@jbrowse/product-core 3.7.0 → 4.0.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (97) hide show
  1. package/esm/RootModel/BaseRootModel.d.ts +52 -37
  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 +189 -127
  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 +178 -122
  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 +175 -121
  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 -534
  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 -1681
  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 -1664
  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 -1657
  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
@@ -1,1664 +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
- getCanonicalRefName2(asmName: string): string;
52
- getRefNameColor(refName: string): string | undefined;
53
- isValidRefName(refName: string): boolean;
54
- } & {
55
- setLoaded({ regions, refNameAliases, cytobands, }: {
56
- regions: import("@jbrowse/core/util").Region[];
57
- refNameAliases: {
58
- [x: string]: string;
59
- };
60
- cytobands: import("@jbrowse/core/util").Feature[];
61
- }): void;
62
- setError(e: unknown): void;
63
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
64
- setRefNameAliases(aliases: {
65
- [x: string]: string;
66
- }): void;
67
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
68
- setLoadingP(p?: Promise<void>): void;
69
- load(): Promise<void>;
70
- loadPre(): Promise<void>;
71
- } & {
72
- getAdapterMapEntry(adapterConf: {
73
- [x: string]: unknown;
74
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
75
- getRefNameMapForAdapter(adapterConf: {
76
- [x: string]: unknown;
77
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
78
- [x: string]: string;
79
- }>;
80
- getReverseRefNameMapForAdapter(adapterConf: {
81
- [x: string]: unknown;
82
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
83
- [x: string]: string;
84
- }>;
85
- afterCreate(): void;
86
- }, 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<{
87
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
88
- }, {
89
- error: unknown;
90
- loadingP: Promise<void> | undefined;
91
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
92
- refNameAliases: {
93
- [x: string]: string;
94
- } | undefined;
95
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
96
- } & {
97
- getConf(arg: string): any;
98
- readonly lowerCaseRefNameAliases: {
99
- [k: string]: string;
100
- } | undefined;
101
- } & {
102
- readonly initialized: boolean;
103
- readonly name: string;
104
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
105
- readonly aliases: string[];
106
- readonly displayName: string;
107
- hasName(name: string): boolean;
108
- readonly allAliases: string[];
109
- readonly allRefNames: string[] | undefined;
110
- readonly lowerCaseRefNames: string[] | undefined;
111
- readonly allRefNamesWithLowerCase: string[] | undefined;
112
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
113
- readonly refNameColors: string[];
114
- } & {
115
- readonly refNames: string[] | undefined;
116
- } & {
117
- getCanonicalRefName(refName: string): string | undefined;
118
- getCanonicalRefName2(asmName: string): string;
119
- getRefNameColor(refName: string): string | undefined;
120
- isValidRefName(refName: string): boolean;
121
- } & {
122
- setLoaded({ regions, refNameAliases, cytobands, }: {
123
- regions: import("@jbrowse/core/util").Region[];
124
- refNameAliases: {
125
- [x: string]: string;
126
- };
127
- cytobands: import("@jbrowse/core/util").Feature[];
128
- }): void;
129
- setError(e: unknown): void;
130
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
131
- setRefNameAliases(aliases: {
132
- [x: string]: string;
133
- }): void;
134
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
135
- setLoadingP(p?: Promise<void>): void;
136
- load(): Promise<void>;
137
- loadPre(): Promise<void>;
138
- } & {
139
- getAdapterMapEntry(adapterConf: {
140
- [x: string]: unknown;
141
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
142
- getRefNameMapForAdapter(adapterConf: {
143
- [x: string]: unknown;
144
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
145
- [x: string]: string;
146
- }>;
147
- getReverseRefNameMapForAdapter(adapterConf: {
148
- [x: string]: unknown;
149
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
150
- [x: string]: string;
151
- }>;
152
- afterCreate(): void;
153
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
154
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
155
- readonly assemblyNameMap: Record<string, {
156
- configuration: any;
157
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
158
- error: unknown;
159
- loadingP: Promise<void> | undefined;
160
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
161
- refNameAliases: {
162
- [x: string]: string;
163
- } | undefined;
164
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
165
- } & {
166
- getConf(arg: string): any;
167
- readonly lowerCaseRefNameAliases: {
168
- [k: string]: string;
169
- } | undefined;
170
- } & {
171
- readonly initialized: boolean;
172
- readonly name: string;
173
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
174
- readonly aliases: string[];
175
- readonly displayName: string;
176
- hasName(name: string): boolean;
177
- readonly allAliases: string[];
178
- readonly allRefNames: string[] | undefined;
179
- readonly lowerCaseRefNames: string[] | undefined;
180
- readonly allRefNamesWithLowerCase: string[] | undefined;
181
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
182
- readonly refNameColors: string[];
183
- } & {
184
- readonly refNames: string[] | undefined;
185
- } & {
186
- getCanonicalRefName(refName: string): string | undefined;
187
- getCanonicalRefName2(asmName: string): string;
188
- getRefNameColor(refName: string): string | undefined;
189
- isValidRefName(refName: string): boolean;
190
- } & {
191
- setLoaded({ regions, refNameAliases, cytobands, }: {
192
- regions: import("@jbrowse/core/util").Region[];
193
- refNameAliases: {
194
- [x: string]: string;
195
- };
196
- cytobands: import("@jbrowse/core/util").Feature[];
197
- }): void;
198
- setError(e: unknown): void;
199
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
200
- setRefNameAliases(aliases: {
201
- [x: string]: string;
202
- }): void;
203
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
204
- setLoadingP(p?: Promise<void>): void;
205
- load(): Promise<void>;
206
- loadPre(): Promise<void>;
207
- } & {
208
- getAdapterMapEntry(adapterConf: {
209
- [x: string]: unknown;
210
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
211
- getRefNameMapForAdapter(adapterConf: {
212
- [x: string]: unknown;
213
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
214
- [x: string]: string;
215
- }>;
216
- getReverseRefNameMapForAdapter(adapterConf: {
217
- [x: string]: unknown;
218
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
219
- [x: string]: string;
220
- }>;
221
- afterCreate(): void;
222
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
223
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
224
- }, {
225
- error: unknown;
226
- loadingP: Promise<void> | undefined;
227
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
228
- refNameAliases: {
229
- [x: string]: string;
230
- } | undefined;
231
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
232
- } & {
233
- getConf(arg: string): any;
234
- readonly lowerCaseRefNameAliases: {
235
- [k: string]: string;
236
- } | undefined;
237
- } & {
238
- readonly initialized: boolean;
239
- readonly name: string;
240
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
241
- readonly aliases: string[];
242
