@jbrowse/product-core 3.6.5 → 4.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (97) hide show
  1. package/esm/RootModel/BaseRootModel.d.ts +53 -30
  2. package/esm/RootModel/BaseRootModel.js +1 -1
  3. package/esm/RootModel/FormatAbout.d.ts +2 -2
  4. package/esm/RootModel/FormatDetails.d.ts +2 -2
  5. package/esm/RootModel/HierarchicalConfig.d.ts +6 -6
  6. package/esm/RootModel/InternetAccounts.d.ts +4 -4
  7. package/esm/RootModel/InternetAccounts.js +3 -3
  8. package/esm/RootModel/index.d.ts +5 -5
  9. package/esm/RootModel/index.js +5 -5
  10. package/esm/Session/BaseSession.d.ts +12 -8
  11. package/esm/Session/BaseSession.js +12 -2
  12. package/esm/Session/Connections.d.ts +7 -144
  13. package/esm/Session/Connections.js +13 -3
  14. package/esm/Session/DialogQueue.d.ts +3 -3
  15. package/esm/Session/DialogQueue.js +4 -6
  16. package/esm/Session/DrawerWidgets.d.ts +17 -9
  17. package/esm/Session/DrawerWidgets.js +32 -8
  18. package/esm/Session/MultipleViews.d.ts +192 -105
  19. package/esm/Session/MultipleViews.js +27 -10
  20. package/esm/Session/ReferenceManagement.d.ts +3 -3
  21. package/esm/Session/ReferenceManagement.js +10 -4
  22. package/esm/Session/SessionTracks.d.ts +181 -100
  23. package/esm/Session/SessionTracks.js +13 -3
  24. package/esm/Session/Themes.d.ts +3 -3
  25. package/esm/Session/Themes.js +3 -3
  26. package/esm/Session/Tracks.d.ts +178 -99
  27. package/esm/Session/Tracks.js +16 -3
  28. package/esm/Session/index.d.ts +10 -10
  29. package/esm/Session/index.js +10 -10
  30. package/esm/index.d.ts +4 -4
  31. package/esm/index.js +4 -4
  32. package/esm/rpcWorker.d.ts +6 -0
  33. package/esm/rpcWorker.js +12 -6
  34. package/esm/ui/AboutDialog.d.ts +4 -2
  35. package/esm/ui/AboutDialog.js +4 -5
  36. package/esm/ui/AboutDialogContents.d.ts +4 -2
  37. package/esm/ui/AboutDialogContents.js +13 -12
  38. package/esm/ui/FileInfoPanel.d.ts +4 -2
  39. package/esm/ui/FileInfoPanel.js +6 -7
  40. package/esm/ui/HeaderButtons.js +4 -4
  41. package/esm/ui/RefNameInfoDialog.d.ts +4 -2
  42. package/esm/ui/RefNameInfoDialog.js +13 -13
  43. package/esm/ui/index.d.ts +1 -1
  44. package/esm/ui/index.js +1 -1
  45. package/esm/ui/util.d.ts +5 -2
  46. package/esm/ui/util.js +23 -5
  47. package/package.json +24 -34
  48. package/dist/RootModel/BaseRootModel.d.ts +0 -526
  49. package/dist/RootModel/BaseRootModel.js +0 -57
  50. package/dist/RootModel/FormatAbout.d.ts +0 -12
  51. package/dist/RootModel/FormatAbout.js +0 -18
  52. package/dist/RootModel/FormatDetails.d.ts +0 -24
  53. package/dist/RootModel/FormatDetails.js +0 -30
  54. package/dist/RootModel/HierarchicalConfig.d.ts +0 -26
  55. package/dist/RootModel/HierarchicalConfig.js +0 -32
  56. package/dist/RootModel/InternetAccounts.d.ts +0 -15
  57. package/dist/RootModel/InternetAccounts.js +0 -79
  58. package/dist/RootModel/index.d.ts +0 -5
  59. package/dist/RootModel/index.js +0 -21
  60. package/dist/Session/BaseSession.d.ts +0 -31
  61. package/dist/Session/BaseSession.js +0 -63
  62. package/dist/Session/Connections.d.ts +0 -158
  63. package/dist/Session/Connections.js +0 -84
  64. package/dist/Session/DialogQueue.d.ts +0 -15
  65. package/dist/Session/DialogQueue.js +0 -37
  66. package/dist/Session/DrawerWidgets.d.ts +0 -28
  67. package/dist/Session/DrawerWidgets.js +0 -107
  68. package/dist/Session/MultipleViews.d.ts +0 -1656
  69. package/dist/Session/MultipleViews.js +0 -75
  70. package/dist/Session/ReferenceManagement.d.ts +0 -15
  71. package/dist/Session/ReferenceManagement.js +0 -71
  72. package/dist/Session/SessionTracks.d.ts +0 -1639
  73. package/dist/Session/SessionTracks.js +0 -54
  74. package/dist/Session/Themes.d.ts +0 -18
  75. package/dist/Session/Themes.js +0 -47
  76. package/dist/Session/Tracks.d.ts +0 -1632
  77. package/dist/Session/Tracks.js +0 -36
  78. package/dist/Session/index.d.ts +0 -10
  79. package/dist/Session/index.js +0 -26
  80. package/dist/index.d.ts +0 -4
  81. package/dist/index.js +0 -20
  82. package/dist/rpcWorker.d.ts +0 -6
  83. package/dist/rpcWorker.js +0 -57
  84. package/dist/ui/AboutDialog.d.ts +0 -5
  85. package/dist/ui/AboutDialog.js +0 -18
  86. package/dist/ui/AboutDialogContents.d.ts +0 -5
  87. package/dist/ui/AboutDialogContents.js +0 -41
  88. package/dist/ui/FileInfoPanel.d.ts +0 -4
  89. package/dist/ui/FileInfoPanel.js +0 -43
  90. package/dist/ui/HeaderButtons.d.ts +0 -6
  91. package/dist/ui/HeaderButtons.js +0 -31
  92. package/dist/ui/RefNameInfoDialog.d.ts +0 -6
  93. package/dist/ui/RefNameInfoDialog.js +0 -87
  94. package/dist/ui/index.d.ts +0 -1
  95. package/dist/ui/index.js +0 -17
  96. package/dist/ui/util.d.ts +0 -12
  97. package/dist/ui/util.js +0 -28
@@ -1,1632 +0,0 @@
1
- import type PluginManager from '@jbrowse/core/PluginManager';
2
- import type { AnyConfiguration, AnyConfigurationModel } from '@jbrowse/core/configuration';
3
- import type { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
4
- export declare function TracksManagerSessionMixin(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
5
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
6
- name: import("mobx-state-tree").ISimpleType<string>;
7
- margin: import("mobx-state-tree").IType<number | undefined, number, number>;
8
- }, {
9
- selection: unknown;
10
- hovered: unknown;
11
- } & {
12
- readonly root: {
13
- jbrowse: any;
14
- session: any;
15
- sessionPath: string;
16
- assemblyManager: {
17
- assemblies: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
18
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
19
- }, {
20
- error: unknown;
21
- loadingP: Promise<void> | undefined;
22
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
23
- refNameAliases: {
24
- [x: string]: string;
25
- } | undefined;
26
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
27
- } & {
28
- getConf(arg: string): any;
29
- readonly lowerCaseRefNameAliases: {
30
- [k: string]: string;
31
- } | undefined;
32
- } & {
33
- readonly initialized: boolean;
34
- readonly name: string;
35
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
36
- readonly aliases: string[];
37
- readonly displayName: string;
38
- hasName(name: string): boolean;
39
- readonly allAliases: string[];
40
- readonly allRefNames: string[] | undefined;
41
- readonly lowerCaseRefNames: string[] | undefined;
42
- readonly allRefNamesWithLowerCase: string[] | undefined;
43
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
44
- readonly refNameColors: string[];
45
- } & {
46
- readonly refNames: string[] | undefined;
47
- } & {
48
- getCanonicalRefName(refName: string): string | undefined;
49
- getRefNameColor(refName: string): string | undefined;
50
- isValidRefName(refName: string): boolean;
51
- } & {
52
- setLoaded({ regions, refNameAliases, cytobands, }: {
53
- regions: import("@jbrowse/core/util").Region[];
54
- refNameAliases: {
55
- [x: string]: string;
56
- };
57
- cytobands: import("@jbrowse/core/util").Feature[];
58
- }): void;
59
- setError(e: unknown): void;
60
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
61
- setRefNameAliases(aliases: {
62
- [x: string]: string;
63
- }): void;
64
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
65
- setLoadingP(p?: Promise<void>): void;
66
- load(): Promise<void>;
67
- loadPre(): Promise<void>;
68
- } & {
69
- getAdapterMapEntry(adapterConf: {
70
- [x: string]: unknown;
71
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
72
- getRefNameMapForAdapter(adapterConf: {
73
- [x: string]: unknown;
74
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
75
- [x: string]: string;
76
- }>;
77
- getReverseRefNameMapForAdapter(adapterConf: {
78
- [x: string]: unknown;
79
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
80
- [x: string]: string;
81
- }>;
82
- afterCreate(): void;
83
- }, 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<{
84
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
85
- }, {
86
- error: unknown;
87
- loadingP: Promise<void> | undefined;
88
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
89
