@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
@@ -1,1639 +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 SessionTracksManagerSessionMixin(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
- sessionTracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
10
- }, {
11
- selection: unknown;
12
- hovered: unknown;
13
- } & {
14
- readonly root: {
15
- jbrowse: any;
16
- session: any;
17
- sessionPath: string;
18
- assemblyManager: {
19
- assemblies: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
20
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
21
- }, {
22
- error: unknown;
23
- loadingP: Promise<void> | undefined;
24
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
25
- refNameAliases: {
26
- [x: string]: string;
27
- } | undefined;
28
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
29
- } & {
30
- getConf(arg: string): any;
31
- readonly lowerCaseRefNameAliases: {
32
- [k: string]: string;
33
- } | undefined;
34
- } & {
35
- readonly initialized: boolean;
36
- readonly name: string;
37
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
38
- readonly aliases: string[];
39
- readonly displayName: string;
40
- hasName(name: string): boolean;
41
- readonly allAliases: string[];
42
- readonly allRefNames: string[] | undefined;
43
- readonly lowerCaseRefNames: string[] | undefined;
44
- readonly allRefNamesWithLowerCase: string[] | undefined;
45
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
46
- readonly refNameColors: string[];
47
- } & {
48
- readonly refNames: string[] | undefined;
49
- } & {
50
- getCanonicalRefName(refName: string): string | undefined;
51
- getRefNameColor(refName: string): string | undefined;
52
- isValidRefName(refName: string): boolean;
53
- } & {
54
- setLoaded({ regions, refNameAliases, cytobands, }: {
55
- regions: import("@jbrowse/core/util").Region[];
56
- refNameAliases: {
57
- [x: string]: string;
58
- };
59
- cytobands: import("@jbrowse/core/util").Feature[];
60
- }): void;
61
- setError(e: unknown): void;
62
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
63
- setRefNameAliases(aliases: {
64
- [x: string]: string;
65
- }): void;
66
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
67
- setLoadingP(p?: Promise<void>): void;
68
- load(): Promise<void>;
69
- loadPre(): Promise<void>;
70
- } & {
71
- getAdapterMapEntry(adapterConf: {
72
- [x: string]: unknown;
73
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
74
- getRefNameMapForAdapter(adapterConf: {
75
- [x: string]: unknown;
76
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
77
- [x: string]: string;
78
- }>;
79
- getReverseRefNameMapForAdapter(adapterConf: {
80
- [x: string]: unknown;
81
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
82
- [x: string]: string;
83
- }>;
84
- afterCreate(): void;
85
- }, 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<{
86
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
87
- }, {
88
- error: unknown;
89
- loadingP: Promise<void> | undefined;
90
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
91
- refNameAliases: {
92
- [x: string]: string;
93
- } | undefined;
94
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
95
- } & {
96
- getConf(arg: string): any;
97
- readonly lowerCaseRefNameAliases: {
98
- [k: string]: string;
99
- } | undefined;
100
- } & {
101
- readonly initialized: boolean;
102
- readonly name: string;
103
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
104
- readonly aliases: string[];
105
- readonly displayName: string;
106
- hasName(name: string): boolean;
107
- readonly allAliases: string[];
108
- readonly allRefNames: string[] | undefined;
109
- readonly lowerCaseRefNames: string[] | undefined;
110
- readonly allRefNamesWithLowerCase: string[] | undefined;
111
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
112
- readonly refNameColors: string[];
113
- } & {
114
- readonly refNames: string[] | undefined;
115
- } & {
116
- getCanonicalRefName(refName: string): string | undefined;
117
- getRefNameColor(refName: string): string | undefined;
118
- isValidRefName(refName: string): boolean;
119
- } & {
120
- setLoaded({ regions, refNameAliases, cytobands, }: {
121
- regions: import("@jbrowse/core/util").Region[];
122
- refNameAliases: {
123
- [x: string]: string;
124
- };
125
- cytobands: import("@jbrowse/core/util").Feature[];
126
- }): void;
127
- setError(e: unknown): void;
128
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
129
- setRefNameAliases(aliases: {
130
- [x: string]: string;
131
- }): void;
132
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
133
- setLoadingP(p?: Promise<void>): void;
134
- load(): Promise<void>;
135
- loadPre(): Promise<void>;
136
- } & {
137
- getAdapterMapEntry(adapterConf: {
138
- [x: string]: unknown;
139
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
140
- getRefNameMapForAdapter(adapterConf: {
141
- [x: string]: unknown;
142
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
143
- [x: string]: string;
144
- }>;
145
- getReverseRefNameMapForAdapter(adapterConf: {
146
- [x: string]: unknown;
147
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
148
- [x: string]: string;
149
- }>;
150
- afterCreate(): void;
151
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
152
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
153
- readonly assemblyNameMap: Record<string, {
154
- configuration: any;
155
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
156
- error: unknown;
157
- loadingP: Promise<void> | undefined;
158
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
159
- refNameAliases: {
160
- [x: string]: string;
161
- } | undefined;
162
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
163
- } & {
164
- getConf(arg: string): any;
165
- readonly lowerCaseRefNameAliases: {
166
- [k: string]: string;
167
- } | undefined;
168
- } & {
169
- readonly initialized: boolean;
170
- readonly name: string;
171
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
172
- readonly aliases: string[];
173
- readonly displayName: string;
174
- hasName(name: string): boolean;
175
- readonly allAliases: string[];
176
- readonly allRefNames: string[] | undefined;
177
- readonly lowerCaseRefNames: string[] | undefined;
178
- readonly allRefNamesWithLowerCase: string[] | undefined;
179
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
180
- readonly refNameColors: string[];
181
- } & {
182
- readonly refNames: string[] | undefined;
183
- } & {
184
- getCanonicalRefName(refName: string): string | undefined;
185
- getRefNameColor(refName: string): string | undefined;
186
- isValidRefName(refName: string): boolean;
187
- } & {
188
- setLoaded({ regions, refNameAliases, cytobands, }: {
189
- regions: import("@jbrowse/core/util").Region[];
190
- refNameAliases: {
191
- [x: string]: string;
192
- };
193
- cytobands: import("@jbrowse/core/util").Feature[];
194
- }): void;
195
- setError(e: unknown): void;
196
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
197
- setRefNameAliases(aliases: {
198
- [x: string]: string;
199
- }): void;
200
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
201
- setLoadingP(p?: Promise<void>): void;
202
- load(): Promise<void>;
203
- loadPre(): Promise<void>;
204
- } & {
205
- getAdapterMapEntry(adapterConf: {
206
- [x: string]: unknown;
207
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
208
- getRefNameMapForAdapter(adapterConf: {
209
- [x: string]: unknown;
210
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