- readonly displayName: string;
243
- hasName(name: string): boolean;
244
- readonly allAliases: string[];
245
- readonly allRefNames: string[] | undefined;
246
- readonly lowerCaseRefNames: string[] | undefined;
247
- readonly allRefNamesWithLowerCase: string[] | undefined;
248
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
249
- readonly refNameColors: string[];
250
- } & {
251
- readonly refNames: string[] | undefined;
252
- } & {
253
- getCanonicalRefName(refName: string): string | undefined;
254
- getCanonicalRefName2(asmName: string): string;
255
- getRefNameColor(refName: string): string | undefined;
256
- isValidRefName(refName: string): boolean;
257
- } & {
258
- setLoaded({ regions, refNameAliases, cytobands, }: {
259
- regions: import("@jbrowse/core/util").Region[];
260
- refNameAliases: {
261
- [x: string]: string;
262
- };
263
- cytobands: import("@jbrowse/core/util").Feature[];
264
- }): void;
265
- setError(e: unknown): void;
266
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
267
- setRefNameAliases(aliases: {
268
- [x: string]: string;
269
- }): void;
270
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
271
- setLoadingP(p?: Promise<void>): void;
272
- load(): Promise<void>;
273
- loadPre(): Promise<void>;
274
- } & {
275
- getAdapterMapEntry(adapterConf: {
276
- [x: string]: unknown;
277
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
278
- getRefNameMapForAdapter(adapterConf: {
279
- [x: string]: unknown;
280
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
281
- [x: string]: string;
282
- }>;
283
- getReverseRefNameMapForAdapter(adapterConf: {
284
- [x: string]: unknown;
285
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
286
- [x: string]: string;
287
- }>;
288
- afterCreate(): void;
289
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
290
- } & {
291
- getCanonicalAssemblyName(asmName: string): string | undefined;
292
- getCanonicalAssemblyName2(asmName: string): string;
293
- get(asmName: string): ({
294
- configuration: any;
295
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
296
- error: unknown;
297
- loadingP: Promise<void> | undefined;
298
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
299
- refNameAliases: {
300
- [x: string]: string;
301
- } | undefined;
302
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
303
- } & {
304
- getConf(arg: string): any;
305
- readonly lowerCaseRefNameAliases: {
306
- [k: string]: string;
307
- } | undefined;
308
- } & {
309
- readonly initialized: boolean;
310
- readonly name: string;
311
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
312
- readonly aliases: string[];
313
- readonly displayName: string;
314
- hasName(name: string): boolean;
315
- readonly allAliases: string[];
316
- readonly allRefNames: string[] | undefined;
317
- readonly lowerCaseRefNames: string[] | undefined;
318
- readonly allRefNamesWithLowerCase: string[] | undefined;
319
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
320
- readonly refNameColors: string[];
321
- } & {
322
- readonly refNames: string[] | undefined;
323
- } & {
324
- getCanonicalRefName(refName: string): string | undefined;
325
- getCanonicalRefName2(asmName: string): string;
326
- getRefNameColor(refName: string): string | undefined;
327
- isValidRefName(refName: string): boolean;
328
- } & {
329
- setLoaded({ regions, refNameAliases, cytobands, }: {
330
- regions: import("@jbrowse/core/util").Region[];
331
- refNameAliases: {
332
- [x: string]: string;
333
- };
334
- cytobands: import("@jbrowse/core/util").Feature[];
335
- }): void;
336
- setError(e: unknown): void;
337
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
338
- setRefNameAliases(aliases: {
339
- [x: string]: string;
340
- }): void;
341
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
342
- setLoadingP(p?: Promise<void>): void;
343
- load(): Promise<void>;
344
- loadPre(): Promise<void>;
345
- } & {
346
- getAdapterMapEntry(adapterConf: {
347
- [x: string]: unknown;
348
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
349
- getRefNameMapForAdapter(adapterConf: {
350
- [x: string]: unknown;
351
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
352
- [x: string]: string;
353
- }>;
354
- getReverseRefNameMapForAdapter(adapterConf: {
355
- [x: string]: unknown;
356
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
357
- [x: string]: string;
358
- }>;
359
- afterCreate(): void;
360
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
361
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
362
- }, {
363
- error: unknown;
364
- loadingP: Promise<void> | undefined;
365
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
366
- refNameAliases: {
367
- [x: string]: string;
368
- } | undefined;
369
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
370
- } & {
371
- getConf(arg: string): any;
372
- readonly lowerCaseRefNameAliases: {
373
- [k: string]: string;
374
- } | undefined;
375
- } & {
376
- readonly initialized: boolean;
377
- readonly name: string;
378
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
379
- readonly aliases: string[];
380
- readonly displayName: string;
381
- hasName(name: string): boolean;
382
- readonly allAliases: string[];
383
- readonly allRefNames: string[] | undefined;
384
- readonly lowerCaseRefNames: string[] | undefined;
385
- readonly allRefNamesWithLowerCase: string[] | undefined;
386
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
387
- readonly refNameColors: string[];
388
- } & {
389
- readonly refNames: string[] | undefined;
390
- } & {
391
- getCanonicalRefName(refName: string): string | undefined;
392
- getCanonicalRefName2(asmName: string): string;
393
- getRefNameColor(refName: string): string | undefined;
394
- isValidRefName(refName: string): boolean;
395
- } & {
396
- setLoaded({ regions, refNameAliases, cytobands, }: {
397
- regions: import("@jbrowse/core/util").Region[];
398
- refNameAliases: {
399
- [x: string]: string;
400
- };
401
- cytobands: import("@jbrowse/core/util").Feature[];
402
- }): void;
403
- setError(e: unknown): void;
404
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
405
- setRefNameAliases(aliases: {
406
- [x: string]: string;
407
- }): void;
408
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
409
- setLoadingP(p?: Promise<void>): void;
410
- load(): Promise<void>;
411
- loadPre(): Promise<void>;
412
- } & {
413
- getAdapterMapEntry(adapterConf: {
414
- [x: string]: unknown;
415
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
416
- getRefNameMapForAdapter(adapterConf: {
417
- [x: string]: unknown;
418
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
419
- [x: string]: string;
420
- }>;
421
- getReverseRefNameMapForAdapter(adapterConf: {
422
- [x: string]: unknown;
423
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
424
- [x: string]: string;
425
- }>;
426
- afterCreate(): void;
427
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
428
- readonly assemblyNamesList: any[];
429
- readonly assemblyList: AnyConfigurationModel[];
430
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
431
- } & {
432
- waitForAssembly(assemblyName: string): Promise<({
433
- configuration: any;
434
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
435
- error: unknown;
436
- loadingP: Promise<void> | undefined;
437
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
438
- refNameAliases: {
439
- [x: string]: string;
440
- } | undefined;
441
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
442
- } & {
443
- getConf(arg: string): any;
444
- readonly lowerCaseRefNameAliases: {
445
- [k: string]: string;
446
- } | undefined;
447
- } & {
448
- readonly initialized: boolean;