- refNameAliases: {
90
- [x: string]: string;
91
- } | undefined;
92
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
93
- } & {
94
- getConf(arg: string): any;
95
- readonly lowerCaseRefNameAliases: {
96
- [k: string]: string;
97
- } | undefined;
98
- } & {
99
- readonly initialized: boolean;
100
- readonly name: string;
101
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
102
- readonly aliases: string[];
103
- readonly displayName: string;
104
- hasName(name: string): boolean;
105
- readonly allAliases: string[];
106
- readonly allRefNames: string[] | undefined;
107
- readonly lowerCaseRefNames: string[] | undefined;
108
- readonly allRefNamesWithLowerCase: string[] | undefined;
109
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
110
- readonly refNameColors: string[];
111
- } & {
112
- readonly refNames: string[] | undefined;
113
- } & {
114
- getCanonicalRefName(refName: string): string | undefined;
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")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
150
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
151
- readonly assemblyNameMap: Record<string, {
152
- configuration: any;
153
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
154
- error: unknown;
155
- loadingP: Promise<void> | undefined;
156
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
157
- refNameAliases: {
158
- [x: string]: string;
159
- } | undefined;
160
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
161
- } & {
162
- getConf(arg: string): any;
163
- readonly lowerCaseRefNameAliases: {
164
- [k: string]: string;
165
- } | undefined;
166
- } & {
167
- readonly initialized: boolean;
168
- readonly name: string;
169
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
170
- readonly aliases: string[];
171
- readonly displayName: string;
172
- hasName(name: string): boolean;
173
- readonly allAliases: string[];
174
- readonly allRefNames: string[] | undefined;
175
- readonly lowerCaseRefNames: string[] | undefined;
176
- readonly allRefNamesWithLowerCase: string[] | undefined;
177
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
178
- readonly refNameColors: string[];
179
- } & {
180
- readonly refNames: string[] | undefined;
181
- } & {
182
- getCanonicalRefName(refName: string): string | undefined;
183
- getRefNameColor(refName: string): string | undefined;
184
- isValidRefName(refName: string): boolean;
185
- } & {
186
- setLoaded({ regions, refNameAliases, cytobands, }: {
187
- regions: import("@jbrowse/core/util").Region[];
188
- refNameAliases: {
189
- [x: string]: string;
190
- };
191
- cytobands: import("@jbrowse/core/util").Feature[];
192
- }): void;
193
- setError(e: unknown): void;
194
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
195
- setRefNameAliases(aliases: {
196
- [x: string]: string;
197
- }): void;
198
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
199
- setLoadingP(p?: Promise<void>): void;
200
- load(): Promise<void>;
201
- loadPre(): Promise<void>;
202
- } & {
203
- getAdapterMapEntry(adapterConf: {
204
- [x: string]: unknown;
205
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
206
- getRefNameMapForAdapter(adapterConf: {
207
- [x: string]: unknown;
208
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
209
- [x: string]: string;
210
- }>;
211
- getReverseRefNameMapForAdapter(adapterConf: {
212
- [x: string]: unknown;
213
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
214
- [x: string]: string;
215
- }>;
216
- afterCreate(): void;
217
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
218
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
219
- }, {
220
- error: unknown;
221
- loadingP: Promise<void> | undefined;
222
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
223
- refNameAliases: {
224
- [x: string]: string;
225
- } | undefined;
226
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
227
- } & {
228
- getConf(arg: string): any;
229
- readonly lowerCaseRefNameAliases: {
230
- [k: string]: string;
231
- } | undefined;
232
- } & {
233
- readonly initialized: boolean;
234
- readonly name: string;
235
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
236
- readonly aliases: string[];
237
- readonly displayName: string;
238
- hasName(name: string): boolean;
239
- readonly allAliases: string[];
240
- readonly allRefNames: string[] | undefined;
241
- readonly lowerCaseRefNames: string[] | undefined;
242
- readonly allRefNamesWithLowerCase: string[] | undefined;
243
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
244
- readonly refNameColors: string[];
245
- } & {
246
- readonly refNames: string[] | undefined;
247
- } & {
248
- getCanonicalRefName(refName: string): string | undefined;
249
- getRefNameColor(refName: string): string | undefined;
250
- isValidRefName(refName: string): boolean;
251
- } & {
252
- setLoaded({ regions, refNameAliases, cytobands, }: {
253
- regions: import("@jbrowse/core/util").Region[];
254
- refNameAliases: {
255
- [x: string]: string;
256
- };
257
- cytobands: import("@jbrowse/core/util").Feature[];
258
- }): void;
259
- setError(e: unknown): void;
260
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
261
- setRefNameAliases(aliases: {
262
- [x: string]: string;
263
- }): void;
264
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
265
- setLoadingP(p?: Promise<void>): void;
266
- load(): Promise<void>;
267
- loadPre(): Promise<void>;
268
- } & {
269
- getAdapterMapEntry(adapterConf: {
270
- [x: string]: unknown;
271
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
272
- getRefNameMapForAdapter(adapterConf: {
273
- [x: string]: unknown;
274
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
275
- [x: string]: string;
276
- }>;
277
- getReverseRefNameMapForAdapter(adapterConf: {
278
- [x: string]: unknown;
279
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
280
- [x: string]: string;
281
- }>;
282
- afterCreate(): void;
283
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
284
- } & {
285
- getCanonicalAssemblyName(asmName: string): string | undefined;
286
- get(asmName: string): ({
287
- configuration: any;
288
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
289
- error: unknown;
290
- loadingP: Promise<void> | undefined;
291
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
292
- refNameAliases: {
293
- [x: string]: string;
294
- } | undefined;
295
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
296
- } & {
297
- getConf(arg: string): any;
298
- readonly lowerCaseRefNameAliases: {
299
- [k: string]: string;
300
- } | undefined;
301
- } & {
302
- readonly initialized: boolean;
303
- readonly name: string;
304
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
305
- readonly aliases: string[];
306
- readonly displayName: string;
307
- hasName(name: string): boolean;
308
- readonly allAliases: string[];
309
- readonly allRefNames: string[] | undefined;
310
- readonly lowerCaseRefNames: string[] | undefined;
311
- readonly allRefNamesWithLowerCase: string[] | undefined;
312
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
313
- readonly refNameColors: string[];
314
- } & {
315
- readonly refNames: string[] | undefined;
316
- } & {
317
- getCanonicalRefName(refName: string): string | undefined;
318
- getRefNameColor(refName: string): string | undefined;
319
- isValidRefName(refName: string): boolean;
320
- } & {
321
- setLoaded({ regions, refNameAliases, cytobands, }: {
322
- regions: import("@jbrowse/core/util").Region[];
323
- refNameAliases: {
324
- [x: string]: string;
325
- };
326
- cytobands: import("@jbrowse/core/util").Feature[];
327
- }): void;
328
- setError(e: unknown): void;
329
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
330
- setRefNameAliases(aliases: {
331
- [x: string]: string;
332
- }): void;
333
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
334
- setLoadingP(p?: Promise<void>): void;
335
- load(): Promise<void>;
336
- loadPre(): Promise<void>;
337
- } & {
338
- getAdapterMapEntry(adapterConf: {
339
- [x: string]: unknown;
340
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