211
- [x: string]: string;
212
- }>;
213
- getReverseRefNameMapForAdapter(adapterConf: {
214
- [x: string]: unknown;
215
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
216
- [x: string]: string;
217
- }>;
218
- afterCreate(): void;
219
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
220
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
221
- }, {
222
- error: unknown;
223
- loadingP: Promise<void> | undefined;
224
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
225
- refNameAliases: {
226
- [x: string]: string;
227
- } | undefined;
228
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
229
- } & {
230
- getConf(arg: string): any;
231
- readonly lowerCaseRefNameAliases: {
232
- [k: string]: string;
233
- } | undefined;
234
- } & {
235
- readonly initialized: boolean;
236
- readonly name: string;
237
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
238
- readonly aliases: string[];
239
- readonly displayName: string;
240
- hasName(name: string): boolean;
241
- readonly allAliases: string[];
242
- readonly allRefNames: string[] | undefined;
243
- readonly lowerCaseRefNames: string[] | undefined;
244
- readonly allRefNamesWithLowerCase: string[] | undefined;
245
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
246
- readonly refNameColors: string[];
247
- } & {
248
- readonly refNames: string[] | undefined;
249
- } & {
250
- getCanonicalRefName(refName: string): string | undefined;
251
- getRefNameColor(refName: string): string | undefined;
252
- isValidRefName(refName: string): boolean;
253
- } & {
254
- setLoaded({ regions, refNameAliases, cytobands, }: {
255
- regions: import("@jbrowse/core/util").Region[];
256
- refNameAliases: {
257
- [x: string]: string;
258
- };
259
- cytobands: import("@jbrowse/core/util").Feature[];
260
- }): void;
261
- setError(e: unknown): void;
262
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
263
- setRefNameAliases(aliases: {
264
- [x: string]: string;
265
- }): void;
266
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
267
- setLoadingP(p?: Promise<void>): void;
268
- load(): Promise<void>;
269
- loadPre(): Promise<void>;
270
- } & {
271
- getAdapterMapEntry(adapterConf: {
272
- [x: string]: unknown;
273
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
274
- getRefNameMapForAdapter(adapterConf: {
275
- [x: string]: unknown;
276
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
277
- [x: string]: string;
278
- }>;
279
- getReverseRefNameMapForAdapter(adapterConf: {
280
- [x: string]: unknown;
281
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
282
- [x: string]: string;
283
- }>;
284
- afterCreate(): void;
285
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
286
- } & {
287
- getCanonicalAssemblyName(asmName: string): string | undefined;
288
- get(asmName: string): ({
289
- configuration: any;
290
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
291
- error: unknown;
292
- loadingP: Promise<void> | undefined;
293
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
294
- refNameAliases: {
295
- [x: string]: string;
296
- } | undefined;
297
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
298
- } & {
299
- getConf(arg: string): any;
300
- readonly lowerCaseRefNameAliases: {
301
- [k: string]: string;
302
- } | undefined;
303
- } & {
304
- readonly initialized: boolean;
305
- readonly name: string;
306
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
307
- readonly aliases: string[];
308
- readonly displayName: string;
309
- hasName(name: string): boolean;
310
- readonly allAliases: string[];
311
- readonly allRefNames: string[] | undefined;
312
- readonly lowerCaseRefNames: string[] | undefined;
313
- readonly allRefNamesWithLowerCase: string[] | undefined;
314
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
315
- readonly refNameColors: string[];
316
- } & {
317
- readonly refNames: string[] | undefined;
318
- } & {
319
- getCanonicalRefName(refName: string): string | undefined;
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").IStateTreeNode<import("mobx-state-tree").IModelType<{
355
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
356
- }, {
357
- error: unknown;
358
- loadingP: Promise<void> | undefined;
359
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
360
- refNameAliases: {
361
- [x: string]: string;
362
- } | undefined;
363
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
364
- } & {
365
- getConf(arg: string): any;
366
- readonly lowerCaseRefNameAliases: {
367
- [k: string]: string;
368
- } | undefined;
369
- } & {
370
- readonly initialized: boolean;
371
- readonly name: string;
372
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
373
- readonly aliases: string[];
374
- readonly displayName: string;
375
- hasName(name: string): boolean;
376
- readonly allAliases: string[];
377
- readonly allRefNames: string[] | undefined;
378
- readonly lowerCaseRefNames: string[] | undefined;
379
- readonly allRefNamesWithLowerCase: string[] | undefined;
380
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
381
- readonly refNameColors: string[];
382
- } & {
383
- readonly refNames: string[] | undefined;
384
- } & {
385
- getCanonicalRefName(refName: string): string | undefined;
386
- getRefNameColor(refName: string): string | undefined;
387
- isValidRefName(refName: string): boolean;
388
- } & {
389
- setLoaded({ regions, refNameAliases, cytobands, }: {
390
- regions: import("@jbrowse/core/util").Region[];
391
- refNameAliases: {
392
- [x: string]: string;
393
- };
394
- cytobands: import("@jbrowse/core/util").Feature[];
395
- }): void;
396
- setError(e: unknown): void;
397
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
398
- setRefNameAliases(aliases: {
399
- [x: string]: string;
400
- }): void;
401
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
402
- setLoadingP(p?: Promise<void>): void;
403
- load(): Promise<void>;
404
- loadPre(): Promise<void>;
405
- } & {
406
- getAdapterMapEntry(adapterConf: {
407
- [x: string]: unknown;
408
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
409
- getRefNameMapForAdapter(adapterConf: {
410
- [x: string]: unknown;
411
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
412
- [x: string]: string;
413
- }>;
414
- getReverseRefNameMapForAdapter(adapterConf: {
415
- [x: string]: unknown;
416
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
417
- [x: string]: string;
418
- }>;
419
- afterCreate(): void;
420
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
421
- readonly assemblyNamesList: any[];
422
- readonly assemblyList: AnyConfigurationModel[];
423
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
424
- } & {
425
- waitForAssembly(assemblyName: string): Promise<({
426
- configuration: any;
427
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
428
- error: unknown;
429
- loadingP: Promise<void> | undefined;
430
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
431
- refNameAliases: {
432
- [x: string]: string;
433
- } | undefined;
434
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
435
- } & {
436
- getConf(arg: string): any;
437
- readonly lowerCaseRefNameAliases: {
438
- [k: string]: string;
439
- } | undefined;
440
- } & {
441
- readonly initialized: boolean;
442
- readonly name: string;
443
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
444
- readonly aliases: string[];
445
- readonly displayName: string;
446
- hasName(name: string): boolean;
447