449
- readonly name: string;
450
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
451
- readonly aliases: string[];
452
- readonly displayName: string;
453
- hasName(name: string): boolean;
454
- readonly allAliases: string[];
455
- readonly allRefNames: string[] | undefined;
456
- readonly lowerCaseRefNames: string[] | undefined;
457
- readonly allRefNamesWithLowerCase: string[] | undefined;
458
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
459
- readonly refNameColors: string[];
460
- } & {
461
- readonly refNames: string[] | undefined;
462
- } & {
463
- getCanonicalRefName(refName: string): string | undefined;
464
- getCanonicalRefName2(asmName: string): string;
465
- getRefNameColor(refName: string): string | undefined;
466
- isValidRefName(refName: string): boolean;
467
- } & {
468
- setLoaded({ regions, refNameAliases, cytobands, }: {
469
- regions: import("@jbrowse/core/util").Region[];
470
- refNameAliases: {
471
- [x: string]: string;
472
- };
473
- cytobands: import("@jbrowse/core/util").Feature[];
474
- }): void;
475
- setError(e: unknown): void;
476
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
477
- setRefNameAliases(aliases: {
478
- [x: string]: string;
479
- }): void;
480
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
481
- setLoadingP(p?: Promise<void>): void;
482
- load(): Promise<void>;
483
- loadPre(): Promise<void>;
484
- } & {
485
- getAdapterMapEntry(adapterConf: {
486
- [x: string]: unknown;
487
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
488
- getRefNameMapForAdapter(adapterConf: {
489
- [x: string]: unknown;
490
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
491
- [x: string]: string;
492
- }>;
493
- getReverseRefNameMapForAdapter(adapterConf: {
494
- [x: string]: unknown;
495
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
496
- [x: string]: string;
497
- }>;
498
- afterCreate(): void;
499
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
500
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
501
- }, {
502
- error: unknown;
503
- loadingP: Promise<void> | undefined;
504
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
505
- refNameAliases: {
506
- [x: string]: string;
507
- } | undefined;
508
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
509
- } & {
510
- getConf(arg: string): any;
511
- readonly lowerCaseRefNameAliases: {
512
- [k: string]: string;
513
- } | undefined;
514
- } & {
515
- readonly initialized: boolean;
516
- readonly name: string;
517
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
518
- readonly aliases: string[];
519
- readonly displayName: string;
520
- hasName(name: string): boolean;
521
- readonly allAliases: string[];
522
- readonly allRefNames: string[] | undefined;
523
- readonly lowerCaseRefNames: string[] | undefined;
524
- readonly allRefNamesWithLowerCase: string[] | undefined;
525
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
526
- readonly refNameColors: string[];
527
- } & {
528
- readonly refNames: string[] | undefined;
529
- } & {
530
- getCanonicalRefName(refName: string): string | undefined;
531
- getCanonicalRefName2(asmName: string): string;
532
- getRefNameColor(refName: string): string | undefined;
533
- isValidRefName(refName: string): boolean;
534
- } & {
535
- setLoaded({ regions, refNameAliases, cytobands, }: {
536
- regions: import("@jbrowse/core/util").Region[];
537
- refNameAliases: {
538
- [x: string]: string;
539
- };
540
- cytobands: import("@jbrowse/core/util").Feature[];
541
- }): void;
542
- setError(e: unknown): void;
543
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
544
- setRefNameAliases(aliases: {
545
- [x: string]: string;
546
- }): void;
547
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
548
- setLoadingP(p?: Promise<void>): void;
549
- load(): Promise<void>;
550
- loadPre(): Promise<void>;
551
- } & {
552
- getAdapterMapEntry(adapterConf: {
553
- [x: string]: unknown;
554
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
555
- getRefNameMapForAdapter(adapterConf: {
556
- [x: string]: unknown;
557
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
558
- [x: string]: string;
559
- }>;
560
- getReverseRefNameMapForAdapter(adapterConf: {
561
- [x: string]: unknown;
562
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
563
- [x: string]: string;
564
- }>;
565
- afterCreate(): void;
566
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
567
- getRefNameMapForAdapter(adapterConf: {
568
- [x: string]: unknown;
569
- }, assemblyName: string | undefined, opts: {
570
- stopToken?: string;
571
- sessionId: string;
572
- }): Promise<{
573
- [x: string]: string;
574
- } | undefined>;
575
- getReverseRefNameMapForAdapter(adapterConf: {
576
- [x: string]: unknown;
577
- }, assemblyName: string | undefined, opts: {
578
- stopToken?: string;
579
- sessionId: string;
580
- }): Promise<{
581
- [x: string]: string;
582
- } | undefined>;
583
- isValidRefName(refName: string, assemblyName: string): boolean;
584
- } & {
585
- afterAttach(): void;
586
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
587
- addAssembly(configuration: any): void;
588
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
589
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
590
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
591
- }, {
592
- error: unknown;
593
- loadingP: Promise<void> | undefined;
594
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
595
- refNameAliases: {
596
- [x: string]: string;
597
- } | undefined;
598
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
599
- } & {
600
- getConf(arg: string): any;
601
- readonly lowerCaseRefNameAliases: {
602
- [k: string]: string;
603
- } | undefined;
604
- } & {
605
- readonly initialized: boolean;
606
- readonly name: string;
607
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
608
- readonly aliases: string[];
609
- readonly displayName: string;
610
- hasName(name: string): boolean;
611
- readonly allAliases: string[];
612
- readonly allRefNames: string[] | undefined;
613
- readonly lowerCaseRefNames: string[] | undefined;
614
- readonly allRefNamesWithLowerCase: string[] | undefined;
615
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
616
- readonly refNameColors: string[];
617
- } & {
618
- readonly refNames: string[] | undefined;
619
- } & {
620
- getCanonicalRefName(refName: string): string | undefined;
621
- getCanonicalRefName2(asmName: string): string;
622
- getRefNameColor(refName: string): string | undefined;
623
- isValidRefName(refName: string): boolean;
624
- } & {
625
- setLoaded({ regions, refNameAliases, cytobands, }: {
626
- regions: import("@jbrowse/core/util").Region[];
627
- refNameAliases: {
628
- [x: string]: string;
629
- };
630
- cytobands: import("@jbrowse/core/util").Feature[];
631
- }): void;
632
- setError(e: unknown): void;
633
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
634
- setRefNameAliases(aliases: {
635
- [x: string]: string;
636
- }): void;
637
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
638
- setLoadingP(p?: Promise<void>): void;
639
- load(): Promise<void>;
640
- loadPre(): Promise<void>;
641
- } & {
642
- getAdapterMapEntry(adapterConf: {
643
- [x: string]: unknown;
644
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
645
- getRefNameMapForAdapter(adapterConf: {
646
- [x: string]: unknown;
647
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
648
- [x: string]: string;
649
- }>;
650
- getReverseRefNameMapForAdapter(adapterConf: {
651
- [x: string]: unknown;
652
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
653
- [x: string]: string;
654
- }>;
655
- afterCreate(): void;
656