341
- getRefNameMapForAdapter(adapterConf: {
342
- [x: string]: unknown;
343
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
344
- [x: string]: string;
345
- }>;
346
- getReverseRefNameMapForAdapter(adapterConf: {
347
- [x: string]: unknown;
348
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
349
- [x: string]: string;
350
- }>;
351
- afterCreate(): void;
352
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
353
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
354
- }, {
355
- error: unknown;
356
- loadingP: Promise<void> | undefined;
357
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
358
- refNameAliases: {
359
- [x: string]: string;
360
- } | undefined;
361
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
362
- } & {
363
- getConf(arg: string): any;
364
- readonly lowerCaseRefNameAliases: {
365
- [k: string]: string;
366
- } | undefined;
367
- } & {
368
- readonly initialized: boolean;
369
- readonly name: string;
370
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
371
- readonly aliases: string[];
372
- readonly displayName: string;
373
- hasName(name: string): boolean;
374
- readonly allAliases: string[];
375
- readonly allRefNames: string[] | undefined;
376
- readonly lowerCaseRefNames: string[] | undefined;
377
- readonly allRefNamesWithLowerCase: string[] | undefined;
378
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
379
- readonly refNameColors: string[];
380
- } & {
381
- readonly refNames: string[] | undefined;
382
- } & {
383
- getCanonicalRefName(refName: string): string | undefined;
384
- getRefNameColor(refName: string): string | undefined;
385
- isValidRefName(refName: string): boolean;
386
- } & {
387
- setLoaded({ regions, refNameAliases, cytobands, }: {
388
- regions: import("@jbrowse/core/util").Region[];
389
- refNameAliases: {
390
- [x: string]: string;
391
- };
392
- cytobands: import("@jbrowse/core/util").Feature[];
393
- }): void;
394
- setError(e: unknown): void;
395
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
396
- setRefNameAliases(aliases: {
397
- [x: string]: string;
398
- }): void;
399
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
400
- setLoadingP(p?: Promise<void>): void;
401
- load(): Promise<void>;
402
- loadPre(): Promise<void>;
403
- } & {
404
- getAdapterMapEntry(adapterConf: {
405
- [x: string]: unknown;
406
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
407
- getRefNameMapForAdapter(adapterConf: {
408
- [x: string]: unknown;
409
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
410
- [x: string]: string;
411
- }>;
412
- getReverseRefNameMapForAdapter(adapterConf: {
413
- [x: string]: unknown;
414
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
415
- [x: string]: string;
416
- }>;
417
- afterCreate(): void;
418
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
419
- readonly assemblyNamesList: any[];
420
- readonly assemblyList: AnyConfigurationModel[];
421
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
422
- } & {
423
- waitForAssembly(assemblyName: string): Promise<({
424
- configuration: any;
425
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
426
- error: unknown;
427
- loadingP: Promise<void> | undefined;
428
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
429
- refNameAliases: {
430
- [x: string]: string;
431
- } | undefined;
432
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
433
- } & {
434
- getConf(arg: string): any;
435
- readonly lowerCaseRefNameAliases: {
436
- [k: string]: string;
437
- } | undefined;
438
- } & {
439
- readonly initialized: boolean;
440
- readonly name: string;
441
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
442
- readonly aliases: string[];
443
- readonly displayName: string;
444
- hasName(name: string): boolean;
445
- readonly allAliases: string[];
446
- readonly allRefNames: string[] | undefined;
447
- readonly lowerCaseRefNames: string[] | undefined;
448
- readonly allRefNamesWithLowerCase: string[] | undefined;
449
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
450
- readonly refNameColors: string[];
451
- } & {
452
- readonly refNames: string[] | undefined;
453
- } & {
454
- getCanonicalRefName(refName: string): string | undefined;
455
- getRefNameColor(refName: string): string | undefined;
456
- isValidRefName(refName: string): boolean;
457
- } & {
458
- setLoaded({ regions, refNameAliases, cytobands, }: {
459
- regions: import("@jbrowse/core/util").Region[];
460
- refNameAliases: {
461
- [x: string]: string;
462
- };
463
- cytobands: import("@jbrowse/core/util").Feature[];
464
- }): void;
465
- setError(e: unknown): void;
466
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
467
- setRefNameAliases(aliases: {
468
- [x: string]: string;
469
- }): void;
470
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
471
- setLoadingP(p?: Promise<void>): void;
472
- load(): Promise<void>;
473
- loadPre(): Promise<void>;
474
- } & {
475
- getAdapterMapEntry(adapterConf: {
476
- [x: string]: unknown;
477
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
478
- getRefNameMapForAdapter(adapterConf: {
479
- [x: string]: unknown;
480
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
481
- [x: string]: string;
482
- }>;
483
- getReverseRefNameMapForAdapter(adapterConf: {
484
- [x: string]: unknown;
485
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
486
- [x: string]: string;
487
- }>;
488
- afterCreate(): void;
489
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
490
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
491
- }, {
492
- error: unknown;
493
- loadingP: Promise<void> | undefined;
494
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
495
- refNameAliases: {
496
- [x: string]: string;
497
- } | undefined;
498
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
499
- } & {
500
- getConf(arg: string): any;
501
- readonly lowerCaseRefNameAliases: {
502
- [k: string]: string;
503
- } | undefined;
504
- } & {
505
- readonly initialized: boolean;
506
- readonly name: string;
507
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
508
- readonly aliases: string[];
509
- readonly displayName: string;
510
- hasName(name: string): boolean;
511
- readonly allAliases: string[];
512
- readonly allRefNames: string[] | undefined;
513
- readonly lowerCaseRefNames: string[] | undefined;
514
- readonly allRefNamesWithLowerCase: string[] | undefined;
515
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
516
- readonly refNameColors: string[];
517
- } & {
518
- readonly refNames: string[] | undefined;
519
- } & {
520
- getCanonicalRefName(refName: string): string | undefined;
521
- getRefNameColor(refName: string): string | undefined;
522
- isValidRefName(refName: string): boolean;
523
- } & {
524
- setLoaded({ regions, refNameAliases, cytobands, }: {
525
- regions: import("@jbrowse/core/util").Region[];
526
- refNameAliases: {
527
- [x: string]: string;
528
- };
529
- cytobands: import("@jbrowse/core/util").Feature[];
530
- }): void;
531
- setError(e: unknown): void;
532
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
533
- setRefNameAliases(aliases: {
534
- [x: string]: string;
535
- }): void;
536
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
537
- setLoadingP(p?: Promise<void>): void;
538
- load(): Promise<void>;
539
- loadPre(): Promise<void>;
540
- } & {
541
- getAdapterMapEntry(adapterConf: {
542
- [x: string]: unknown;
543
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
544
- getRefNameMapForAdapter(adapterConf: {
545
- [x: string]: unknown;
546
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
547
- [x: string]: string;
548
- }>;
549
- getReverseRefNameMapForAdapter(adapterConf: {
550
- [x: string]: unknown;
551
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
552
- [x: string]: string;
553
- }>;
554
- afterCreate(): void;
555
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
556
- getRefNameMapForAdapter(adapterConf: {
557
- [x: string]: unknown;
558
- }, assemblyName: string | undefined, opts: {
559
- stopToken?: string;
560