- readonly allAliases: string[];
448
- readonly allRefNames: string[] | undefined;
449
- readonly lowerCaseRefNames: string[] | undefined;
450
- readonly allRefNamesWithLowerCase: string[] | undefined;
451
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
452
- readonly refNameColors: string[];
453
- } & {
454
- readonly refNames: string[] | undefined;
455
- } & {
456
- getCanonicalRefName(refName: string): string | undefined;
457
- getRefNameColor(refName: string): string | undefined;
458
- isValidRefName(refName: string): boolean;
459
- } & {
460
- setLoaded({ regions, refNameAliases, cytobands, }: {
461
- regions: import("@jbrowse/core/util").Region[];
462
- refNameAliases: {
463
- [x: string]: string;
464
- };
465
- cytobands: import("@jbrowse/core/util").Feature[];
466
- }): void;
467
- setError(e: unknown): void;
468
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
469
- setRefNameAliases(aliases: {
470
- [x: string]: string;
471
- }): void;
472
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
473
- setLoadingP(p?: Promise<void>): void;
474
- load(): Promise<void>;
475
- loadPre(): Promise<void>;
476
- } & {
477
- getAdapterMapEntry(adapterConf: {
478
- [x: string]: unknown;
479
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
480
- getRefNameMapForAdapter(adapterConf: {
481
- [x: string]: unknown;
482
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
483
- [x: string]: string;
484
- }>;
485
- getReverseRefNameMapForAdapter(adapterConf: {
486
- [x: string]: unknown;
487
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
488
- [x: string]: string;
489
- }>;
490
- afterCreate(): void;
491
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
492
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
493
- }, {
494
- error: unknown;
495
- loadingP: Promise<void> | undefined;
496
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
497
- refNameAliases: {
498
- [x: string]: string;
499
- } | undefined;
500
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
501
- } & {
502
- getConf(arg: string): any;
503
- readonly lowerCaseRefNameAliases: {
504
- [k: string]: string;
505
- } | undefined;
506
- } & {
507
- readonly initialized: boolean;
508
- readonly name: string;
509
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
510
- readonly aliases: string[];
511
- readonly displayName: string;
512
- hasName(name: string): boolean;
513
- readonly allAliases: string[];
514
- readonly allRefNames: string[] | undefined;
515
- readonly lowerCaseRefNames: string[] | undefined;
516
- readonly allRefNamesWithLowerCase: string[] | undefined;
517
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
518
- readonly refNameColors: string[];
519
- } & {
520
- readonly refNames: string[] | undefined;
521
- } & {
522
- getCanonicalRefName(refName: string): string | undefined;
523
- getRefNameColor(refName: string): string | undefined;
524
- isValidRefName(refName: string): boolean;
525
- } & {
526
- setLoaded({ regions, refNameAliases, cytobands, }: {
527
- regions: import("@jbrowse/core/util").Region[];
528
- refNameAliases: {
529
- [x: string]: string;
530
- };
531
- cytobands: import("@jbrowse/core/util").Feature[];
532
- }): void;
533
- setError(e: unknown): void;
534
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
535
- setRefNameAliases(aliases: {
536
- [x: string]: string;
537
- }): void;
538
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
539
- setLoadingP(p?: Promise<void>): void;
540
- load(): Promise<void>;
541
- loadPre(): Promise<void>;
542
- } & {
543
- getAdapterMapEntry(adapterConf: {
544
- [x: string]: unknown;
545
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
546
- getRefNameMapForAdapter(adapterConf: {
547
- [x: string]: unknown;
548
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
549
- [x: string]: string;
550
- }>;
551
- getReverseRefNameMapForAdapter(adapterConf: {
552
- [x: string]: unknown;
553
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
554
- [x: string]: string;
555
- }>;
556
- afterCreate(): void;
557
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
558
- getRefNameMapForAdapter(adapterConf: {
559
- [x: string]: unknown;
560
- }, assemblyName: string | undefined, opts: {
561
- stopToken?: string;
562
- sessionId: string;
563
- }): Promise<{
564
- [x: string]: string;
565
- } | undefined>;
566
- getReverseRefNameMapForAdapter(adapterConf: {
567
- [x: string]: unknown;
568
- }, assemblyName: string | undefined, opts: {
569
- stopToken?: string;
570
- sessionId: string;
571
- }): Promise<{
572
- [x: string]: string;
573
- } | undefined>;
574
- isValidRefName(refName: string, assemblyName: string): boolean;
575
- } & {
576
- afterAttach(): void;
577
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
578
- addAssembly(configuration: any): void;
579
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
580
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
581
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
582
- }, {
583
- error: unknown;
584
- loadingP: Promise<void> | undefined;
585
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
586
- refNameAliases: {
587
- [x: string]: string;
588
- } | undefined;
589
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
590
- } & {
591
- getConf(arg: string): any;
592
- readonly lowerCaseRefNameAliases: {
593
- [k: string]: string;
594
- } | undefined;
595
- } & {
596
- readonly initialized: boolean;
597
- readonly name: string;
598
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
599
- readonly aliases: string[];
600
- readonly displayName: string;
601
- hasName(name: string): boolean;
602
- readonly allAliases: string[];
603
- readonly allRefNames: string[] | undefined;
604
- readonly lowerCaseRefNames: string[] | undefined;
605
- readonly allRefNamesWithLowerCase: string[] | undefined;
606
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
607
- readonly refNameColors: string[];
608
- } & {
609
- readonly refNames: string[] | undefined;
610
- } & {
611
- getCanonicalRefName(refName: string): string | undefined;
612
- getRefNameColor(refName: string): string | undefined;
613
- isValidRefName(refName: string): boolean;
614
- } & {
615
- setLoaded({ regions, refNameAliases, cytobands, }: {
616
- regions: import("@jbrowse/core/util").Region[];
617
- refNameAliases: {
618
- [x: string]: string;
619
- };
620
- cytobands: import("@jbrowse/core/util").Feature[];
621
- }): void;
622
- setError(e: unknown): void;
623
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
624
- setRefNameAliases(aliases: {
625
- [x: string]: string;
626
- }): void;
627
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
628
- setLoadingP(p?: Promise<void>): void;
629
- load(): Promise<void>;
630
- loadPre(): Promise<void>;
631
- } & {
632
- getAdapterMapEntry(adapterConf: {
633
- [x: string]: unknown;
634
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
635
- getRefNameMapForAdapter(adapterConf: {
636
- [x: string]: unknown;
637
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
638
- [x: string]: string;
639
- }>;
640
- getReverseRefNameMapForAdapter(adapterConf: {
641
- [x: string]: unknown;
642
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
643
- [x: string]: string;
644
- }>;
645
- afterCreate(): void;
646
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
647
- }, {
648
- readonly assemblyNameMap: Record<string, {
649
- configuration: any;
650
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
651