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
657
- }, {
658
- readonly assemblyNameMap: Record<string, {
659
- configuration: any;
660
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
661
- error: unknown;
662
- loadingP: Promise<void> | undefined;
663
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
664
- refNameAliases: {
665
- [x: string]: string;
666
- } | undefined;
667
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
668
- } & {
669
- getConf(arg: string): any;
670
- readonly lowerCaseRefNameAliases: {
671
- [k: string]: string;
672
- } | undefined;
673
- } & {
674
- readonly initialized: boolean;
675
- readonly name: string;
676
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
677
- readonly aliases: string[];
678
- readonly displayName: string;
679
- hasName(name: string): boolean;
680
- readonly allAliases: string[];
681
- readonly allRefNames: string[] | undefined;
682
- readonly lowerCaseRefNames: string[] | undefined;
683
- readonly allRefNamesWithLowerCase: string[] | undefined;
684
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
685
- readonly refNameColors: string[];
686
- } & {
687
- readonly refNames: string[] | undefined;
688
- } & {
689
- getCanonicalRefName(refName: string): string | undefined;
690
- getCanonicalRefName2(asmName: string): string;
691
- getRefNameColor(refName: string): string | undefined;
692
- isValidRefName(refName: string): boolean;
693
- } & {
694
- setLoaded({ regions, refNameAliases, cytobands, }: {
695
- regions: import("@jbrowse/core/util").Region[];
696
- refNameAliases: {
697
- [x: string]: string;
698
- };
699
- cytobands: import("@jbrowse/core/util").Feature[];
700
- }): void;
701
- setError(e: unknown): void;
702
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
703
- setRefNameAliases(aliases: {
704
- [x: string]: string;
705
- }): void;
706
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
707
- setLoadingP(p?: Promise<void>): void;
708
- load(): Promise<void>;
709
- loadPre(): Promise<void>;
710
- } & {
711
- getAdapterMapEntry(adapterConf: {
712
- [x: string]: unknown;
713
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
714
- getRefNameMapForAdapter(adapterConf: {
715
- [x: string]: unknown;
716
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
717
- [x: string]: string;
718
- }>;
719
- getReverseRefNameMapForAdapter(adapterConf: {
720
- [x: string]: unknown;
721
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
722
- [x: string]: string;
723
- }>;
724
- afterCreate(): void;
725
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
726
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
727
- }, {
728
- error: unknown;
729
- loadingP: Promise<void> | undefined;
730
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
731
- refNameAliases: {
732
- [x: string]: string;
733
- } | undefined;
734
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
735
- } & {
736
- getConf(arg: string): any;
737
- readonly lowerCaseRefNameAliases: {
738
- [k: string]: string;
739
- } | undefined;
740
- } & {
741
- readonly initialized: boolean;
742
- readonly name: string;
743
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
744
- readonly aliases: string[];
745
- readonly displayName: string;
746
- hasName(name: string): boolean;
747
- readonly allAliases: string[];
748
- readonly allRefNames: string[] | undefined;
749
- readonly lowerCaseRefNames: string[] | undefined;
750
- readonly allRefNamesWithLowerCase: string[] | undefined;
751
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
752
- readonly refNameColors: string[];
753
- } & {
754
- readonly refNames: string[] | undefined;
755
- } & {
756
- getCanonicalRefName(refName: string): string | undefined;
757
- getCanonicalRefName2(asmName: string): string;
758
- getRefNameColor(refName: string): string | undefined;
759
- isValidRefName(refName: string): boolean;
760
- } & {
761
- setLoaded({ regions, refNameAliases, cytobands, }: {
762
- regions: import("@jbrowse/core/util").Region[];
763
- refNameAliases: {
764
- [x: string]: string;
765
- };
766
- cytobands: import("@jbrowse/core/util").Feature[];
767
- }): void;
768
- setError(e: unknown): void;
769
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
770
- setRefNameAliases(aliases: {
771
- [x: string]: string;
772
- }): void;
773
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
774
- setLoadingP(p?: Promise<void>): void;
775
- load(): Promise<void>;
776
- loadPre(): Promise<void>;
777
- } & {
778
- getAdapterMapEntry(adapterConf: {
779
- [x: string]: unknown;
780
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
781
- getRefNameMapForAdapter(adapterConf: {
782
- [x: string]: unknown;
783
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
784
- [x: string]: string;
785
- }>;
786
- getReverseRefNameMapForAdapter(adapterConf: {
787
- [x: string]: unknown;
788
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
789
- [x: string]: string;
790
- }>;
791
- afterCreate(): void;
792
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
793
- } & {
794
- getCanonicalAssemblyName(asmName: string): string | undefined;
795
- getCanonicalAssemblyName2(asmName: string): string;
796
- get(asmName: string): ({
797
- configuration: any;
798
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
799
- error: unknown;
800
- loadingP: Promise<void> | undefined;
801
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
802
- refNameAliases: {
803
- [x: string]: string;
804
- } | undefined;
805
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
806
- } & {
807
- getConf(arg: string): any;
808
- readonly lowerCaseRefNameAliases: {
809
- [k: string]: string;
810
- } | undefined;
811
- } & {
812
- readonly initialized: boolean;
813
- readonly name: string;
814
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
815
- readonly aliases: string[];
816
- readonly displayName: string;
817
- hasName(name: string): boolean;
818
- readonly allAliases: string[];
819
- readonly allRefNames: string[] | undefined;
820
- readonly lowerCaseRefNames: string[] | undefined;
821
- readonly allRefNamesWithLowerCase: string[] | undefined;
822
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
823
- readonly refNameColors: string[];
824
- } & {
825
- readonly refNames: string[] | undefined;
826
- } & {
827
- getCanonicalRefName(refName: string): string | undefined;
828
- getCanonicalRefName2(asmName: string): string;
829
- getRefNameColor(refName: string): string | undefined;
830
- isValidRefName(refName: string): boolean;
831
- } & {
832
- setLoaded({ regions, refNameAliases, cytobands, }: {
833
- regions: import("@jbrowse/core/util").Region[];
834
- refNameAliases: {
835
- [x: string]: string;
836
- };
837
- cytobands: import("@jbrowse/core/util").Feature[];
838
- }): void;
839
- setError(e: unknown): void;
840
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
841
- setRefNameAliases(aliases: {
842
- [x: string]: string;
843
- }): void;
844
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
845
- setLoadingP(p?: Promise<void>): void;
846
- load(): Promise<void>;
847
- loadPre(): Promise<void>;
848
- } & {
849
- getAdapterMapEntry(adapterConf: {
850
- [x: string]: unknown;
851
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
852
- getRefNameMapForAdapter(adapterConf: {
853
- [x: string]: unknown;
854
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
855
- [x: string]: string;
856
- }>;
857
- getReverseRefNameMapForAdapter(adapterConf: {
858
- [x: string]: unknown;
859
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
860
- [x: string]: string;
861
- }>;
862
- afterCreate(): void;
863
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