- sessionId: string;
561
- }): Promise<{
562
- [x: string]: string;
563
- } | undefined>;
564
- getReverseRefNameMapForAdapter(adapterConf: {
565
- [x: string]: unknown;
566
- }, assemblyName: string | undefined, opts: {
567
- stopToken?: string;
568
- sessionId: string;
569
- }): Promise<{
570
- [x: string]: string;
571
- } | undefined>;
572
- isValidRefName(refName: string, assemblyName: string): boolean;
573
- } & {
574
- afterAttach(): void;
575
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
576
- addAssembly(configuration: any): void;
577
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
578
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
579
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
580
- }, {
581
- error: unknown;
582
- loadingP: Promise<void> | undefined;
583
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
584
- refNameAliases: {
585
- [x: string]: string;
586
- } | undefined;
587
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
588
- } & {
589
- getConf(arg: string): any;
590
- readonly lowerCaseRefNameAliases: {
591
- [k: string]: string;
592
- } | undefined;
593
- } & {
594
- readonly initialized: boolean;
595
- readonly name: string;
596
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
597
- readonly aliases: string[];
598
- readonly displayName: string;
599
- hasName(name: string): boolean;
600
- readonly allAliases: string[];
601
- readonly allRefNames: string[] | undefined;
602
- readonly lowerCaseRefNames: string[] | undefined;
603
- readonly allRefNamesWithLowerCase: string[] | undefined;
604
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
605
- readonly refNameColors: string[];
606
- } & {
607
- readonly refNames: string[] | undefined;
608
- } & {
609
- getCanonicalRefName(refName: string): string | undefined;
610
- getRefNameColor(refName: string): string | undefined;
611
- isValidRefName(refName: string): boolean;
612
- } & {
613
- setLoaded({ regions, refNameAliases, cytobands, }: {
614
- regions: import("@jbrowse/core/util").Region[];
615
- refNameAliases: {
616
- [x: string]: string;
617
- };
618
- cytobands: import("@jbrowse/core/util").Feature[];
619
- }): void;
620
- setError(e: unknown): void;
621
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
622
- setRefNameAliases(aliases: {
623
- [x: string]: string;
624
- }): void;
625
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
626
- setLoadingP(p?: Promise<void>): void;
627
- load(): Promise<void>;
628
- loadPre(): Promise<void>;
629
- } & {
630
- getAdapterMapEntry(adapterConf: {
631
- [x: string]: unknown;
632
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
633
- getRefNameMapForAdapter(adapterConf: {
634
- [x: string]: unknown;
635
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
636
- [x: string]: string;
637
- }>;
638
- getReverseRefNameMapForAdapter(adapterConf: {
639
- [x: string]: unknown;
640
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
641
- [x: string]: string;
642
- }>;
643
- afterCreate(): void;
644
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
645
- }, {
646
- readonly assemblyNameMap: Record<string, {
647
- configuration: any;
648
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
649
- error: unknown;
650
- loadingP: Promise<void> | undefined;
651
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
652
- refNameAliases: {
653
- [x: string]: string;
654
- } | undefined;
655
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
656
- } & {
657
- getConf(arg: string): any;
658
- readonly lowerCaseRefNameAliases: {
659
- [k: string]: string;
660
- } | undefined;
661
- } & {
662
- readonly initialized: boolean;
663
- readonly name: string;
664
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
665
- readonly aliases: string[];
666
- readonly displayName: string;
667
- hasName(name: string): boolean;
668
- readonly allAliases: string[];
669
- readonly allRefNames: string[] | undefined;
670
- readonly lowerCaseRefNames: string[] | undefined;
671
- readonly allRefNamesWithLowerCase: string[] | undefined;
672
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
673
- readonly refNameColors: string[];
674
- } & {
675
- readonly refNames: string[] | undefined;
676
- } & {
677
- getCanonicalRefName(refName: string): string | undefined;
678
- getRefNameColor(refName: string): string | undefined;
679
- isValidRefName(refName: string): boolean;
680
- } & {
681
- setLoaded({ regions, refNameAliases, cytobands, }: {
682
- regions: import("@jbrowse/core/util").Region[];
683
- refNameAliases: {
684
- [x: string]: string;
685
- };
686
- cytobands: import("@jbrowse/core/util").Feature[];
687
- }): void;
688
- setError(e: unknown): void;
689
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
690
- setRefNameAliases(aliases: {
691
- [x: string]: string;
692
- }): void;
693
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
694
- setLoadingP(p?: Promise<void>): void;
695
- load(): Promise<void>;
696
- loadPre(): Promise<void>;
697
- } & {
698
- getAdapterMapEntry(adapterConf: {
699
- [x: string]: unknown;
700
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
701
- getRefNameMapForAdapter(adapterConf: {
702
- [x: string]: unknown;
703
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
704
- [x: string]: string;
705
- }>;
706
- getReverseRefNameMapForAdapter(adapterConf: {
707
- [x: string]: unknown;
708
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
709
- [x: string]: string;
710
- }>;
711
- afterCreate(): void;
712
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
713
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
714
- }, {
715
- error: unknown;
716
- loadingP: Promise<void> | undefined;
717
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
718
- refNameAliases: {
719
- [x: string]: string;
720
- } | undefined;
721
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
722
- } & {
723
- getConf(arg: string): any;
724
- readonly lowerCaseRefNameAliases: {
725
- [k: string]: string;
726
- } | undefined;
727
- } & {
728
- readonly initialized: boolean;
729
- readonly name: string;
730
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
731
- readonly aliases: string[];
732
- readonly displayName: string;
733
- hasName(name: string): boolean;
734
- readonly allAliases: string[];
735
- readonly allRefNames: string[] | undefined;
736
- readonly lowerCaseRefNames: string[] | undefined;
737
- readonly allRefNamesWithLowerCase: string[] | undefined;
738
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
739
- readonly refNameColors: string[];
740
- } & {
741
- readonly refNames: string[] | undefined;
742
- } & {
743
- getCanonicalRefName(refName: string): string | undefined;
744
- getRefNameColor(refName: string): string | undefined;
745
- isValidRefName(refName: string): boolean;
746
- } & {
747
- setLoaded({ regions, refNameAliases, cytobands, }: {
748
- regions: import("@jbrowse/core/util").Region[];
749
- refNameAliases: {
750
- [x: string]: string;
751
- };
752
- cytobands: import("@jbrowse/core/util").Feature[];
753
- }): void;
754
- setError(e: unknown): void;
755
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
756
- setRefNameAliases(aliases: {
757
- [x: string]: string;
758
- }): void;
759
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
760
- setLoadingP(p?: Promise<void>): void;
761
- load(): Promise<void>;
762
- loadPre(): Promise<void>;
763
- } & {
764
- getAdapterMapEntry(adapterConf: {
765
- [x: string]: unknown;
766
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
767
- getRefNameMapForAdapter(adapterConf: {
768
- [x: string]: unknown;
769
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
770
- [x: string]: string;
771
- }>;
772
- getReverseRefNameMapForAdapter(adapterConf: {
773
- [x: string]: unknown;
774
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
775
- [x: string]: string;
776
- }>;
777
- afterCreate(): void;
778
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
779
- } & {
780
- getCanonicalAssemblyName(asmName: string): string | undefined;
781
- get(asmName: string): ({
