285
- }>;
286
- afterCreate(): void;
287
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
288
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
289
- }, {
290
- error: unknown;
291
- loadingP: Promise<void> | undefined;
292
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
293
- refNameAliases: {
294
- [x: string]: string;
295
- } | undefined;
296
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
297
- } & {
298
- getConf(arg: string): any;
299
- readonly lowerCaseRefNameAliases: {
300
- [k: string]: string;
301
- } | undefined;
302
- } & {
303
- readonly initialized: boolean;
304
- readonly name: string;
305
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
306
- readonly aliases: string[];
307
- readonly displayName: string;
308
- hasName(name: string): boolean;
309
- readonly allAliases: string[];
310
- readonly allRefNames: string[] | undefined;
311
- readonly lowerCaseRefNames: string[] | undefined;
312
- readonly allRefNamesWithLowerCase: string[] | undefined;
313
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
314
- readonly refNameColors: string[];
315
- } & {
316
- readonly refNames: string[] | undefined;
317
- } & {
318
- getCanonicalRefName(refName: string): string | undefined;
319
- getCanonicalRefName2(asmName: string): string;
320
- getRefNameColor(refName: string): string | undefined;
321
- isValidRefName(refName: string): boolean;
322
- } & {
323
- setLoaded({ regions, refNameAliases, cytobands, }: {
324
- regions: import("@jbrowse/core/util").Region[];
325
- refNameAliases: {
326
- [x: string]: string;
327
- };
328
- cytobands: import("@jbrowse/core/util").Feature[];
329
- }): void;
330
- setError(e: unknown): void;
331
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
332
- setRefNameAliases(aliases: {
333
- [x: string]: string;
334
- }): void;
335
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
336
- setLoadingP(p?: Promise<void>): void;
337
- load(): Promise<void>;
338
- loadPre(): Promise<void>;
339
- } & {
340
- getAdapterMapEntry(adapterConf: {
341
- [x: string]: unknown;
342
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
343
- getRefNameMapForAdapter(adapterConf: {
344
- [x: string]: unknown;
345
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
346
- [x: string]: string;
347
- }>;
348
- getReverseRefNameMapForAdapter(adapterConf: {
349
- [x: string]: unknown;
350
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
351
- [x: string]: string;
352
- }>;
353
- afterCreate(): void;
354
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
355
- readonly assemblyNamesList: any[];
356
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
357
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
358
- } & {
359
- waitForAssembly(assemblyName: string): Promise<({
360
- configuration: any;
361
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
362
- error: unknown;
363
- loadingP: Promise<void> | undefined;
364
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
365
- refNameAliases: {
366
- [x: string]: string;
367
- } | undefined;
368
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
369
- } & {
370
- getConf(arg: string): any;
371
- readonly lowerCaseRefNameAliases: {
372
- [k: string]: string;
373
- } | undefined;
374
- } & {
375
- readonly initialized: boolean;
376
- readonly name: string;
377
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
378
- readonly aliases: string[];
379
- readonly displayName: string;
380
- hasName(name: string): boolean;
381
- readonly allAliases: string[];
382
- readonly allRefNames: string[] | undefined;
383
- readonly lowerCaseRefNames: string[] | undefined;
384
- readonly allRefNamesWithLowerCase: string[] | undefined;
385
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
386
- readonly refNameColors: string[];
387
- } & {
388
- readonly refNames: string[] | undefined;
389
- } & {
390
- getCanonicalRefName(refName: string): string | undefined;
391
- getCanonicalRefName2(asmName: string): string;
392
- getRefNameColor(refName: string): string | undefined;
393
- isValidRefName(refName: string): boolean;
394
- } & {
395
- setLoaded({ regions, refNameAliases, cytobands, }: {
396
- regions: import("@jbrowse/core/util").Region[];
397
- refNameAliases: {
398
- [x: string]: string;
399
- };
400
- cytobands: import("@jbrowse/core/util").Feature[];
401
- }): void;
402
- setError(e: unknown): void;
403
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
404
- setRefNameAliases(aliases: {
405
- [x: string]: string;
406
- }): void;
407
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
408
- setLoadingP(p?: Promise<void>): void;
409
- load(): Promise<void>;
410
- loadPre(): Promise<void>;
411
- } & {
412
- getAdapterMapEntry(adapterConf: {
413
- [x: string]: unknown;
414
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
415
- getRefNameMapForAdapter(adapterConf: {
416
- [x: string]: unknown;
417
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
418
- [x: string]: string;
419
- }>;
420
- getReverseRefNameMapForAdapter(adapterConf: {
421
- [x: string]: unknown;
422
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
423
- [x: string]: string;
424
- }>;
425
- afterCreate(): void;
426
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
427
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
428
- }, {
429
- error: unknown;
430
- loadingP: Promise<void> | undefined;
431
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
432
- refNameAliases: {
433
- [x: string]: string;
434
- } | undefined;
435
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
436
- } & {
437
- getConf(arg: string): any;
438
- readonly lowerCaseRefNameAliases: {
439
- [k: string]: string;
440
- } | undefined;
441
- } & {
442
- readonly initialized: boolean;
443
- readonly name: string;
444
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
445
- readonly aliases: string[];
446
- readonly displayName: string;
447
- hasName(name: string): boolean;
448
- readonly allAliases: string[];
449
- readonly allRefNames: string[] | undefined;