864
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
865
- }, {
866
- error: unknown;
867
- loadingP: Promise<void> | undefined;
868
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
869
- refNameAliases: {
870
- [x: string]: string;
871
- } | undefined;
872
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
873
- } & {
874
- getConf(arg: string): any;
875
- readonly lowerCaseRefNameAliases: {
876
- [k: string]: string;
877
- } | undefined;
878
- } & {
879
- readonly initialized: boolean;
880
- readonly name: string;
881
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
882
- readonly aliases: string[];
883
- readonly displayName: string;
884
- hasName(name: string): boolean;
885
- readonly allAliases: string[];
886
- readonly allRefNames: string[] | undefined;
887
- readonly lowerCaseRefNames: string[] | undefined;
888
- readonly allRefNamesWithLowerCase: string[] | undefined;
889
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
890
- readonly refNameColors: string[];
891
- } & {
892
- readonly refNames: string[] | undefined;
893
- } & {
894
- getCanonicalRefName(refName: string): string | undefined;
895
- getCanonicalRefName2(asmName: string): string;
896
- getRefNameColor(refName: string): string | undefined;
897
- isValidRefName(refName: string): boolean;
898
- } & {
899
- setLoaded({ regions, refNameAliases, cytobands, }: {
900
- regions: import("@jbrowse/core/util").Region[];
901
- refNameAliases: {
902
- [x: string]: string;
903
- };
904
- cytobands: import("@jbrowse/core/util").Feature[];
905
- }): void;
906
- setError(e: unknown): void;
907
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
908
- setRefNameAliases(aliases: {
909
- [x: string]: string;
910
- }): void;
911
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
912
- setLoadingP(p?: Promise<void>): void;
913
- load(): Promise<void>;
914
- loadPre(): Promise<void>;
915
- } & {
916
- getAdapterMapEntry(adapterConf: {
917
- [x: string]: unknown;
918
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
919
- getRefNameMapForAdapter(adapterConf: {
920
- [x: string]: unknown;
921
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
922
- [x: string]: string;
923
- }>;
924
- getReverseRefNameMapForAdapter(adapterConf: {
925
- [x: string]: unknown;
926
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
927
- [x: string]: string;
928
- }>;
929
- afterCreate(): void;
930
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
931
- readonly assemblyNamesList: any[];
932
- readonly assemblyList: AnyConfigurationModel[];
933
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
934
- } & {
935
- waitForAssembly(assemblyName: string): Promise<({
936
- configuration: any;
937
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
938
- error: unknown;
939
- loadingP: Promise<void> | undefined;
940
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
941
- refNameAliases: {
942
- [x: string]: string;
943
- } | undefined;
944
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
945
- } & {
946
- getConf(arg: string): any;
947
- readonly lowerCaseRefNameAliases: {
948
- [k: string]: string;
949
- } | undefined;
950
- } & {
951
- readonly initialized: boolean;
952
- readonly name: string;
953
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
954
- readonly aliases: string[];
955
- readonly displayName: string;
956
- hasName(name: string): boolean;
957
- readonly allAliases: string[];
958
- readonly allRefNames: string[] | undefined;
959
- readonly lowerCaseRefNames: string[] | undefined;
960
- readonly allRefNamesWithLowerCase: string[] | undefined;
961
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
962
- readonly refNameColors: string[];
963
- } & {
964
- readonly refNames: string[] | undefined;
965
- } & {
966
- getCanonicalRefName(refName: string): string | undefined;
967
- getCanonicalRefName2(asmName: string): string;
968
- getRefNameColor(refName: string): string | undefined;
969
- isValidRefName(refName: string): boolean;
970
- } & {
971
- setLoaded({ regions, refNameAliases, cytobands, }: {
972
- regions: import("@jbrowse/core/util").Region[];
973
- refNameAliases: {
974
- [x: string]: string;
975
- };
976
- cytobands: import("@jbrowse/core/util").Feature[];
977
- }): void;
978
- setError(e: unknown): void;
979
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
980
- setRefNameAliases(aliases: {
981
- [x: string]: string;
982
- }): void;
983
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
984
- setLoadingP(p?: Promise<void>): void;
985
- load(): Promise<void>;
986
- loadPre(): Promise<void>;
987
- } & {
988
- getAdapterMapEntry(adapterConf: {
989
- [x: string]: unknown;
990
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
991
- getRefNameMapForAdapter(adapterConf: {
992
- [x: string]: unknown;
993
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
994
- [x: string]: string;
995
- }>;
996
- getReverseRefNameMapForAdapter(adapterConf: {
997
- [x: string]: unknown;
998
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
999
- [x: string]: string;
1000
- }>;
1001
- afterCreate(): void;
1002
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1003
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1004
- }, {
1005
- error: unknown;
1006
- loadingP: Promise<void> | undefined;
1007
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1008
- refNameAliases: {
1009
- [x: string]: string;
1010
- } | undefined;
1011
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1012
- } & {
1013
- getConf(arg: string): any;
1014
- readonly lowerCaseRefNameAliases: {
1015
- [k: string]: string;
1016
- } | undefined;
1017
- } & {
1018
- readonly initialized: boolean;
1019
- readonly name: string;
1020
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1021
- readonly aliases: string[];
1022
- readonly displayName: string;
1023
- hasName(name: string): boolean;
1024
- readonly allAliases: string[];
1025
- readonly allRefNames: string[] | undefined;
1026
- readonly lowerCaseRefNames: string[] | undefined;
1027
- readonly allRefNamesWithLowerCase: string[] | undefined;
1028
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1029
- readonly refNameColors: string[];
1030
- } & {
1031
- readonly refNames: string[] | undefined;
1032
- } & {
1033
- getCanonicalRefName(refName: string): string | undefined;
1034
- getCanonicalRefName2(asmName: string): string;
1035
- getRefNameColor(refName: string): string | undefined;
1036
- isValidRefName(refName: string): boolean;
1037
- } & {
1038
- setLoaded({ regions, refNameAliases, cytobands, }: {
1039
- regions: import("@jbrowse/core/util").Region[];
1040
- refNameAliases: {
1041
- [x: string]: string;
1042
- };
1043
- cytobands: import("@jbrowse/core/util").Feature[];
1044
- }): void;
1045
- setError(e: unknown): void;
1046
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1047
- setRefNameAliases(aliases: {
1048
- [x: string]: string;
1049
- }): void;
1050
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1051
- setLoadingP(p?: Promise<void>): void;
1052
- load(): Promise<void>;
1053
- loadPre(): Promise<void>;
1054
- } & {
1055
- getAdapterMapEntry(adapterConf: {
1056
- [x: string]: unknown;
1057
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1058
- getRefNameMapForAdapter(adapterConf: {
1059
- [x: string]: unknown;
1060
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1061
- [x: string]: string;
1062
- }>;
1063
- getReverseRefNameMapForAdapter(adapterConf: {
1064
- [x: string]: unknown;
1065
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1066
- [x: string]: string;
1067
- }>;
1068
- afterCreate(): void;
1069
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1070