- error: unknown;
652
- loadingP: Promise<void> | undefined;
653
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
654
- refNameAliases: {
655
- [x: string]: string;
656
- } | undefined;
657
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
658
- } & {
659
- getConf(arg: string): any;
660
- readonly lowerCaseRefNameAliases: {
661
- [k: string]: string;
662
- } | undefined;
663
- } & {
664
- readonly initialized: boolean;
665
- readonly name: string;
666
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
667
- readonly aliases: string[];
668
- readonly displayName: string;
669
- hasName(name: string): boolean;
670
- readonly allAliases: string[];
671
- readonly allRefNames: string[] | undefined;
672
- readonly lowerCaseRefNames: string[] | undefined;
673
- readonly allRefNamesWithLowerCase: string[] | undefined;
674
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
675
- readonly refNameColors: string[];
676
- } & {
677
- readonly refNames: string[] | undefined;
678
- } & {
679
- getCanonicalRefName(refName: string): string | undefined;
680
- getRefNameColor(refName: string): string | undefined;
681
- isValidRefName(refName: string): boolean;
682
- } & {
683
- setLoaded({ regions, refNameAliases, cytobands, }: {
684
- regions: import("@jbrowse/core/util").Region[];
685
- refNameAliases: {
686
- [x: string]: string;
687
- };
688
- cytobands: import("@jbrowse/core/util").Feature[];
689
- }): void;
690
- setError(e: unknown): void;
691
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
692
- setRefNameAliases(aliases: {
693
- [x: string]: string;
694
- }): void;
695
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
696
- setLoadingP(p?: Promise<void>): void;
697
- load(): Promise<void>;
698
- loadPre(): Promise<void>;
699
- } & {
700
- getAdapterMapEntry(adapterConf: {
701
- [x: string]: unknown;
702
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
703
- getRefNameMapForAdapter(adapterConf: {
704
- [x: string]: unknown;
705
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
706
- [x: string]: string;
707
- }>;
708
- getReverseRefNameMapForAdapter(adapterConf: {
709
- [x: string]: unknown;
710
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
711
- [x: string]: string;
712
- }>;
713
- afterCreate(): void;
714
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
715
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
716
- }, {
717
- error: unknown;
718
- loadingP: Promise<void> | undefined;
719
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
720
- refNameAliases: {
721
- [x: string]: string;
722
- } | undefined;
723
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
724
- } & {
725
- getConf(arg: string): any;
726
- readonly lowerCaseRefNameAliases: {
727
- [k: string]: string;
728
- } | undefined;
729
- } & {
730
- readonly initialized: boolean;
731
- readonly name: string;
732
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
733
- readonly aliases: string[];
734
- readonly displayName: string;
735
- hasName(name: string): boolean;
736
- readonly allAliases: string[];
737
- readonly allRefNames: string[] | undefined;
738
- readonly lowerCaseRefNames: string[] | undefined;
739
- readonly allRefNamesWithLowerCase: string[] | undefined;
740
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
741
- readonly refNameColors: string[];
742
- } & {
743
- readonly refNames: string[] | undefined;
744
- } & {
745
- getCanonicalRefName(refName: string): string | undefined;
746
- getRefNameColor(refName: string): string | undefined;
747
- isValidRefName(refName: string): boolean;
748
- } & {
749
- setLoaded({ regions, refNameAliases, cytobands, }: {
750
- regions: import("@jbrowse/core/util").Region[];
751
- refNameAliases: {
752
- [x: string]: string;
753
- };
754
- cytobands: import("@jbrowse/core/util").Feature[];
755
- }): void;
756
- setError(e: unknown): void;
757
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
758
- setRefNameAliases(aliases: {
759
- [x: string]: string;
760
- }): void;
761
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
762
- setLoadingP(p?: Promise<void>): void;
763
- load(): Promise<void>;
764
- loadPre(): Promise<void>;
765
- } & {
766
- getAdapterMapEntry(adapterConf: {
767
- [x: string]: unknown;
768
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
769
- getRefNameMapForAdapter(adapterConf: {
770
- [x: string]: unknown;
771
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
772
- [x: string]: string;
773
- }>;
774
- getReverseRefNameMapForAdapter(adapterConf: {
775
- [x: string]: unknown;
776
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
777
- [x: string]: string;
778
- }>;
779
- afterCreate(): void;
780
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
781
- } & {
782
- getCanonicalAssemblyName(asmName: string): string | undefined;
783
- get(asmName: string): ({
784
- configuration: any;
785
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
786
- error: unknown;
787
- loadingP: Promise<void> | undefined;
788
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
789
- refNameAliases: {
790
- [x: string]: string;
791
- } | undefined;
792
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
793
- } & {
794
- getConf(arg: string): any;
795
- readonly lowerCaseRefNameAliases: {
796
- [k: string]: string;
797
- } | undefined;
798
- } & {
799
- readonly initialized: boolean;
800
- readonly name: string;
801
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
802
- readonly aliases: string[];
803
- readonly displayName: string;
804
- hasName(name: string): boolean;
805
- readonly allAliases: string[];
806
- readonly allRefNames: string[] | undefined;
807
- readonly lowerCaseRefNames: string[] | undefined;
808
- readonly allRefNamesWithLowerCase: string[] | undefined;
809
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
810
- readonly refNameColors: string[];
811
- } & {
812
- readonly refNames: string[] | undefined;
813
- } & {
814
- getCanonicalRefName(refName: string): string | undefined;
815
- getRefNameColor(refName: string): string | undefined;
816
- isValidRefName(refName: string): boolean;
817
- } & {
818
- setLoaded({ regions, refNameAliases, cytobands, }: {
819
- regions: import("@jbrowse/core/util").Region[];
820
- refNameAliases: {
821
- [x: string]: string;
822
- };
823
- cytobands: import("@jbrowse/core/util").Feature[];
824
- }): void;
825
- setError(e: unknown): void;
826
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
827
- setRefNameAliases(aliases: {
828
- [x: string]: string;
829
- }): void;
830
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
831
- setLoadingP(p?: Promise<void>): void;
832
- load(): Promise<void>;
833
- loadPre(): Promise<void>;
834
- } & {
835
- getAdapterMapEntry(adapterConf: {
836
- [x: string]: unknown;
837
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
838
- getRefNameMapForAdapter(adapterConf: {
839
- [x: string]: unknown;
840
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
841
- [x: string]: string;
842
- }>;
843
- getReverseRefNameMapForAdapter(adapterConf: {
844
- [x: string]: unknown;
845
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
846
- [x: string]: string;
847
- }>;
848
- afterCreate(): void;
849
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
850
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
851
- }, {
852
- error: unknown;
853
- loadingP: Promise<void> | undefined;
854
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
855