782
- configuration: any;
783
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
784
- error: unknown;
785
- loadingP: Promise<void> | undefined;
786
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
787
- refNameAliases: {
788
- [x: string]: string;
789
- } | undefined;
790
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
791
- } & {
792
- getConf(arg: string): any;
793
- readonly lowerCaseRefNameAliases: {
794
- [k: string]: string;
795
- } | undefined;
796
- } & {
797
- readonly initialized: boolean;
798
- readonly name: string;
799
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
800
- readonly aliases: string[];
801
- readonly displayName: string;
802
- hasName(name: string): boolean;
803
- readonly allAliases: string[];
804
- readonly allRefNames: string[] | undefined;
805
- readonly lowerCaseRefNames: string[] | undefined;
806
- readonly allRefNamesWithLowerCase: string[] | undefined;
807
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
808
- readonly refNameColors: string[];
809
- } & {
810
- readonly refNames: string[] | undefined;
811
- } & {
812
- getCanonicalRefName(refName: string): string | undefined;
813
- getRefNameColor(refName: string): string | undefined;
814
- isValidRefName(refName: string): boolean;
815
- } & {
816
- setLoaded({ regions, refNameAliases, cytobands, }: {
817
- regions: import("@jbrowse/core/util").Region[];
818
- refNameAliases: {
819
- [x: string]: string;
820
- };
821
- cytobands: import("@jbrowse/core/util").Feature[];
822
- }): void;
823
- setError(e: unknown): void;
824
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
825
- setRefNameAliases(aliases: {
826
- [x: string]: string;
827
- }): void;
828
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
829
- setLoadingP(p?: Promise<void>): void;
830
- load(): Promise<void>;
831
- loadPre(): Promise<void>;
832
- } & {
833
- getAdapterMapEntry(adapterConf: {
834
- [x: string]: unknown;
835
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
836
- getRefNameMapForAdapter(adapterConf: {
837
- [x: string]: unknown;
838
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
839
- [x: string]: string;
840
- }>;
841
- getReverseRefNameMapForAdapter(adapterConf: {
842
- [x: string]: unknown;
843
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
844
- [x: string]: string;
845
- }>;
846
- afterCreate(): void;
847
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
848
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
849
- }, {
850
- error: unknown;
851
- loadingP: Promise<void> | undefined;
852
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
853
- refNameAliases: {
854
- [x: string]: string;
855
- } | undefined;
856
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
857
- } & {
858
- getConf(arg: string): any;
859
- readonly lowerCaseRefNameAliases: {
860
- [k: string]: string;
861
- } | undefined;
862
- } & {
863
- readonly initialized: boolean;
864
- readonly name: string;
865
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
866
- readonly aliases: string[];
867
- readonly displayName: string;
868
- hasName(name: string): boolean;
869
- readonly allAliases: string[];
870
- readonly allRefNames: string[] | undefined;
871
- readonly lowerCaseRefNames: string[] | undefined;
872
- readonly allRefNamesWithLowerCase: string[] | undefined;
873
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
874
- readonly refNameColors: string[];
875
- } & {
876
- readonly refNames: string[] | undefined;
877
- } & {
878
- getCanonicalRefName(refName: string): string | undefined;
879
- getRefNameColor(refName: string): string | undefined;
880
- isValidRefName(refName: string): boolean;
881
- } & {
882
- setLoaded({ regions, refNameAliases, cytobands, }: {
883
- regions: import("@jbrowse/core/util").Region[];
884
- refNameAliases: {
885
- [x: string]: string;
886
- };
887
- cytobands: import("@jbrowse/core/util").Feature[];
888
- }): void;
889
- setError(e: unknown): void;
890
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
891
- setRefNameAliases(aliases: {
892
- [x: string]: string;
893
- }): void;
894
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
895
- setLoadingP(p?: Promise<void>): void;
896
- load(): Promise<void>;
897
- loadPre(): Promise<void>;
898
- } & {
899
- getAdapterMapEntry(adapterConf: {
900
- [x: string]: unknown;
901
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
902
- getRefNameMapForAdapter(adapterConf: {
903
- [x: string]: unknown;
904
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
905
- [x: string]: string;
906
- }>;
907
- getReverseRefNameMapForAdapter(adapterConf: {
908
- [x: string]: unknown;
909
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
910
- [x: string]: string;
911
- }>;
912
- afterCreate(): void;
913
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
914
- readonly assemblyNamesList: any[];
915
- readonly assemblyList: AnyConfigurationModel[];
916
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
917
- } & {
918
- waitForAssembly(assemblyName: string): Promise<({
919
- configuration: any;
920
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
921
- error: unknown;
922
- loadingP: Promise<void> | undefined;
923
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
924
- refNameAliases: {
925
- [x: string]: string;
926
- } | undefined;
927
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
928
- } & {
929
- getConf(arg: string): any;
930
- readonly lowerCaseRefNameAliases: {
931
- [k: string]: string;
932
- } | undefined;
933
- } & {
934
- readonly initialized: boolean;
935
- readonly name: string;
936
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
937
- readonly aliases: string[];
938
- readonly displayName: string;
939
- hasName(name: string): boolean;
940
- readonly allAliases: string[];
941
- readonly allRefNames: string[] | undefined;
942
- readonly lowerCaseRefNames: string[] | undefined;
943
- readonly allRefNamesWithLowerCase: string[] | undefined;
944
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
945
- readonly refNameColors: string[];
946
- } & {
947
- readonly refNames: string[] | undefined;
948
- } & {
949
- getCanonicalRefName(refName: string): string | undefined;
950
- getRefNameColor(refName: string): string | undefined;
951
- isValidRefName(refName: string): boolean;
952
- } & {
953
- setLoaded({ regions, refNameAliases, cytobands, }: {
954
- regions: import("@jbrowse/core/util").Region[];
955
- refNameAliases: {
956
- [x: string]: string;
957
- };
958
- cytobands: import("@jbrowse/core/util").Feature[];
959
- }): void;
960
- setError(e: unknown): void;
961
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
962
- setRefNameAliases(aliases: {
963
- [x: string]: string;
964
- }): void;
965
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
966
- setLoadingP(p?: Promise<void>): void;
967
- load(): Promise<void>;
968
- loadPre(): Promise<void>;
969
- } & {
970
- getAdapterMapEntry(adapterConf: {
971
- [x: string]: unknown;
972
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
973
- getRefNameMapForAdapter(adapterConf: {
974
- [x: string]: unknown;
975
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
976
- [x: string]: string;
977
- }>;
978
- getReverseRefNameMapForAdapter(adapterConf: {
979
- [x: string]: unknown;
980
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
981
- [x: string]: string;
982
- }>;
983
- afterCreate(): void;
984
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
985
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
986
- }, {
987
- error: unknown;
988
- loadingP: Promise<void> | undefined;
989
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
990
- refNameAliases: {
991
- [x: string]: string;
992
- } | undefined;
993
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
994
- } & {
995
- getConf(arg: string): any;
996
- readonly lowerCaseRefNameAliases: {
997
- [k: string]: string;
998
- } | undefined;
999
- } & {
1000
- readonly initialized: boolean;
1001
- readonly name: string;
1002
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1003
