@jbrowse/product-core 3.7.0 → 4.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (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
@@ -1,1681 +0,0 @@
1
- import type PluginManager from '@jbrowse/core/PluginManager';
2
- import type { IBaseViewModel } from '@jbrowse/core/pluggableElementTypes';
3
- import type { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
4
- export declare function MultipleViewsSessionMixin(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
- drawerPosition: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
10
- drawerWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
11
- widgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyType>;
12
- activeWidgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>>;
13
- minimized: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
14
- } & {
15
- views: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
16
- stickyViewHeaders: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
17
- }, {
18
- selection: unknown;
19
- hovered: unknown;
20
- } & {
21
- readonly root: {
22
- jbrowse: any;
23
- session: any;
24
- sessionPath: string;
25
- assemblyManager: {
26
- assemblies: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
27
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
28
- }, {
29
- error: unknown;
30
- loadingP: Promise<void> | undefined;
31
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
32
- refNameAliases: {
33
- [x: string]: string;
34
- } | undefined;
35
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
36
- } & {
37
- getConf(arg: string): any;
38
- readonly lowerCaseRefNameAliases: {
39
- [k: string]: string;
40
- } | undefined;
41
- } & {
42
- readonly initialized: boolean;
43
- readonly name: string;
44
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
45
- readonly aliases: string[];
46
- readonly displayName: string;
47
- hasName(name: string): boolean;
48
- readonly allAliases: string[];
49
- readonly allRefNames: string[] | undefined;
50
- readonly lowerCaseRefNames: string[] | undefined;
51
- readonly allRefNamesWithLowerCase: string[] | undefined;
52
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
53
- readonly refNameColors: string[];
54
- } & {
55
- readonly refNames: string[] | undefined;
56
- } & {
57
- getCanonicalRefName(refName: string): string | undefined;
58
- getCanonicalRefName2(asmName: string): string;
59
- getRefNameColor(refName: string): string | undefined;
60
- isValidRefName(refName: string): boolean;
61
- } & {
62
- setLoaded({ regions, refNameAliases, cytobands, }: {
63
- regions: import("@jbrowse/core/util").Region[];
64
- refNameAliases: {
65
- [x: string]: string;
66
- };
67
- cytobands: import("@jbrowse/core/util").Feature[];
68
- }): void;
69
- setError(e: unknown): void;
70
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
71
- setRefNameAliases(aliases: {
72
- [x: string]: string;
73
- }): void;
74
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
75
- setLoadingP(p?: Promise<void>): void;
76
- load(): Promise<void>;
77
- loadPre(): Promise<void>;
78
- } & {
79
- getAdapterMapEntry(adapterConf: {
80
- [x: string]: unknown;
81
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
82
- getRefNameMapForAdapter(adapterConf: {
83
- [x: string]: unknown;
84
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
85
- [x: string]: string;
86
- }>;
87
- getReverseRefNameMapForAdapter(adapterConf: {
88
- [x: string]: unknown;
89
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
90
- [x: string]: string;
91
- }>;
92
- afterCreate(): void;
93
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
94
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
95
- }, {
96
- error: unknown;
97
- loadingP: Promise<void> | undefined;
98
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
99
- refNameAliases: {
100
- [x: string]: string;
101
- } | undefined;
102
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
103
- } & {
104
- getConf(arg: string): any;
105
- readonly lowerCaseRefNameAliases: {
106
- [k: string]: string;
107
- } | undefined;
108
- } & {
109
- readonly initialized: boolean;
110
- readonly name: string;
111
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
112
- readonly aliases: string[];
113
- readonly displayName: string;
114
- hasName(name: string): boolean;
115
- readonly allAliases: string[];
116
- readonly allRefNames: string[] | undefined;