- refNameAliases: {
856
- [x: string]: string;
857
- } | undefined;
858
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
859
- } & {
860
- getConf(arg: string): any;
861
- readonly lowerCaseRefNameAliases: {
862
- [k: string]: string;
863
- } | undefined;
864
- } & {
865
- readonly initialized: boolean;
866
- readonly name: string;
867
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
868
- readonly aliases: string[];
869
- readonly displayName: string;
870
- hasName(name: string): boolean;
871
- readonly allAliases: string[];
872
- readonly allRefNames: string[] | undefined;
873
- readonly lowerCaseRefNames: string[] | undefined;
874
- readonly allRefNamesWithLowerCase: string[] | undefined;
875
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
876
- readonly refNameColors: string[];
877
- } & {
878
- readonly refNames: string[] | undefined;
879
- } & {
880
- getCanonicalRefName(refName: string): string | undefined;
881
- getRefNameColor(refName: string): string | undefined;
882
- isValidRefName(refName: string): boolean;
883
- } & {
884
- setLoaded({ regions, refNameAliases, cytobands, }: {
885
- regions: import("@jbrowse/core/util").Region[];
886
- refNameAliases: {
887
- [x: string]: string;
888
- };
889
- cytobands: import("@jbrowse/core/util").Feature[];
890
- }): void;
891
- setError(e: unknown): void;
892
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
893
- setRefNameAliases(aliases: {
894
- [x: string]: string;
895
- }): void;
896
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
897
- setLoadingP(p?: Promise<void>): void;
898
- load(): Promise<void>;
899
- loadPre(): Promise<void>;
900
- } & {
901
- getAdapterMapEntry(adapterConf: {
902
- [x: string]: unknown;
903
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
904
- getRefNameMapForAdapter(adapterConf: {
905
- [x: string]: unknown;
906
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
907
- [x: string]: string;
908
- }>;
909
- getReverseRefNameMapForAdapter(adapterConf: {
910
- [x: string]: unknown;
911
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
912
- [x: string]: string;
913
- }>;
914
- afterCreate(): void;
915
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
916
- readonly assemblyNamesList: any[];
917
- readonly assemblyList: AnyConfigurationModel[];
918
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
919
- } & {
920
- waitForAssembly(assemblyName: string): Promise<({
921
- configuration: any;
922
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
923
- error: unknown;
924
- loadingP: Promise<void> | undefined;
925
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
926
- refNameAliases: {
927
- [x: string]: string;
928
- } | undefined;
929
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
930
- } & {
931
- getConf(arg: string): any;
932
- readonly lowerCaseRefNameAliases: {
933
- [k: string]: string;
934
- } | undefined;
935
- } & {
936
- readonly initialized: boolean;
937
- readonly name: string;
938
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
939
- readonly aliases: string[];
940
- readonly displayName: string;
941
- hasName(name: string): boolean;
942
- readonly allAliases: string[];
943
- readonly allRefNames: string[] | undefined;
944
- readonly lowerCaseRefNames: string[] | undefined;
945
- readonly allRefNamesWithLowerCase: string[] | undefined;
946
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
947
- readonly refNameColors: string[];
948
- } & {
949
- readonly refNames: string[] | undefined;
950
- } & {
951
- getCanonicalRefName(refName: string): string | undefined;
952
- getRefNameColor(refName: string): string | undefined;
953
- isValidRefName(refName: string): boolean;
954
- } & {
955
- setLoaded({ regions, refNameAliases, cytobands, }: {
956
- regions: import("@jbrowse/core/util").Region[];
957
- refNameAliases: {
958
- [x: string]: string;
959
- };
960
- cytobands: import("@jbrowse/core/util").Feature[];
961
- }): void;
962
- setError(e: unknown): void;
963
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
964
- setRefNameAliases(aliases: {
965
- [x: string]: string;
966
- }): void;
967
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
968
- setLoadingP(p?: Promise<void>): void;
969
- load(): Promise<void>;
970
- loadPre(): Promise<void>;
971
- } & {
972
- getAdapterMapEntry(adapterConf: {
973
- [x: string]: unknown;
974
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
975
- getRefNameMapForAdapter(adapterConf: {
976
- [x: string]: unknown;
977
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
978
- [x: string]: string;
979
- }>;
980
- getReverseRefNameMapForAdapter(adapterConf: {
981
- [x: string]: unknown;
982
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
983
- [x: string]: string;
984
- }>;
985
- afterCreate(): void;
986
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
987
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
988
- }, {
989
- error: unknown;
990
- loadingP: Promise<void> | undefined;
991
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
992
- refNameAliases: {
993
- [x: string]: string;
994
- } | undefined;
995
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
996
- } & {
997
- getConf(arg: string): any;
998
- readonly lowerCaseRefNameAliases: {
999
- [k: string]: string;
1000
- } | undefined;
1001
- } & {
1002
- readonly initialized: boolean;
1003
- readonly name: string;
1004
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1005
- readonly aliases: string[];
1006
- readonly displayName: string;
1007
- hasName(name: string): boolean;
1008
- readonly allAliases: string[];
1009
- readonly allRefNames: string[] | undefined;
1010
- readonly lowerCaseRefNames: string[] | undefined;
1011
- readonly allRefNamesWithLowerCase: string[] | undefined;
1012
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1013
- readonly refNameColors: string[];
1014
- } & {
1015
- readonly refNames: string[] | undefined;
1016
- } & {
1017
- getCanonicalRefName(refName: string): string | undefined;
1018
- getRefNameColor(refName: string): string | undefined;
1019
- isValidRefName(refName: string): boolean;
1020
- } & {
1021
- setLoaded({ regions, refNameAliases, cytobands, }: {
1022
- regions: import("@jbrowse/core/util").Region[];
1023
- refNameAliases: {
1024
- [x: string]: string;
1025
- };
1026
- cytobands: import("@jbrowse/core/util").Feature[];
1027
- }): void;
1028
- setError(e: unknown): void;
1029
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1030
- setRefNameAliases(aliases: {
1031
- [x: string]: string;
1032
- }): void;
1033
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1034
- setLoadingP(p?: Promise<void>): void;
1035
- load(): Promise<void>;
1036
- loadPre(): Promise<void>;
1037
- } & {
1038
- getAdapterMapEntry(adapterConf: {
1039
- [x: string]: unknown;
1040
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1041
- getRefNameMapForAdapter(adapterConf: {
1042
- [x: string]: unknown;
1043
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1044
- [x: string]: string;
1045
- }>;
1046
- getReverseRefNameMapForAdapter(adapterConf: {
1047
- [x: string]: unknown;
1048
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1049
- [x: string]: string;
1050
- }>;
1051
- afterCreate(): void;
1052
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1053
- getRefNameMapForAdapter(adapterConf: {
1054
- [x: string]: unknown;
1055
- }, assemblyName: string | undefined, opts: {
1056
- stopToken?: string;
1057