450
- readonly lowerCaseRefNames: string[] | undefined;
451
- readonly allRefNamesWithLowerCase: string[] | undefined;
452
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
453
- readonly refNameColors: string[];
454
- } & {
455
- readonly refNames: string[] | undefined;
456
- } & {
457
- getCanonicalRefName(refName: string): string | undefined;
458
- getCanonicalRefName2(asmName: string): string;
459
- getRefNameColor(refName: string): string | undefined;
460
- isValidRefName(refName: string): boolean;
461
- } & {
462
- setLoaded({ regions, refNameAliases, cytobands, }: {
463
- regions: import("@jbrowse/core/util").Region[];
464
- refNameAliases: {
465
- [x: string]: string;
466
- };
467
- cytobands: import("@jbrowse/core/util").Feature[];
468
- }): void;
469
- setError(e: unknown): void;
470
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
471
- setRefNameAliases(aliases: {
472
- [x: string]: string;
473
- }): void;
474
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
475
- setLoadingP(p?: Promise<void>): void;
476
- load(): Promise<void>;
477
- loadPre(): Promise<void>;
478
- } & {
479
- getAdapterMapEntry(adapterConf: {
480
- [x: string]: unknown;
481
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
482
- getRefNameMapForAdapter(adapterConf: {
483
- [x: string]: unknown;
484
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
485
- [x: string]: string;
486
- }>;
487
- getReverseRefNameMapForAdapter(adapterConf: {
488
- [x: string]: unknown;
489
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
490
- [x: string]: string;
491
- }>;
492
- afterCreate(): void;
493
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
494
- getRefNameMapForAdapter(adapterConf: {
495
- [x: string]: unknown;
496
- }, assemblyName: string | undefined, opts: {
497
- stopToken?: string;
498
- sessionId: string;
499
- }): Promise<{
500
- [x: string]: string;
501
- } | undefined>;
502
- getReverseRefNameMapForAdapter(adapterConf: {
503
- [x: string]: unknown;
504
- }, assemblyName: string | undefined, opts: {
505
- stopToken?: string;
506
- sessionId: string;
507
- }): Promise<{
508
- [x: string]: string;
509
- } | undefined>;
510
- isValidRefName(refName: string, assemblyName: string): boolean;
511
- } & {
512
- afterAttach(): void;
513
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
514
- addAssembly(configuration: any): void;
515
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
516
- } & {
517
- internetAccounts: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
518
- }, {
519
- rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
520
- adminMode: boolean;
521
- error: unknown;
522
- textSearchManager: import("@jbrowse/core/util").TextSearchManager;
523
- pluginManager: PluginManager;
524
- } & {
525
- setError(error: unknown): void;
526
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
527
- setDefaultSession(): void;
528
- setSessionPath(path: string): void;
529
- renameCurrentSession(newName: string): void;
530
- } & {
531
- initializeInternetAccount(internetAccountConfig: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: {}): any;
532
- createEphemeralInternetAccount(internetAccountId: string, initialSnapshot: Record<string, unknown>, url: string): any;
533
- findAppropriateInternetAccount(location: import("@jbrowse/core/util").UriLocation): any;
534
- } & {
535
- afterCreate(): void;
536
- } & {
537
- mutableMenuActions: import("@jbrowse/app-core").MenuAction[];
538
- } & {
539
- setMenus(newMenus: import("@jbrowse/app-core").Menu[]): void;
540
- appendMenu(menuName: string): void;
541
- insertMenu(menuName: string, position: number): void;
542
- appendToMenu(menuName: string, menuItem: import("@jbrowse/core/ui").MenuItem): void;
543
- insertInMenu(menuName: string, menuItem: import("@jbrowse/core/ui").MenuItem, position: number): void;
544
- appendToSubMenu(menuPath: string[], menuItem: import("@jbrowse/core/ui").MenuItem): void;
545
- insertInSubMenu(menuPath: string[], menuItem: import("@jbrowse/core/ui").MenuItem, position: number): void;
546
- } & {
547
- version: string;
548
- pluginsUpdated: boolean;
549
- rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
550
- textSearchManager: import("@jbrowse/core/util").TextSearchManager;
551
- error: unknown;
552
- } & {
553
- afterCreate(): void;
554
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("@jbrowse/product-core").BaseSessionType>): void;
555
- setPluginsUpdated(flag: boolean): void;
556
- setDefaultSession(): void;
557
- renameCurrentSession(sessionName: string): void;
558
- setError(error?: unknown): void;
559
- } & {
560
- menus(): import("@jbrowse/app-core").Menu[];
561
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
562
- pluginManager: PluginManager;
563
- };
564
- export type ViewStateModel = ReturnType<typeof createModel>['model'];
565
- export type ViewModel = Instance<ViewStateModel>;
@@ -1,26 +0,0 @@
1
- "use strict";
2
- var __importDefault = (this && this.__importDefault) || function (mod) {
3
- return (mod && mod.__esModule) ? mod : { "default": mod };
4
- };
5
- Object.defineProperty(exports, "__esModule", { value: true });
6
- exports.default = createModel;
7
- const PluginManager_1 = __importDefault(require("@jbrowse/core/PluginManager"));
8
- const corePlugins_1 = __importDefault(require("./corePlugins"));
9
- const rootModel_1 = __importDefault(require("./rootModel/rootModel"));
10
- const sessionModel_1 = __importDefault(require("./sessionModel"));
11
- function createModel({ runtimePlugins, makeWorkerInstance = () => {
12
- throw new Error('no makeWorkerInstance supplied');
13
- }, }) {
14
- const pluginManager = new PluginManager_1.default([
15
- ...corePlugins_1.default.map(P => ({ plugin: new P(), metadata: { isCore: true } })),
16
- ...runtimePlugins.map(P => new P()),
17
- ]).createPluggableElements();
18
- return {
19
- model: (0, rootModel_1.default)({
20
- pluginManager,
21
- sessionModelFactory: sessionModel_1.default,
22
- makeWorkerInstance,
23
- }),
24
- pluginManager,
25
- };
26
- }