- readonly aliases: string[];
1004
- readonly displayName: string;
1005
- hasName(name: string): boolean;
1006
- readonly allAliases: string[];
1007
- readonly allRefNames: string[] | undefined;
1008
- readonly lowerCaseRefNames: string[] | undefined;
1009
- readonly allRefNamesWithLowerCase: string[] | undefined;
1010
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1011
- readonly refNameColors: string[];
1012
- } & {
1013
- readonly refNames: string[] | undefined;
1014
- } & {
1015
- getCanonicalRefName(refName: string): string | undefined;
1016
- getRefNameColor(refName: string): string | undefined;
1017
- isValidRefName(refName: string): boolean;
1018
- } & {
1019
- setLoaded({ regions, refNameAliases, cytobands, }: {
1020
- regions: import("@jbrowse/core/util").Region[];
1021
- refNameAliases: {
1022
- [x: string]: string;
1023
- };
1024
- cytobands: import("@jbrowse/core/util").Feature[];
1025
- }): void;
1026
- setError(e: unknown): void;
1027
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1028
- setRefNameAliases(aliases: {
1029
- [x: string]: string;
1030
- }): void;
1031
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1032
- setLoadingP(p?: Promise<void>): void;
1033
- load(): Promise<void>;
1034
- loadPre(): Promise<void>;
1035
- } & {
1036
- getAdapterMapEntry(adapterConf: {
1037
- [x: string]: unknown;
1038
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1039
- getRefNameMapForAdapter(adapterConf: {
1040
- [x: string]: unknown;
1041
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1042
- [x: string]: string;
1043
- }>;
1044
- getReverseRefNameMapForAdapter(adapterConf: {
1045
- [x: string]: unknown;
1046
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1047
- [x: string]: string;
1048
- }>;
1049
- afterCreate(): void;
1050
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1051
- getRefNameMapForAdapter(adapterConf: {
1052
- [x: string]: unknown;
1053
- }, assemblyName: string | undefined, opts: {
1054
- stopToken?: string;
1055
- sessionId: string;
1056
- }): Promise<{
1057
- [x: string]: string;
1058
- } | undefined>;
1059
- getReverseRefNameMapForAdapter(adapterConf: {
1060
- [x: string]: unknown;
1061
- }, assemblyName: string | undefined, opts: {
1062
- stopToken?: string;
1063
- sessionId: string;
1064
- }): Promise<{
1065
- [x: string]: string;
1066
- } | undefined>;
1067
- isValidRefName(refName: string, assemblyName: string): boolean;
1068
- } & {
1069
- afterAttach(): void;
1070
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1071
- addAssembly(configuration: any): void;
1072
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
1073
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1074
- rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1075
- adminMode: boolean;
1076
- error: unknown;
1077
- textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1078
- pluginManager: PluginManager;
1079
- } & {
1080
- setError(error: unknown): void;
1081
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1082
- setDefaultSession(): void;
1083
- setSessionPath(path: string): void;
1084
- renameCurrentSession(newName: string): void;
1085
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1086
- jbrowse: import("mobx-state-tree").IAnyType;
1087
- session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
1088
- sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1089
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1090
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1091
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1092
- }, {
1093
- error: unknown;
1094
- loadingP: Promise<void> | undefined;
1095
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1096
- refNameAliases: {
1097
- [x: string]: string;
1098
- } | undefined;
1099
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1100
- } & {
1101
- getConf(arg: string): any;
1102
- readonly lowerCaseRefNameAliases: {
1103
- [k: string]: string;
1104
- } | undefined;
1105
- } & {
1106
- readonly initialized: boolean;
1107
- readonly name: string;
1108
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1109
- readonly aliases: string[];
1110
- readonly displayName: string;
1111
- hasName(name: string): boolean;
1112
- readonly allAliases: string[];
1113
- readonly allRefNames: string[] | undefined;
1114
- readonly lowerCaseRefNames: string[] | undefined;
1115
- readonly allRefNamesWithLowerCase: string[] | undefined;
1116
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1117
- readonly refNameColors: string[];
1118
- } & {
1119
- readonly refNames: string[] | undefined;
1120
- } & {
1121
- getCanonicalRefName(refName: string): string | undefined;
1122
- getRefNameColor(refName: string): string | undefined;
1123
- isValidRefName(refName: string): boolean;
1124
- } & {
1125
- setLoaded({ regions, refNameAliases, cytobands, }: {
1126
- regions: import("@jbrowse/core/util").Region[];
1127
- refNameAliases: {
1128
- [x: string]: string;
1129
- };
1130
- cytobands: import("@jbrowse/core/util").Feature[];
1131
- }): void;
1132
- setError(e: unknown): void;
1133
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1134
- setRefNameAliases(aliases: {
1135
- [x: string]: string;
1136
- }): void;
1137
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1138
- setLoadingP(p?: Promise<void>): void;
1139
- load(): Promise<void>;
1140
- loadPre(): Promise<void>;
1141
- } & {
1142
- getAdapterMapEntry(adapterConf: {
1143
- [x: string]: unknown;
1144
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1145
- getRefNameMapForAdapter(adapterConf: {
1146
- [x: string]: unknown;
1147
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1148
- [x: string]: string;
1149
- }>;
1150
- getReverseRefNameMapForAdapter(adapterConf: {
1151
- [x: string]: unknown;
1152
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1153
- [x: string]: string;
1154
- }>;
1155
- afterCreate(): void;
1156
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1157
- }, {
1158
- readonly assemblyNameMap: Record<string, {
1159
- configuration: any;
1160
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1161
- error: unknown;
1162
- loadingP: Promise<void> | undefined;
1163
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1164
- refNameAliases: {
1165
- [x: string]: string;
1166
- } | undefined;
1167
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1168
- } & {
1169
- getConf(arg: string): any;
1170
- readonly lowerCaseRefNameAliases: {
1171
- [k: string]: string;
1172
- } | undefined;
1173
- } & {
1174
- readonly initialized: boolean;
1175
- readonly name: string;
1176
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1177
- readonly aliases: string[];
1178
- readonly displayName: string;
1179
- hasName(name: string): boolean;
1180
- readonly allAliases: string[];
1181
- readonly allRefNames: string[] | undefined;
1182
- readonly lowerCaseRefNames: string[] | undefined;
1183
- readonly allRefNamesWithLowerCase: string[] | undefined;
1184
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1185
- readonly refNameColors: string[];
1186
- } & {
1187
- readonly refNames: string[] | undefined;
1188
- } & {
1189
- getCanonicalRefName(refName: string): string | undefined;
1190
- getRefNameColor(refName: string): string | undefined;
1191
- isValidRefName(refName: string): boolean;
1192
- } & {
1193
- setLoaded({ regions, refNameAliases, cytobands, }: {
1194
- regions: import("@jbrowse/core/util").Region[];
1195
- refNameAliases: {
1196
- [x: string]: string;
1197
- };
1198
- cytobands: import("@jbrowse/core/util").Feature[];
1199
- }): void;
1200
- setError(e: unknown): void;
1201
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1202
- setRefNameAliases(aliases: {
1203
- [x: string]: string;
1204
- }): void;
1205
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1206
- setLoadingP(p?: Promise<void>): void;
1207
- load(): Promise<void>;
1208
- loadPre(): Promise<void>;
1209
- } & {
1210
- getAdapterMapEntry(adapterConf: {
1211
- [x: string]: unknown;
1212
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1213