- sessionId: string;
1058
- }): Promise<{
1059
- [x: string]: string;
1060
- } | undefined>;
1061
- getReverseRefNameMapForAdapter(adapterConf: {
1062
- [x: string]: unknown;
1063
- }, assemblyName: string | undefined, opts: {
1064
- stopToken?: string;
1065
- sessionId: string;
1066
- }): Promise<{
1067
- [x: string]: string;
1068
- } | undefined>;
1069
- isValidRefName(refName: string, assemblyName: string): boolean;
1070
- } & {
1071
- afterAttach(): void;
1072
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1073
- addAssembly(configuration: any): void;
1074
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
1075
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1076
- rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1077
- adminMode: boolean;
1078
- error: unknown;
1079
- textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1080
- pluginManager: PluginManager;
1081
- } & {
1082
- setError(error: unknown): void;
1083
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1084
- setDefaultSession(): void;
1085
- setSessionPath(path: string): void;
1086
- renameCurrentSession(newName: string): void;
1087
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1088
- jbrowse: import("mobx-state-tree").IAnyType;
1089
- session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
1090
- sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1091
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1092
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1093
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1094
- }, {
1095
- error: unknown;
1096
- loadingP: Promise<void> | undefined;
1097
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1098
- refNameAliases: {
1099
- [x: string]: string;
1100
- } | undefined;
1101
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1102
- } & {
1103
- getConf(arg: string): any;
1104
- readonly lowerCaseRefNameAliases: {
1105
- [k: string]: string;
1106
- } | undefined;
1107
- } & {
1108
- readonly initialized: boolean;
1109
- readonly name: string;
1110
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1111
- readonly aliases: string[];
1112
- readonly displayName: string;
1113
- hasName(name: string): boolean;
1114
- readonly allAliases: string[];
1115
- readonly allRefNames: string[] | undefined;
1116
- readonly lowerCaseRefNames: string[] | undefined;
1117
- readonly allRefNamesWithLowerCase: string[] | undefined;
1118
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1119
- readonly refNameColors: string[];
1120
- } & {
1121
- readonly refNames: string[] | undefined;
1122
- } & {
1123
- getCanonicalRefName(refName: string): string | undefined;
1124
- getRefNameColor(refName: string): string | undefined;
1125
- isValidRefName(refName: string): boolean;
1126
- } & {
1127
- setLoaded({ regions, refNameAliases, cytobands, }: {
1128
- regions: import("@jbrowse/core/util").Region[];
1129
- refNameAliases: {
1130
- [x: string]: string;
1131
- };
1132
- cytobands: import("@jbrowse/core/util").Feature[];
1133
- }): void;
1134
- setError(e: unknown): void;
1135
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1136
- setRefNameAliases(aliases: {
1137
- [x: string]: string;
1138
- }): void;
1139
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1140
- setLoadingP(p?: Promise<void>): void;
1141
- load(): Promise<void>;
1142
- loadPre(): Promise<void>;
1143
- } & {
1144
- getAdapterMapEntry(adapterConf: {
1145
- [x: string]: unknown;
1146
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1147
- getRefNameMapForAdapter(adapterConf: {
1148
- [x: string]: unknown;
1149
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1150
- [x: string]: string;
1151
- }>;
1152
- getReverseRefNameMapForAdapter(adapterConf: {
1153
- [x: string]: unknown;
1154
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1155
- [x: string]: string;
1156
- }>;
1157
- afterCreate(): void;
1158
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1159
- }, {
1160
- readonly assemblyNameMap: Record<string, {
1161
- configuration: any;
1162
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1163
- error: unknown;
1164
- loadingP: Promise<void> | undefined;
1165
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1166
- refNameAliases: {
1167
- [x: string]: string;
1168
- } | undefined;
1169
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1170
- } & {
1171
- getConf(arg: string): any;
1172
- readonly lowerCaseRefNameAliases: {
1173
- [k: string]: string;
1174
- } | undefined;
1175
- } & {
1176
- readonly initialized: boolean;
1177
- readonly name: string;
1178
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1179
- readonly aliases: string[];
1180
- readonly displayName: string;
1181
- hasName(name: string): boolean;
1182
- readonly allAliases: string[];
1183
- readonly allRefNames: string[] | undefined;
1184
- readonly lowerCaseRefNames: string[] | undefined;
1185
- readonly allRefNamesWithLowerCase: string[] | undefined;
1186
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1187
- readonly refNameColors: string[];
1188
- } & {
1189
- readonly refNames: string[] | undefined;
1190
- } & {
1191
- getCanonicalRefName(refName: string): string | undefined;
1192
- getRefNameColor(refName: string): string | undefined;
1193
- isValidRefName(refName: string): boolean;
1194
- } & {
1195
- setLoaded({ regions, refNameAliases, cytobands, }: {
1196
- regions: import("@jbrowse/core/util").Region[];
1197
- refNameAliases: {
1198
- [x: string]: string;
1199
- };
1200
- cytobands: import("@jbrowse/core/util").Feature[];
1201
- }): void;
1202
- setError(e: unknown): void;
1203
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1204
- setRefNameAliases(aliases: {
1205
- [x: string]: string;
1206
- }): void;
1207
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1208
- setLoadingP(p?: Promise<void>): void;
1209
- load(): Promise<void>;
1210
- loadPre(): Promise<void>;
1211
- } & {
1212
- getAdapterMapEntry(adapterConf: {
1213
- [x: string]: unknown;
1214
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1215
- getRefNameMapForAdapter(adapterConf: {
1216
- [x: string]: unknown;
1217
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1218
- [x: string]: string;
1219
- }>;
1220
- getReverseRefNameMapForAdapter(adapterConf: {
1221
- [x: string]: unknown;
1222
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1223
- [x: string]: string;
1224
- }>;
1225
- afterCreate(): void;
1226
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1227
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1228
- }, {
1229
- error: unknown;
1230
- loadingP: Promise<void> | undefined;
1231
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1232
- refNameAliases: {
1233
- [x: string]: string;
1234
- } | undefined;
1235
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1236
- } & {
1237
- getConf(arg: string): any;
1238
- readonly lowerCaseRefNameAliases: {
1239
- [k: string]: string;
1240
- } | undefined;
1241
- } & {
1242
- readonly initialized: boolean;
1243
- readonly name: string;
1244
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1245
- readonly aliases: string[];
1246
- readonly displayName: string;
1247
- hasName(name: string): boolean;
1248
- readonly allAliases: string[];
1249
- readonly allRefNames: string[] | undefined;
1250
- readonly lowerCaseRefNames: string[] | undefined;
1251
- readonly allRefNamesWithLowerCase: string[] | undefined;
1252
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1253