117
- readonly lowerCaseRefNames: string[] | undefined;
118
- readonly allRefNamesWithLowerCase: string[] | undefined;
119
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
120
- readonly refNameColors: string[];
121
- } & {
122
- readonly refNames: string[] | undefined;
123
- } & {
124
- getCanonicalRefName(refName: string): string | undefined;
125
- getCanonicalRefName2(asmName: string): string;
126
- getRefNameColor(refName: string): string | undefined;
127
- isValidRefName(refName: string): boolean;
128
- } & {
129
- setLoaded({ regions, refNameAliases, cytobands, }: {
130
- regions: import("@jbrowse/core/util").Region[];
131
- refNameAliases: {
132
- [x: string]: string;
133
- };
134
- cytobands: import("@jbrowse/core/util").Feature[];
135
- }): void;
136
- setError(e: unknown): void;
137
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
138
- setRefNameAliases(aliases: {
139
- [x: string]: string;
140
- }): void;
141
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
142
- setLoadingP(p?: Promise<void>): void;
143
- load(): Promise<void>;
144
- loadPre(): Promise<void>;
145
- } & {
146
- getAdapterMapEntry(adapterConf: {
147
- [x: string]: unknown;
148
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
149
- getRefNameMapForAdapter(adapterConf: {
150
- [x: string]: unknown;
151
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
152
- [x: string]: string;
153
- }>;
154
- getReverseRefNameMapForAdapter(adapterConf: {
155
- [x: string]: unknown;
156
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
157
- [x: string]: string;
158
- }>;
159
- afterCreate(): void;
160
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
161
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
162
- readonly assemblyNameMap: Record<string, {
163
- configuration: any;
164
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
165
- error: unknown;
166
- loadingP: Promise<void> | undefined;
167
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
168
- refNameAliases: {
169
- [x: string]: string;
170
- } | undefined;
171
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
172
- } & {
173
- getConf(arg: string): any;
174
- readonly lowerCaseRefNameAliases: {
175
- [k: string]: string;
176
- } | undefined;
177
- } & {
178
- readonly initialized: boolean;
179
- readonly name: string;
180
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
181
- readonly aliases: string[];
182
- readonly displayName: string;
183
- hasName(name: string): boolean;
184
- readonly allAliases: string[];
185
- readonly allRefNames: string[] | undefined;
186
- readonly lowerCaseRefNames: string[] | undefined;
187
- readonly allRefNamesWithLowerCase: string[] | undefined;
188
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
189
- readonly refNameColors: string[];
190
- } & {
191
- readonly refNames: string[] | undefined;
192
- } & {
193
- getCanonicalRefName(refName: string): string | undefined;
194
- getCanonicalRefName2(asmName: string): string;
195
- getRefNameColor(refName: string): string | undefined;
196
- isValidRefName(refName: string): boolean;
197
- } & {
198
- setLoaded({ regions, refNameAliases, cytobands, }: {
199
- regions: import("@jbrowse/core/util").Region[];
200
- refNameAliases: {
201
- [x: string]: string;
202
- };
203
- cytobands: import("@jbrowse/core/util").Feature[];
204
- }): void;
205
- setError(e: unknown): void;
206
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
207
- setRefNameAliases(aliases: {
208
- [x: string]: string;
209
- }): void;
210
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
211
- setLoadingP(p?: Promise<void>): void;
212
- load(): Promise<void>;
213
- loadPre(): Promise<void>;
214
- } & {
215
- getAdapterMapEntry(adapterConf: {
216
- [x: string]: unknown;
217
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
218
- getRefNameMapForAdapter(adapterConf: {
219
- [x: string]: unknown;
220
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
221
- [x: string]: string;
222
- }>;
223
- getReverseRefNameMapForAdapter(adapterConf: {
224
- [x: string]: unknown;
225
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
226
- [x: string]: string;
227
- }>;
228
- afterCreate(): void;
229
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
230
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
231
- }, {
232
- error: unknown;
233
- loadingP: Promise<void> | undefined;