- getRefNameMapForAdapter(adapterConf: {
1071
- [x: string]: unknown;
1072
- }, assemblyName: string | undefined, opts: {
1073
- stopToken?: string;
1074
- sessionId: string;
1075
- }): Promise<{
1076
- [x: string]: string;
1077
- } | undefined>;
1078
- getReverseRefNameMapForAdapter(adapterConf: {
1079
- [x: string]: unknown;
1080
- }, assemblyName: string | undefined, opts: {
1081
- stopToken?: string;
1082
- sessionId: string;
1083
- }): Promise<{
1084
- [x: string]: string;
1085
- } | undefined>;
1086
- isValidRefName(refName: string, assemblyName: string): boolean;
1087
- } & {
1088
- afterAttach(): void;
1089
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1090
- addAssembly(configuration: any): void;
1091
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
1092
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1093
- rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1094
- adminMode: boolean;
1095
- error: unknown;
1096
- textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1097
- pluginManager: PluginManager;
1098
- } & {
1099
- setError(error: unknown): void;
1100
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1101
- setDefaultSession(): void;
1102
- setSessionPath(path: string): void;
1103
- renameCurrentSession(newName: string): void;
1104
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1105
- jbrowse: import("mobx-state-tree").IAnyType;
1106
- session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
1107
- sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1108
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1109
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1110
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1111
- }, {
1112
- error: unknown;
1113
- loadingP: Promise<void> | undefined;
1114
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1115
- refNameAliases: {
1116
- [x: string]: string;
1117
- } | undefined;
1118
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1119
- } & {
1120
- getConf(arg: string): any;
1121
- readonly lowerCaseRefNameAliases: {
1122
- [k: string]: string;
1123
- } | undefined;
1124
- } & {
1125
- readonly initialized: boolean;
1126
- readonly name: string;
1127
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1128
- readonly aliases: string[];
1129
- readonly displayName: string;
1130
- hasName(name: string): boolean;
1131
- readonly allAliases: string[];
1132
- readonly allRefNames: string[] | undefined;
1133
- readonly lowerCaseRefNames: string[] | undefined;
1134
- readonly allRefNamesWithLowerCase: string[] | undefined;
1135
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1136
- readonly refNameColors: string[];
1137
- } & {
1138
- readonly refNames: string[] | undefined;
1139
- } & {
1140
- getCanonicalRefName(refName: string): string | undefined;
1141
- getCanonicalRefName2(asmName: string): string;
1142
- getRefNameColor(refName: string): string | undefined;
1143
- isValidRefName(refName: string): boolean;
1144
- } & {
1145
- setLoaded({ regions, refNameAliases, cytobands, }: {
1146
- regions: import("@jbrowse/core/util").Region[];
1147
- refNameAliases: {
1148
- [x: string]: string;
1149
- };
1150
- cytobands: import("@jbrowse/core/util").Feature[];
1151
- }): void;
1152
- setError(e: unknown): void;
1153
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1154
- setRefNameAliases(aliases: {
1155
- [x: string]: string;
1156
- }): void;
1157
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1158
- setLoadingP(p?: Promise<void>): void;
1159
- load(): Promise<void>;
1160
- loadPre(): Promise<void>;
1161
- } & {
1162
- getAdapterMapEntry(adapterConf: {
1163
- [x: string]: unknown;
1164
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1165
- getRefNameMapForAdapter(adapterConf: {
1166
- [x: string]: unknown;
1167
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1168
- [x: string]: string;
1169
- }>;
1170
- getReverseRefNameMapForAdapter(adapterConf: {
1171
- [x: string]: unknown;
1172
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1173
- [x: string]: string;
1174
- }>;
1175
- afterCreate(): void;
1176
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1177
- }, {
1178
- readonly assemblyNameMap: Record<string, {
1179
- configuration: any;
1180
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1181
- error: unknown;
1182
- loadingP: Promise<void> | undefined;
1183
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1184
- refNameAliases: {
1185
- [x: string]: string;
1186
- } | undefined;
1187
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1188
- } & {
1189
- getConf(arg: string): any;
1190
- readonly lowerCaseRefNameAliases: {
1191
- [k: string]: string;
1192
- } | undefined;
1193
- } & {
1194
- readonly initialized: boolean;
1195
- readonly name: string;
1196
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1197
- readonly aliases: string[];
1198
- readonly displayName: string;
1199
- hasName(name: string): boolean;
1200
- readonly allAliases: string[];
1201
- readonly allRefNames: string[] | undefined;
1202
- readonly lowerCaseRefNames: string[] | undefined;
1203
- readonly allRefNamesWithLowerCase: string[] | undefined;
1204
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1205
- readonly refNameColors: string[];
1206
- } & {
1207
- readonly refNames: string[] | undefined;
1208
- } & {
1209
- getCanonicalRefName(refName: string): string | undefined;
1210
- getCanonicalRefName2(asmName: string): string;
1211
- getRefNameColor(refName: string): string | undefined;
1212
- isValidRefName(refName: string): boolean;
1213
- } & {
1214
- setLoaded({ regions, refNameAliases, cytobands, }: {
1215
- regions: import("@jbrowse/core/util").Region[];
1216
- refNameAliases: {
1217
- [x: string]: string;
1218
- };
1219
- cytobands: import("@jbrowse/core/util").Feature[];
1220
- }): void;
1221
- setError(e: unknown): void;
1222
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1223
- setRefNameAliases(aliases: {
1224
- [x: string]: string;
1225
- }): void;
1226
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1227
- setLoadingP(p?: Promise<void>): void;
1228
- load(): Promise<void>;
1229
- loadPre(): Promise<void>;
1230
- } & {
1231
- getAdapterMapEntry(adapterConf: {
1232
- [x: string]: unknown;
1233
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1234
- getRefNameMapForAdapter(adapterConf: {
1235
- [x: string]: unknown;
1236
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1237
- [x: string]: string;
1238
- }>;
1239
- getReverseRefNameMapForAdapter(adapterConf: {
1240
- [x: string]: unknown;
1241
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1242
- [x: string]: string;
1243
- }>;
1244
- afterCreate(): void;
1245
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1246
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1247
- }, {
1248
- error: unknown;
1249
- loadingP: Promise<void> | undefined;
1250
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1251
- refNameAliases: {
1252
- [x: string]: string;
1253
- } | undefined;
1254
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1255
- } & {
1256
- getConf(arg: string): any;
1257
- readonly lowerCaseRefNameAliases: {
1258
- [k: string]: string;
1259
- } | undefined;
1260
- } & {
1261
- readonly initialized: boolean;
1262
- readonly name: string;
1263
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1264
- readonly aliases: string[];
1265
- readonly displayName: string;
1266
- hasName(name: string): boolean;
1267
- readonly allAliases: string[];
1268
- readonly allRefNames: string[] | undefined;
1269
- readonly lowerCaseRefNames: string[] | undefined;
1270
- readonly allRefNamesWithLowerCase: string[] | undefined;