- getRefNameMapForAdapter(adapterConf: {
1214
- [x: string]: unknown;
1215
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1216
- [x: string]: string;
1217
- }>;
1218
- getReverseRefNameMapForAdapter(adapterConf: {
1219
- [x: string]: unknown;
1220
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1221
- [x: string]: string;
1222
- }>;
1223
- afterCreate(): void;
1224
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1225
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1226
- }, {
1227
- error: unknown;
1228
- loadingP: Promise<void> | undefined;
1229
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1230
- refNameAliases: {
1231
- [x: string]: string;
1232
- } | undefined;
1233
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1234
- } & {
1235
- getConf(arg: string): any;
1236
- readonly lowerCaseRefNameAliases: {
1237
- [k: string]: string;
1238
- } | undefined;
1239
- } & {
1240
- readonly initialized: boolean;
1241
- readonly name: string;
1242
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1243
- readonly aliases: string[];
1244
- readonly displayName: string;
1245
- hasName(name: string): boolean;
1246
- readonly allAliases: string[];
1247
- readonly allRefNames: string[] | undefined;
1248
- readonly lowerCaseRefNames: string[] | undefined;
1249
- readonly allRefNamesWithLowerCase: string[] | undefined;
1250
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1251
- readonly refNameColors: string[];
1252
- } & {
1253
- readonly refNames: string[] | undefined;
1254
- } & {
1255
- getCanonicalRefName(refName: string): string | undefined;
1256
- getRefNameColor(refName: string): string | undefined;
1257
- isValidRefName(refName: string): boolean;
1258
- } & {
1259
- setLoaded({ regions, refNameAliases, cytobands, }: {
1260
- regions: import("@jbrowse/core/util").Region[];
1261
- refNameAliases: {
1262
- [x: string]: string;
1263
- };
1264
- cytobands: import("@jbrowse/core/util").Feature[];
1265
- }): void;
1266
- setError(e: unknown): void;
1267
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1268
- setRefNameAliases(aliases: {
1269
- [x: string]: string;
1270
- }): void;
1271
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1272
- setLoadingP(p?: Promise<void>): void;
1273
- load(): Promise<void>;
1274
- loadPre(): Promise<void>;
1275
- } & {
1276
- getAdapterMapEntry(adapterConf: {
1277
- [x: string]: unknown;
1278
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1279
- getRefNameMapForAdapter(adapterConf: {
1280
- [x: string]: unknown;
1281
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1282
- [x: string]: string;
1283
- }>;
1284
- getReverseRefNameMapForAdapter(adapterConf: {
1285
- [x: string]: unknown;
1286
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1287
- [x: string]: string;
1288
- }>;
1289
- afterCreate(): void;
1290
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
1291
- } & {
1292
- getCanonicalAssemblyName(asmName: string): string | undefined;
1293
- get(asmName: string): ({
1294
- configuration: any;
1295
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1296
- error: unknown;
1297
- loadingP: Promise<void> | undefined;
1298
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1299
- refNameAliases: {
1300
- [x: string]: string;
1301
- } | undefined;
1302
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1303
- } & {
1304
- getConf(arg: string): any;
1305
- readonly lowerCaseRefNameAliases: {
1306
- [k: string]: string;
1307
- } | undefined;
1308
- } & {
1309
- readonly initialized: boolean;
1310
- readonly name: string;
1311
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1312
- readonly aliases: string[];
1313
- readonly displayName: string;
1314
- hasName(name: string): boolean;
1315
- readonly allAliases: string[];
1316
- readonly allRefNames: string[] | undefined;
1317
- readonly lowerCaseRefNames: string[] | undefined;
1318
- readonly allRefNamesWithLowerCase: string[] | undefined;
1319
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1320
- readonly refNameColors: string[];
1321
- } & {
1322
- readonly refNames: string[] | undefined;
1323
- } & {
1324
- getCanonicalRefName(refName: string): string | undefined;
1325
- getRefNameColor(refName: string): string | undefined;
1326
- isValidRefName(refName: string): boolean;
1327
- } & {
1328
- setLoaded({ regions, refNameAliases, cytobands, }: {
1329
- regions: import("@jbrowse/core/util").Region[];
1330
- refNameAliases: {
1331
- [x: string]: string;
1332
- };
1333
- cytobands: import("@jbrowse/core/util").Feature[];
1334
- }): void;
1335
- setError(e: unknown): void;
1336
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1337
- setRefNameAliases(aliases: {
1338
- [x: string]: string;
1339
- }): void;
1340
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1341
- setLoadingP(p?: Promise<void>): void;
1342
- load(): Promise<void>;
1343
- loadPre(): Promise<void>;
1344
- } & {
1345
- getAdapterMapEntry(adapterConf: {
1346
- [x: string]: unknown;
1347
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1348
- getRefNameMapForAdapter(adapterConf: {
1349
- [x: string]: unknown;
1350
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1351
- [x: string]: string;
1352
- }>;
1353
- getReverseRefNameMapForAdapter(adapterConf: {
1354
- [x: string]: unknown;
1355
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1356
- [x: string]: string;
1357
- }>;
1358
- afterCreate(): void;
1359
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1360
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1361
- }, {
1362
- error: unknown;
1363
- loadingP: Promise<void> | undefined;
1364
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1365
- refNameAliases: {
1366
- [x: string]: string;
1367
- } | undefined;
1368
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1369
- } & {
1370
- getConf(arg: string): any;
1371
- readonly lowerCaseRefNameAliases: {
1372
- [k: string]: string;
1373
- } | undefined;
1374
- } & {
1375
- readonly initialized: boolean;
1376
- readonly name: string;
1377
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1378
- readonly aliases: string[];
1379
- readonly displayName: string;
1380
- hasName(name: string): boolean;
1381
- readonly allAliases: string[];
1382
- readonly allRefNames: string[] | undefined;
1383
- readonly lowerCaseRefNames: string[] | undefined;
1384
- readonly allRefNamesWithLowerCase: string[] | undefined;
1385
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1386
- readonly refNameColors: string[];
1387
- } & {
1388
- readonly refNames: string[] | undefined;
1389
- } & {
1390
- getCanonicalRefName(refName: string): string | undefined;
1391
- getRefNameColor(refName: string): string | undefined;
1392
- isValidRefName(refName: string): boolean;
1393
- } & {
1394
- setLoaded({ regions, refNameAliases, cytobands, }: {
1395
- regions: import("@jbrowse/core/util").Region[];
1396
- refNameAliases: {
1397
- [x: string]: string;
1398
- };
1399
- cytobands: import("@jbrowse/core/util").Feature[];
1400
- }): void;
1401
- setError(e: unknown): void;
1402
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1403
- setRefNameAliases(aliases: {
1404
- [x: string]: string;
1405
- }): void;
1406
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1407
- setLoadingP(p?: Promise<void>): void;
1408
- load(): Promise<void>;
1409
- loadPre(): Promise<void>;
1410
- } & {
1411
- getAdapterMapEntry(adapterConf: {
1412
- [x: string]: unknown;
1413
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1414
- getRefNameMapForAdapter(adapterConf: {
1415
- [x: string]: unknown;
1416
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1417
- [x: string]: string;
1418
- }>;
1419
- getReverseRefNameMapForAdapter(adapterConf: {
1420
- [x: string]: unknown;
1421
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1422
- [x: string]: string;
1423
- }>;
1424
- afterCreate(): void;
1425
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1426
- readonly assemblyNamesList: any[];
1427
- readonly assemblyList: AnyConfigurationModel[];
1428