234
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
235
- refNameAliases: {
236
- [x: string]: string;
237
- } | undefined;
238
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
239
- } & {
240
- getConf(arg: string): any;
241
- readonly lowerCaseRefNameAliases: {
242
- [k: string]: string;
243
- } | undefined;
244
- } & {
245
- readonly initialized: boolean;
246
- readonly name: string;
247
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
248
- readonly aliases: string[];
249
- readonly displayName: string;
250
- hasName(name: string): boolean;
251
- readonly allAliases: string[];
252
- readonly allRefNames: string[] | undefined;
253
- readonly lowerCaseRefNames: string[] | undefined;
254
- readonly allRefNamesWithLowerCase: string[] | undefined;
255
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
256
- readonly refNameColors: string[];
257
- } & {
258
- readonly refNames: string[] | undefined;
259
- } & {
260
- getCanonicalRefName(refName: string): string | undefined;
261
- getCanonicalRefName2(asmName: string): string;
262
- getRefNameColor(refName: string): string | undefined;
263
- isValidRefName(refName: string): boolean;
264
- } & {
265
- setLoaded({ regions, refNameAliases, cytobands, }: {
266
- regions: import("@jbrowse/core/util").Region[];
267
- refNameAliases: {
268
- [x: string]: string;
269
- };
270
- cytobands: import("@jbrowse/core/util").Feature[];
271
- }): void;
272
- setError(e: unknown): void;
273
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
274
- setRefNameAliases(aliases: {
275
- [x: string]: string;
276
- }): void;
277
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
278
- setLoadingP(p?: Promise<void>): void;
279
- load(): Promise<void>;
280
- loadPre(): Promise<void>;
281
- } & {
282
- getAdapterMapEntry(adapterConf: {
283
- [x: string]: unknown;
284
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
285
- getRefNameMapForAdapter(adapterConf: {
286
- [x: string]: unknown;
287
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
288
- [x: string]: string;
289
- }>;
290
- getReverseRefNameMapForAdapter(adapterConf: {
291
- [x: string]: unknown;
292
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
293
- [x: string]: string;
294
- }>;
295
- afterCreate(): void;
296
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
297
- } & {
298
- getCanonicalAssemblyName(asmName: string): string | undefined;
299
- getCanonicalAssemblyName2(asmName: string): string;
300
- get(asmName: string): ({
301
- configuration: any;
302
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
303
- error: unknown;
304
- loadingP: Promise<void> | undefined;
305
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
306
- refNameAliases: {
307
- [x: string]: string;
308
- } | undefined;
309
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
310
- } & {
311
- getConf(arg: string): any;
312
- readonly lowerCaseRefNameAliases: {
313
- [k: string]: string;
314
- } | undefined;
315
- } & {
316
- readonly initialized: boolean;
317
- readonly name: string;
318
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
319
- readonly aliases: string[];
320
- readonly displayName: string;
321
- hasName(name: string): boolean;
322
- readonly allAliases: string[];
323
- readonly allRefNames: string[] | undefined;
324
- readonly lowerCaseRefNames: string[] | undefined;
325
- readonly allRefNamesWithLowerCase: string[] | undefined;
326
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
327
- readonly refNameColors: string[];
328
- } & {
329
- readonly refNames: string[] | undefined;
330
- } & {
331
- getCanonicalRefName(refName: string): string | undefined;
332
- getCanonicalRefName2(asmName: string): string;
333
- getRefNameColor(refName: string): string | undefined;
334
- isValidRefName(refName: string): boolean;
335
- } & {
336
- setLoaded({ regions, refNameAliases, cytobands, }: {
337
- regions: import("@jbrowse/core/util").Region[];
338
- refNameAliases: {
339
- [x: string]: string;
340
- };
341
- cytobands: import("@jbrowse/core/util").Feature[];
342
- }): void;
343
- setError(e: unknown): void;
344
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
345
- setRefNameAliases(aliases: {
346
- [x: string]: string;
347
- }): void;
348
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
349
- setLoadingP(p?: Promise<void>): void;
350
- load(): Promise<void>;
351