1271
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1272
- readonly refNameColors: string[];
1273
- } & {
1274
- readonly refNames: string[] | undefined;
1275
- } & {
1276
- getCanonicalRefName(refName: string): string | undefined;
1277
- getCanonicalRefName2(asmName: string): string;
1278
- getRefNameColor(refName: string): string | undefined;
1279
- isValidRefName(refName: string): boolean;
1280
- } & {
1281
- setLoaded({ regions, refNameAliases, cytobands, }: {
1282
- regions: import("@jbrowse/core/util").Region[];
1283
- refNameAliases: {
1284
- [x: string]: string;
1285
- };
1286
- cytobands: import("@jbrowse/core/util").Feature[];
1287
- }): void;
1288
- setError(e: unknown): void;
1289
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1290
- setRefNameAliases(aliases: {
1291
- [x: string]: string;
1292
- }): void;
1293
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1294
- setLoadingP(p?: Promise<void>): void;
1295
- load(): Promise<void>;
1296
- loadPre(): Promise<void>;
1297
- } & {
1298
- getAdapterMapEntry(adapterConf: {
1299
- [x: string]: unknown;
1300
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1301
- getRefNameMapForAdapter(adapterConf: {
1302
- [x: string]: unknown;
1303
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1304
- [x: string]: string;
1305
- }>;
1306
- getReverseRefNameMapForAdapter(adapterConf: {
1307
- [x: string]: unknown;
1308
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1309
- [x: string]: string;
1310
- }>;
1311
- afterCreate(): void;
1312
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
1313
- } & {
1314
- getCanonicalAssemblyName(asmName: string): string | undefined;
1315
- getCanonicalAssemblyName2(asmName: string): string;
1316
- get(asmName: string): ({
1317
- configuration: any;
1318
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1319
- error: unknown;
1320
- loadingP: Promise<void> | undefined;
1321
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1322
- refNameAliases: {
1323
- [x: string]: string;
1324
- } | undefined;
1325
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1326
- } & {
1327
- getConf(arg: string): any;
1328
- readonly lowerCaseRefNameAliases: {
1329
- [k: string]: string;
1330
- } | undefined;
1331
- } & {
1332
- readonly initialized: boolean;
1333
- readonly name: string;
1334
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1335
- readonly aliases: string[];
1336
- readonly displayName: string;
1337
- hasName(name: string): boolean;
1338
- readonly allAliases: string[];
1339
- readonly allRefNames: string[] | undefined;
1340
- readonly lowerCaseRefNames: string[] | undefined;
1341
- readonly allRefNamesWithLowerCase: string[] | undefined;
1342
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1343
- readonly refNameColors: string[];
1344
- } & {
1345
- readonly refNames: string[] | undefined;
1346
- } & {
1347
- getCanonicalRefName(refName: string): string | undefined;
1348
- getCanonicalRefName2(asmName: string): string;
1349
- getRefNameColor(refName: string): string | undefined;
1350
- isValidRefName(refName: string): boolean;
1351
- } & {
1352
- setLoaded({ regions, refNameAliases, cytobands, }: {
1353
- regions: import("@jbrowse/core/util").Region[];
1354
- refNameAliases: {
1355
- [x: string]: string;
1356
- };
1357
- cytobands: import("@jbrowse/core/util").Feature[];
1358
- }): void;
1359
- setError(e: unknown): void;
1360
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1361
- setRefNameAliases(aliases: {
1362
- [x: string]: string;
1363
- }): void;
1364
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1365
- setLoadingP(p?: Promise<void>): void;
1366
- load(): Promise<void>;
1367
- loadPre(): Promise<void>;
1368
- } & {
1369
- getAdapterMapEntry(adapterConf: {
1370
- [x: string]: unknown;
1371
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1372
- getRefNameMapForAdapter(adapterConf: {
1373
- [x: string]: unknown;
1374
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1375
- [x: string]: string;
1376
- }>;
1377
- getReverseRefNameMapForAdapter(adapterConf: {
1378
- [x: string]: unknown;
1379
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1380
- [x: string]: string;
1381
- }>;
1382
- afterCreate(): void;
1383
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1384
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1385
- }, {
1386
- error: unknown;
1387
- loadingP: Promise<void> | undefined;
1388
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1389
- refNameAliases: {
1390
- [x: string]: string;
1391
- } | undefined;
1392
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1393
- } & {
1394
- getConf(arg: string): any;
1395
- readonly lowerCaseRefNameAliases: {
1396
- [k: string]: string;
1397
- } | undefined;
1398
- } & {
1399
- readonly initialized: boolean;
1400
- readonly name: string;
1401
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1402
- readonly aliases: string[];
1403
- readonly displayName: string;
1404
- hasName(name: string): boolean;
1405
- readonly allAliases: string[];
1406
- readonly allRefNames: string[] | undefined;
1407
- readonly lowerCaseRefNames: string[] | undefined;
1408
- readonly allRefNamesWithLowerCase: string[] | undefined;
1409
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1410
- readonly refNameColors: string[];
1411
- } & {
1412
- readonly refNames: string[] | undefined;
1413
- } & {
1414
- getCanonicalRefName(refName: string): string | undefined;
1415
- getCanonicalRefName2(asmName: string): string;
1416
- getRefNameColor(refName: string): string | undefined;
1417
- isValidRefName(refName: string): boolean;
1418
- } & {
1419
- setLoaded({ regions, refNameAliases, cytobands, }: {
1420
- regions: import("@jbrowse/core/util").Region[];
1421
- refNameAliases: {
1422
- [x: string]: string;
1423
- };
1424
- cytobands: import("@jbrowse/core/util").Feature[];
1425
- }): void;
1426
- setError(e: unknown): void;
1427
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1428
- setRefNameAliases(aliases: {
1429
- [x: string]: string;
1430
- }): void;
1431
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1432
- setLoadingP(p?: Promise<void>): void;
1433
- load(): Promise<void>;
1434
- loadPre(): Promise<void>;
1435
- } & {
1436
- getAdapterMapEntry(adapterConf: {
1437
- [x: string]: unknown;
1438
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1439
- getRefNameMapForAdapter(adapterConf: {
1440
- [x: string]: unknown;
1441
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1442
- [x: string]: string;
1443
- }>;
1444
- getReverseRefNameMapForAdapter(adapterConf: {
1445
- [x: string]: unknown;
1446
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1447
- [x: string]: string;
1448
- }>;
1449
- afterCreate(): void;
1450
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1451
- readonly assemblyNamesList: any[];
1452
- readonly assemblyList: AnyConfigurationModel[];
1453
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1454
- } & {
1455
- waitForAssembly(assemblyName: string): Promise<({
1456
- configuration: any;
1457
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1458
- error: unknown;
1459
- loadingP: Promise<void> | undefined;
1460
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1461
- refNameAliases: {
1462
- [x: string]: string;
1463
- } | undefined;
1464
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1465
- } & {
1466
- getConf(arg: string): any;
1467
- readonly lowerCaseRefNameAliases: {
1468
- [k: string]: string;
1469
- } | undefined;
1470
- } & {
1471
- readonly initialized: boolean;
1472
- readonly name: string;
1473
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1474