- readonly refNameColors: string[];
1254
- } & {
1255
- readonly refNames: string[] | undefined;
1256
- } & {
1257
- getCanonicalRefName(refName: string): string | undefined;
1258
- getRefNameColor(refName: string): string | undefined;
1259
- isValidRefName(refName: string): boolean;
1260
- } & {
1261
- setLoaded({ regions, refNameAliases, cytobands, }: {
1262
- regions: import("@jbrowse/core/util").Region[];
1263
- refNameAliases: {
1264
- [x: string]: string;
1265
- };
1266
- cytobands: import("@jbrowse/core/util").Feature[];
1267
- }): void;
1268
- setError(e: unknown): void;
1269
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1270
- setRefNameAliases(aliases: {
1271
- [x: string]: string;
1272
- }): void;
1273
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1274
- setLoadingP(p?: Promise<void>): void;
1275
- load(): Promise<void>;
1276
- loadPre(): Promise<void>;
1277
- } & {
1278
- getAdapterMapEntry(adapterConf: {
1279
- [x: string]: unknown;
1280
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1281
- getRefNameMapForAdapter(adapterConf: {
1282
- [x: string]: unknown;
1283
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1284
- [x: string]: string;
1285
- }>;
1286
- getReverseRefNameMapForAdapter(adapterConf: {
1287
- [x: string]: unknown;
1288
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1289
- [x: string]: string;
1290
- }>;
1291
- afterCreate(): void;
1292
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
1293
- } & {
1294
- getCanonicalAssemblyName(asmName: string): string | undefined;
1295
- get(asmName: string): ({
1296
- configuration: any;
1297
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1298
- error: unknown;
1299
- loadingP: Promise<void> | undefined;
1300
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1301
- refNameAliases: {
1302
- [x: string]: string;
1303
- } | undefined;
1304
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1305
- } & {
1306
- getConf(arg: string): any;
1307
- readonly lowerCaseRefNameAliases: {
1308
- [k: string]: string;
1309
- } | undefined;
1310
- } & {
1311
- readonly initialized: boolean;
1312
- readonly name: string;
1313
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1314
- readonly aliases: string[];
1315
- readonly displayName: string;
1316
- hasName(name: string): boolean;
1317
- readonly allAliases: string[];
1318
- readonly allRefNames: string[] | undefined;
1319
- readonly lowerCaseRefNames: string[] | undefined;
1320
- readonly allRefNamesWithLowerCase: string[] | undefined;
1321
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1322
- readonly refNameColors: string[];
1323
- } & {
1324
- readonly refNames: string[] | undefined;
1325
- } & {
1326
- getCanonicalRefName(refName: string): string | undefined;
1327
- getRefNameColor(refName: string): string | undefined;
1328
- isValidRefName(refName: string): boolean;
1329
- } & {
1330
- setLoaded({ regions, refNameAliases, cytobands, }: {
1331
- regions: import("@jbrowse/core/util").Region[];
1332
- refNameAliases: {
1333
- [x: string]: string;
1334
- };
1335
- cytobands: import("@jbrowse/core/util").Feature[];
1336
- }): void;
1337
- setError(e: unknown): void;
1338
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1339
- setRefNameAliases(aliases: {
1340
- [x: string]: string;
1341
- }): void;
1342
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1343
- setLoadingP(p?: Promise<void>): void;
1344
- load(): Promise<void>;
1345
- loadPre(): Promise<void>;
1346
- } & {
1347
- getAdapterMapEntry(adapterConf: {
1348
- [x: string]: unknown;
1349
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1350
- getRefNameMapForAdapter(adapterConf: {
1351
- [x: string]: unknown;
1352
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1353
- [x: string]: string;
1354
- }>;
1355
- getReverseRefNameMapForAdapter(adapterConf: {
1356
- [x: string]: unknown;
1357
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1358
- [x: string]: string;
1359
- }>;
1360
- afterCreate(): void;
1361
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1362
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1363
- }, {
1364
- error: unknown;
1365
- loadingP: Promise<void> | undefined;
1366
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1367
- refNameAliases: {
1368
- [x: string]: string;
1369
- } | undefined;
1370
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1371
- } & {
1372
- getConf(arg: string): any;
1373
- readonly lowerCaseRefNameAliases: {
1374
- [k: string]: string;
1375
- } | undefined;
1376
- } & {
1377
- readonly initialized: boolean;
1378
- readonly name: string;
1379
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1380
- readonly aliases: string[];
1381
- readonly displayName: string;
1382
- hasName(name: string): boolean;
1383
- readonly allAliases: string[];
1384
- readonly allRefNames: string[] | undefined;
1385
- readonly lowerCaseRefNames: string[] | undefined;
1386
- readonly allRefNamesWithLowerCase: string[] | undefined;
1387
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1388
- readonly refNameColors: string[];
1389
- } & {
1390
- readonly refNames: string[] | undefined;
1391
- } & {
1392
- getCanonicalRefName(refName: string): string | undefined;
1393
- getRefNameColor(refName: string): string | undefined;
1394
- isValidRefName(refName: string): boolean;
1395
- } & {
1396
- setLoaded({ regions, refNameAliases, cytobands, }: {
1397
- regions: import("@jbrowse/core/util").Region[];
1398
- refNameAliases: {
1399
- [x: string]: string;
1400
- };
1401
- cytobands: import("@jbrowse/core/util").Feature[];
1402
- }): void;
1403
- setError(e: unknown): void;
1404
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1405
- setRefNameAliases(aliases: {
1406
- [x: string]: string;
1407
- }): void;
1408
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1409
- setLoadingP(p?: Promise<void>): void;
1410
- load(): Promise<void>;
1411
- loadPre(): Promise<void>;
1412
- } & {
1413
- getAdapterMapEntry(adapterConf: {
1414
- [x: string]: unknown;
1415
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1416
- getRefNameMapForAdapter(adapterConf: {
1417
- [x: string]: unknown;
1418
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1419
- [x: string]: string;
1420
- }>;
1421
- getReverseRefNameMapForAdapter(adapterConf: {
1422
- [x: string]: unknown;
1423
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1424
- [x: string]: string;
1425
- }>;
1426
- afterCreate(): void;
1427
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1428
- readonly assemblyNamesList: any[];
1429
- readonly assemblyList: AnyConfigurationModel[];
1430
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1431
- } & {
1432
- waitForAssembly(assemblyName: string): Promise<({
1433
- configuration: any;
1434
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1435
- error: unknown;
1436
- loadingP: Promise<void> | undefined;
1437
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1438
- refNameAliases: {
1439
- [x: string]: string;
1440
- } | undefined;
1441
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1442
- } & {
1443
- getConf(arg: string): any;
1444
- readonly lowerCaseRefNameAliases: {
1445
- [k: string]: string;
1446
- } | undefined;
1447
- } & {
1448
- readonly initialized: boolean;
1449
- readonly name: string;
1450
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1451
- readonly aliases: string[];
1452
- readonly displayName: string;
1453