- loadPre(): Promise<void>;
352
- } & {
353
- getAdapterMapEntry(adapterConf: {
354
- [x: string]: unknown;
355
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
356
- getRefNameMapForAdapter(adapterConf: {
357
- [x: string]: unknown;
358
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
359
- [x: string]: string;
360
- }>;
361
- getReverseRefNameMapForAdapter(adapterConf: {
362
- [x: string]: unknown;
363
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
364
- [x: string]: string;
365
- }>;
366
- afterCreate(): void;
367
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
368
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
369
- }, {
370
- error: unknown;
371
- loadingP: Promise<void> | undefined;
372
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
373
- refNameAliases: {
374
- [x: string]: string;
375
- } | undefined;
376
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
377
- } & {
378
- getConf(arg: string): any;
379
- readonly lowerCaseRefNameAliases: {
380
- [k: string]: string;
381
- } | undefined;
382
- } & {
383
- readonly initialized: boolean;
384
- readonly name: string;
385
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
386
- readonly aliases: string[];
387
- readonly displayName: string;
388
- hasName(name: string): boolean;
389
- readonly allAliases: string[];
390
- readonly allRefNames: string[] | undefined;
391
- readonly lowerCaseRefNames: string[] | undefined;
392
- readonly allRefNamesWithLowerCase: string[] | undefined;
393
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
394
- readonly refNameColors: string[];
395
- } & {
396
- readonly refNames: string[] | undefined;
397
- } & {
398
- getCanonicalRefName(refName: string): string | undefined;
399
- getCanonicalRefName2(asmName: string): string;
400
- getRefNameColor(refName: string): string | undefined;
401
- isValidRefName(refName: string): boolean;
402
- } & {
403
- setLoaded({ regions, refNameAliases, cytobands, }: {
404
- regions: import("@jbrowse/core/util").Region[];
405
- refNameAliases: {
406
- [x: string]: string;
407
- };
408
- cytobands: import("@jbrowse/core/util").Feature[];
409
- }): void;
410
- setError(e: unknown): void;
411
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
412
- setRefNameAliases(aliases: {
413
- [x: string]: string;
414
- }): void;
415
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
416
- setLoadingP(p?: Promise<void>): void;
417
- load(): Promise<void>;
418
- loadPre(): Promise<void>;
419
- } & {
420
- getAdapterMapEntry(adapterConf: {
421
- [x: string]: unknown;
422
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
423
- getRefNameMapForAdapter(adapterConf: {
424
- [x: string]: unknown;
425
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
426
- [x: string]: string;
427
- }>;
428
- getReverseRefNameMapForAdapter(adapterConf: {
429
- [x: string]: unknown;
430
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
431
- [x: string]: string;
432
- }>;
433
- afterCreate(): void;
434
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
435
- readonly assemblyNamesList: any[];
436
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
437
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
438
- } & {
439
- waitForAssembly(assemblyName: string): Promise<({
440
- configuration: any;
441
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
442
- error: unknown;
443
- loadingP: Promise<void> | undefined;
444
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
445
- refNameAliases: {
446
- [x: string]: string;
447
- } | undefined;
448
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
449
- } & {
450
- getConf(arg: string): any;
451
- readonly lowerCaseRefNameAliases: {
452
- [k: string]: string;
453
- } | undefined;
454
- } & {
455
- readonly initialized: boolean;
456
- readonly name: string;
457
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
458
- readonly aliases: string[];
459
- readonly displayName: string;
460
- hasName(name: string): boolean;
461
- readonly allAliases: string[];
462
- readonly allRefNames: string[] | undefined;
463
- readonly lowerCaseRefNames: string[] | undefined;
464
- readonly allRefNamesWithLowerCase: string[] | undefined;
465
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
466
- readonly refNameColors: string[];
467
- } & {
468
- readonly refNames: string[] | undefined;
469
- } & {
470
- getCanonicalRefName(refName: string): string | undefined;