- readonly aliases: string[];
1475
- readonly displayName: string;
1476
- hasName(name: string): boolean;
1477
- readonly allAliases: string[];
1478
- readonly allRefNames: string[] | undefined;
1479
- readonly lowerCaseRefNames: string[] | undefined;
1480
- readonly allRefNamesWithLowerCase: string[] | undefined;
1481
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1482
- readonly refNameColors: string[];
1483
- } & {
1484
- readonly refNames: string[] | undefined;
1485
- } & {
1486
- getCanonicalRefName(refName: string): string | undefined;
1487
- getCanonicalRefName2(asmName: string): string;
1488
- getRefNameColor(refName: string): string | undefined;
1489
- isValidRefName(refName: string): boolean;
1490
- } & {
1491
- setLoaded({ regions, refNameAliases, cytobands, }: {
1492
- regions: import("@jbrowse/core/util").Region[];
1493
- refNameAliases: {
1494
- [x: string]: string;
1495
- };
1496
- cytobands: import("@jbrowse/core/util").Feature[];
1497
- }): void;
1498
- setError(e: unknown): void;
1499
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1500
- setRefNameAliases(aliases: {
1501
- [x: string]: string;
1502
- }): void;
1503
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1504
- setLoadingP(p?: Promise<void>): void;
1505
- load(): Promise<void>;
1506
- loadPre(): Promise<void>;
1507
- } & {
1508
- getAdapterMapEntry(adapterConf: {
1509
- [x: string]: unknown;
1510
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1511
- getRefNameMapForAdapter(adapterConf: {
1512
- [x: string]: unknown;
1513
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1514
- [x: string]: string;
1515
- }>;
1516
- getReverseRefNameMapForAdapter(adapterConf: {
1517
- [x: string]: unknown;
1518
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1519
- [x: string]: string;
1520
- }>;
1521
- afterCreate(): void;
1522
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1523
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1524
- }, {
1525
- error: unknown;
1526
- loadingP: Promise<void> | undefined;
1527
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1528
- refNameAliases: {
1529
- [x: string]: string;
1530
- } | undefined;
1531
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1532
- } & {
1533
- getConf(arg: string): any;
1534
- readonly lowerCaseRefNameAliases: {
1535
- [k: string]: string;
1536
- } | undefined;
1537
- } & {
1538
- readonly initialized: boolean;
1539
- readonly name: string;
1540
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1541
- readonly aliases: string[];
1542
- readonly displayName: string;
1543
- hasName(name: string): boolean;
1544
- readonly allAliases: string[];
1545
- readonly allRefNames: string[] | undefined;
1546
- readonly lowerCaseRefNames: string[] | undefined;
1547
- readonly allRefNamesWithLowerCase: string[] | undefined;
1548
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1549
- readonly refNameColors: string[];
1550
- } & {
1551
- readonly refNames: string[] | undefined;
1552
- } & {
1553
- getCanonicalRefName(refName: string): string | undefined;
1554
- getCanonicalRefName2(asmName: string): string;
1555
- getRefNameColor(refName: string): string | undefined;
1556
- isValidRefName(refName: string): boolean;
1557
- } & {
1558
- setLoaded({ regions, refNameAliases, cytobands, }: {
1559
- regions: import("@jbrowse/core/util").Region[];
1560
- refNameAliases: {
1561
- [x: string]: string;
1562
- };
1563
- cytobands: import("@jbrowse/core/util").Feature[];
1564
- }): void;
1565
- setError(e: unknown): void;
1566
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1567
- setRefNameAliases(aliases: {
1568
- [x: string]: string;
1569
- }): void;
1570
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1571
- setLoadingP(p?: Promise<void>): void;
1572
- load(): Promise<void>;
1573
- loadPre(): Promise<void>;
1574
- } & {
1575
- getAdapterMapEntry(adapterConf: {
1576
- [x: string]: unknown;
1577
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1578
- getRefNameMapForAdapter(adapterConf: {
1579
- [x: string]: unknown;
1580
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1581
- [x: string]: string;
1582
- }>;
1583
- getReverseRefNameMapForAdapter(adapterConf: {
1584
- [x: string]: unknown;
1585
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1586
- [x: string]: string;
1587
- }>;
1588
- afterCreate(): void;
1589
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1590
- getRefNameMapForAdapter(adapterConf: {
1591
- [x: string]: unknown;
1592
- }, assemblyName: string | undefined, opts: {
1593
- stopToken?: string;
1594
- sessionId: string;
1595
- }): Promise<{
1596
- [x: string]: string;
1597
- } | undefined>;
1598
- getReverseRefNameMapForAdapter(adapterConf: {
1599
- [x: string]: unknown;
1600
- }, assemblyName: string | undefined, opts: {
1601
- stopToken?: string;
1602
- sessionId: string;
1603
- }): Promise<{
1604
- [x: string]: string;
1605
- } | undefined>;
1606
- isValidRefName(refName: string, assemblyName: string): boolean;
1607
- } & {
1608
- afterAttach(): void;
1609
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1610
- addAssembly(configuration: any): void;
1611
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
1612
- }, {
1613
- rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1614
- adminMode: boolean;
1615
- error: unknown;
1616
- textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1617
- pluginManager: PluginManager;
1618
- } & {
1619
- setError(error: unknown): void;
1620
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1621
- setDefaultSession(): void;
1622
- setSessionPath(path: string): void;
1623
- renameCurrentSession(newName: string): void;
1624
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1625
- } & {
1626
- readonly jbrowse: any;
1627
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1628
- readonly configuration: {
1629
- [x: string]: any;
1630
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1631
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1632
- [x: string]: any;
1633
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1634
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1635
- [x: string]: any;
1636
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1637
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1638
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1639
- readonly adminMode: boolean;
1640
- readonly textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1641
- } & {
1642
- readonly assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
1643
- } & {
1644
- setSelection(thing: unknown): void;
1645
- clearSelection(): void;
1646
- setHovered(thing: unknown): void;
1647
- } & {
1648
- getReferring(object: IAnyStateTreeNode): import("./ReferenceManagement").ReferringNode[];
1649
- } & {
1650
- removeReferring(referring: import("./ReferenceManagement").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
1651
- } & {
1652
- readonly tracks: AnyConfigurationModel[];
1653
- } & {
1654
- addTrackConf(trackConf: AnyConfiguration): any;
1655
- deleteTrackConf(trackConf: AnyConfigurationModel): any;
1656
- } & {
1657
- readonly tracks: AnyConfigurationModel[];
1658
- } & {
1659
- addTrackConf(trackConf: AnyConfiguration): any;
1660
- deleteTrackConf(trackConf: AnyConfigurationModel): any;
1661
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
1662
- export type SessionWithSessionTracksType = ReturnType<typeof SessionTracksManagerSessionMixin>;
1663
- export type SessionWithSessionTracks = Instance<SessionWithSessionTracksType>;
1664
- export declare function isSessionWithSessionTracks(thing: IAnyStateTreeNode): thing is SessionWithSessionTracks;