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1429
- } & {
1430
- waitForAssembly(assemblyName: string): Promise<({
1431
- configuration: any;
1432
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1433
- error: unknown;
1434
- loadingP: Promise<void> | undefined;
1435
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1436
- refNameAliases: {
1437
- [x: string]: string;
1438
- } | undefined;
1439
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1440
- } & {
1441
- getConf(arg: string): any;
1442
- readonly lowerCaseRefNameAliases: {
1443
- [k: string]: string;
1444
- } | undefined;
1445
- } & {
1446
- readonly initialized: boolean;
1447
- readonly name: string;
1448
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1449
- readonly aliases: string[];
1450
- readonly displayName: string;
1451
- hasName(name: string): boolean;
1452
- readonly allAliases: string[];
1453
- readonly allRefNames: string[] | undefined;
1454
- readonly lowerCaseRefNames: string[] | undefined;
1455
- readonly allRefNamesWithLowerCase: string[] | undefined;
1456
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1457
- readonly refNameColors: string[];
1458
- } & {
1459
- readonly refNames: string[] | undefined;
1460
- } & {
1461
- getCanonicalRefName(refName: string): string | undefined;
1462
- getRefNameColor(refName: string): string | undefined;
1463
- isValidRefName(refName: string): boolean;
1464
- } & {
1465
- setLoaded({ regions, refNameAliases, cytobands, }: {
1466
- regions: import("@jbrowse/core/util").Region[];
1467
- refNameAliases: {
1468
- [x: string]: string;
1469
- };
1470
- cytobands: import("@jbrowse/core/util").Feature[];
1471
- }): void;
1472
- setError(e: unknown): void;
1473
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1474
- setRefNameAliases(aliases: {
1475
- [x: string]: string;
1476
- }): void;
1477
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1478
- setLoadingP(p?: Promise<void>): void;
1479
- load(): Promise<void>;
1480
- loadPre(): Promise<void>;
1481
- } & {
1482
- getAdapterMapEntry(adapterConf: {
1483
- [x: string]: unknown;
1484
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1485
- getRefNameMapForAdapter(adapterConf: {
1486
- [x: string]: unknown;
1487
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1488
- [x: string]: string;
1489
- }>;
1490
- getReverseRefNameMapForAdapter(adapterConf: {
1491
- [x: string]: unknown;
1492
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1493
- [x: string]: string;
1494
- }>;
1495
- afterCreate(): void;
1496
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1497
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1498
- }, {
1499
- error: unknown;
1500
- loadingP: Promise<void> | undefined;
1501
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1502
- refNameAliases: {
1503
- [x: string]: string;
1504
- } | undefined;
1505
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1506
- } & {
1507
- getConf(arg: string): any;
1508
- readonly lowerCaseRefNameAliases: {
1509
- [k: string]: string;
1510
- } | undefined;
1511
- } & {
1512
- readonly initialized: boolean;
1513
- readonly name: string;
1514
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1515
- readonly aliases: string[];
1516
- readonly displayName: string;
1517
- hasName(name: string): boolean;
1518
- readonly allAliases: string[];
1519
- readonly allRefNames: string[] | undefined;
1520
- readonly lowerCaseRefNames: string[] | undefined;
1521
- readonly allRefNamesWithLowerCase: string[] | undefined;
1522
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1523
- readonly refNameColors: string[];
1524
- } & {
1525
- readonly refNames: string[] | undefined;
1526
- } & {
1527
- getCanonicalRefName(refName: string): string | undefined;
1528
- getRefNameColor(refName: string): string | undefined;
1529
- isValidRefName(refName: string): boolean;
1530
- } & {
1531
- setLoaded({ regions, refNameAliases, cytobands, }: {
1532
- regions: import("@jbrowse/core/util").Region[];
1533
- refNameAliases: {
1534
- [x: string]: string;
1535
- };
1536
- cytobands: import("@jbrowse/core/util").Feature[];
1537
- }): void;
1538
- setError(e: unknown): void;
1539
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1540
- setRefNameAliases(aliases: {
1541
- [x: string]: string;
1542
- }): void;
1543
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1544
- setLoadingP(p?: Promise<void>): void;
1545
- load(): Promise<void>;
1546
- loadPre(): Promise<void>;
1547
- } & {
1548
- getAdapterMapEntry(adapterConf: {
1549
- [x: string]: unknown;
1550
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1551
- getRefNameMapForAdapter(adapterConf: {
1552
- [x: string]: unknown;
1553
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1554
- [x: string]: string;
1555
- }>;
1556
- getReverseRefNameMapForAdapter(adapterConf: {
1557
- [x: string]: unknown;
1558
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1559
- [x: string]: string;
1560
- }>;
1561
- afterCreate(): void;
1562
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1563
- getRefNameMapForAdapter(adapterConf: {
1564
- [x: string]: unknown;
1565
- }, assemblyName: string | undefined, opts: {
1566
- stopToken?: string;
1567
- sessionId: string;
1568
- }): Promise<{
1569
- [x: string]: string;
1570
- } | undefined>;
1571
- getReverseRefNameMapForAdapter(adapterConf: {
1572
- [x: string]: unknown;
1573
- }, assemblyName: string | undefined, opts: {
1574
- stopToken?: string;
1575
- sessionId: string;
1576
- }): Promise<{
1577
- [x: string]: string;
1578
- } | undefined>;
1579
- isValidRefName(refName: string, assemblyName: string): boolean;
1580
- } & {
1581
- afterAttach(): void;
1582
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1583
- addAssembly(configuration: any): void;
1584
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
1585
- }, {
1586
- rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1587
- adminMode: boolean;
1588
- error: unknown;
1589
- textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1590
- pluginManager: PluginManager;
1591
- } & {
1592
- setError(error: unknown): void;
1593
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1594
- setDefaultSession(): void;
1595
- setSessionPath(path: string): void;
1596
- renameCurrentSession(newName: string): void;
1597
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1598
- } & {
1599
- readonly jbrowse: any;
1600
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1601
- readonly configuration: {
1602
- [x: string]: any;
1603
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1604
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1605
- [x: string]: any;
1606
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1607
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1608
- [x: string]: any;
1609
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1610
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1611
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1612
- readonly adminMode: boolean;
1613
- readonly textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1614
- } & {
1615
- readonly assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
1616
- } & {
1617
- setSelection(thing: unknown): void;
1618
- clearSelection(): void;
1619
- setHovered(thing: unknown): void;
1620
- } & {
1621
- getReferring(object: IAnyStateTreeNode): import("./ReferenceManagement").ReferringNode[];
1622
- } & {
1623
- removeReferring(referring: import("./ReferenceManagement").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
1624
- } & {
1625
- readonly tracks: AnyConfigurationModel[];
1626
- } & {
1627
- addTrackConf(trackConf: AnyConfiguration): any;
1628
- deleteTrackConf(trackConf: AnyConfigurationModel): any;
1629
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
1630
- export type SessionWithTracksType = ReturnType<typeof TracksManagerSessionMixin>;
1631
- export type SessionWithTracks = Instance<SessionWithTracksType>;
1632
- export declare function isSessionWithTracks(thing: IAnyStateTreeNode): thing is SessionWithTracks;