- hasName(name: string): boolean;
1454
- readonly allAliases: string[];
1455
- readonly allRefNames: string[] | undefined;
1456
- readonly lowerCaseRefNames: string[] | undefined;
1457
- readonly allRefNamesWithLowerCase: string[] | undefined;
1458
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1459
- readonly refNameColors: string[];
1460
- } & {
1461
- readonly refNames: string[] | undefined;
1462
- } & {
1463
- getCanonicalRefName(refName: string): string | undefined;
1464
- getRefNameColor(refName: string): string | undefined;
1465
- isValidRefName(refName: string): boolean;
1466
- } & {
1467
- setLoaded({ regions, refNameAliases, cytobands, }: {
1468
- regions: import("@jbrowse/core/util").Region[];
1469
- refNameAliases: {
1470
- [x: string]: string;
1471
- };
1472
- cytobands: import("@jbrowse/core/util").Feature[];
1473
- }): void;
1474
- setError(e: unknown): void;
1475
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1476
- setRefNameAliases(aliases: {
1477
- [x: string]: string;
1478
- }): void;
1479
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1480
- setLoadingP(p?: Promise<void>): void;
1481
- load(): Promise<void>;
1482
- loadPre(): Promise<void>;
1483
- } & {
1484
- getAdapterMapEntry(adapterConf: {
1485
- [x: string]: unknown;
1486
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1487
- getRefNameMapForAdapter(adapterConf: {
1488
- [x: string]: unknown;
1489
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1490
- [x: string]: string;
1491
- }>;
1492
- getReverseRefNameMapForAdapter(adapterConf: {
1493
- [x: string]: unknown;
1494
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1495
- [x: string]: string;
1496
- }>;
1497
- afterCreate(): void;
1498
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1499
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1500
- }, {
1501
- error: unknown;
1502
- loadingP: Promise<void> | undefined;
1503
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1504
- refNameAliases: {
1505
- [x: string]: string;
1506
- } | undefined;
1507
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1508
- } & {
1509
- getConf(arg: string): any;
1510
- readonly lowerCaseRefNameAliases: {
1511
- [k: string]: string;
1512
- } | undefined;
1513
- } & {
1514
- readonly initialized: boolean;
1515
- readonly name: string;
1516
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1517
- readonly aliases: string[];
1518
- readonly displayName: string;
1519
- hasName(name: string): boolean;
1520
- readonly allAliases: string[];
1521
- readonly allRefNames: string[] | undefined;
1522
- readonly lowerCaseRefNames: string[] | undefined;
1523
- readonly allRefNamesWithLowerCase: string[] | undefined;
1524
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1525
- readonly refNameColors: string[];
1526
- } & {
1527
- readonly refNames: string[] | undefined;
1528
- } & {
1529
- getCanonicalRefName(refName: string): string | undefined;
1530
- getRefNameColor(refName: string): string | undefined;
1531
- isValidRefName(refName: string): boolean;
1532
- } & {
1533
- setLoaded({ regions, refNameAliases, cytobands, }: {
1534
- regions: import("@jbrowse/core/util").Region[];
1535
- refNameAliases: {
1536
- [x: string]: string;
1537
- };
1538
- cytobands: import("@jbrowse/core/util").Feature[];
1539
- }): void;
1540
- setError(e: unknown): void;
1541
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1542
- setRefNameAliases(aliases: {
1543
- [x: string]: string;
1544
- }): void;
1545
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1546
- setLoadingP(p?: Promise<void>): void;
1547
- load(): Promise<void>;
1548
- loadPre(): Promise<void>;
1549
- } & {
1550
- getAdapterMapEntry(adapterConf: {
1551
- [x: string]: unknown;
1552
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1553
- getRefNameMapForAdapter(adapterConf: {
1554
- [x: string]: unknown;
1555
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1556
- [x: string]: string;
1557
- }>;
1558
- getReverseRefNameMapForAdapter(adapterConf: {
1559
- [x: string]: unknown;
1560
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1561
- [x: string]: string;
1562
- }>;
1563
- afterCreate(): void;
1564
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1565
- getRefNameMapForAdapter(adapterConf: {
1566
- [x: string]: unknown;
1567
- }, assemblyName: string | undefined, opts: {
1568
- stopToken?: string;
1569
- sessionId: string;
1570
- }): Promise<{
1571
- [x: string]: string;
1572
- } | undefined>;
1573
- getReverseRefNameMapForAdapter(adapterConf: {
1574
- [x: string]: unknown;
1575
- }, assemblyName: string | undefined, opts: {
1576
- stopToken?: string;
1577
- sessionId: string;
1578
- }): Promise<{
1579
- [x: string]: string;
1580
- } | undefined>;
1581
- isValidRefName(refName: string, assemblyName: string): boolean;
1582
- } & {
1583
- afterAttach(): void;
1584
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1585
- addAssembly(configuration: any): void;
1586
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
1587
- }, {
1588
- rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1589
- adminMode: boolean;
1590
- error: unknown;
1591
- textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1592
- pluginManager: PluginManager;
1593
- } & {
1594
- setError(error: unknown): void;
1595
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1596
- setDefaultSession(): void;
1597
- setSessionPath(path: string): void;
1598
- renameCurrentSession(newName: string): void;
1599
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1600
- } & {
1601
- readonly jbrowse: any;
1602
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1603
- readonly configuration: {
1604
- [x: string]: any;
1605
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1606
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1607
- [x: string]: any;
1608
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1609
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1610
- [x: string]: any;
1611
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1612
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1613
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1614
- readonly adminMode: boolean;
1615
- readonly textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1616
- } & {
1617
- readonly assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
1618
- } & {
1619
- setSelection(thing: unknown): void;
1620
- clearSelection(): void;
1621
- setHovered(thing: unknown): void;
1622
- } & {
1623
- getReferring(object: IAnyStateTreeNode): import("./ReferenceManagement").ReferringNode[];
1624
- } & {
1625
- removeReferring(referring: import("./ReferenceManagement").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
1626
- } & {
1627
- readonly tracks: AnyConfigurationModel[];
1628
- } & {
1629
- addTrackConf(trackConf: AnyConfiguration): any;
1630
- deleteTrackConf(trackConf: AnyConfigurationModel): any;
1631
- } & {
1632
- readonly tracks: AnyConfigurationModel[];
1633
- } & {
1634
- addTrackConf(trackConf: AnyConfiguration): any;
1635
- deleteTrackConf(trackConf: AnyConfigurationModel): any;
1636
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
1637
- export type SessionWithSessionTracksType = ReturnType<typeof SessionTracksManagerSessionMixin>;
1638
- export type SessionWithSessionTracks = Instance<SessionWithSessionTracksType>;
1639
- export declare function isSessionWithSessionTracks(thing: IAnyStateTreeNode): thing is SessionWithSessionTracks;