471
- getCanonicalRefName2(asmName: string): string;
472
- getRefNameColor(refName: string): string | undefined;
473
- isValidRefName(refName: string): boolean;
474
- } & {
475
- setLoaded({ regions, refNameAliases, cytobands, }: {
476
- regions: import("@jbrowse/core/util").Region[];
477
- refNameAliases: {
478
- [x: string]: string;
479
- };
480
- cytobands: import("@jbrowse/core/util").Feature[];
481
- }): void;
482
- setError(e: unknown): void;
483
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
484
- setRefNameAliases(aliases: {
485
- [x: string]: string;
486
- }): void;
487
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
488
- setLoadingP(p?: Promise<void>): void;
489
- load(): Promise<void>;
490
- loadPre(): Promise<void>;
491
- } & {
492
- getAdapterMapEntry(adapterConf: {
493
- [x: string]: unknown;
494
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
495
- getRefNameMapForAdapter(adapterConf: {
496
- [x: string]: unknown;
497
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
498
- [x: string]: string;
499
- }>;
500
- getReverseRefNameMapForAdapter(adapterConf: {
501
- [x: string]: unknown;
502
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
503
- [x: string]: string;
504
- }>;
505
- afterCreate(): void;
506
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
507
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
508
- }, {
509
- error: unknown;
510
- loadingP: Promise<void> | undefined;
511
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
512
- refNameAliases: {
513
- [x: string]: string;
514
- } | undefined;
515
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
516
- } & {
517
- getConf(arg: string): any;
518
- readonly lowerCaseRefNameAliases: {
519
- [k: string]: string;
520
- } | undefined;
521
- } & {
522
- readonly initialized: boolean;
523
- readonly name: string;
524
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
525
- readonly aliases: string[];
526
- readonly displayName: string;
527
- hasName(name: string): boolean;
528
- readonly allAliases: string[];
529
- readonly allRefNames: string[] | undefined;
530
- readonly lowerCaseRefNames: string[] | undefined;
531
- readonly allRefNamesWithLowerCase: string[] | undefined;
532
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
533
- readonly refNameColors: string[];
534
- } & {
535
- readonly refNames: string[] | undefined;
536
- } & {
537
- getCanonicalRefName(refName: string): string | undefined;
538
- getCanonicalRefName2(asmName: string): string;
539
- getRefNameColor(refName: string): string | undefined;
540
- isValidRefName(refName: string): boolean;
541
- } & {
542
- setLoaded({ regions, refNameAliases, cytobands, }: {
543
- regions: import("@jbrowse/core/util").Region[];
544
- refNameAliases: {
545
- [x: string]: string;
546
- };
547
- cytobands: import("@jbrowse/core/util").Feature[];
548
- }): void;
549
- setError(e: unknown): void;
550
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
551
- setRefNameAliases(aliases: {
552
- [x: string]: string;
553
- }): void;
554
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
555
- setLoadingP(p?: Promise<void>): void;
556
- load(): Promise<void>;
557
- loadPre(): Promise<void>;
558
- } & {
559
- getAdapterMapEntry(adapterConf: {
560
- [x: string]: unknown;
561
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
562
- getRefNameMapForAdapter(adapterConf: {
563
- [x: string]: unknown;
564
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
565
- [x: string]: string;
566
- }>;
567
- getReverseRefNameMapForAdapter(adapterConf: {
568
- [x: string]: unknown;
569
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
570
- [x: string]: string;
571
- }>;
572
- afterCreate(): void;
573
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
574
- getRefNameMapForAdapter(adapterConf: {
575
- [x: string]: unknown;
576
- }, assemblyName: string | undefined, opts: {
577
- stopToken?: string;
578
- sessionId: string;
579
- }): Promise<{
580
- [x: string]: string;
581
- } | undefined>;
582
- getReverseRefNameMapForAdapter(adapterConf: {
583
- [x: string]: unknown;
584
- }, assemblyName: string | undefined, opts: {
585
- stopToken?: string;
586
- sessionId: string;
587
- }): Promise<{
588
- [x: string]: string;
589
- } | undefined>;
590
- isValidRefName(refName: string, assemblyName: string): boolean;
591
- } & {
592
- afterAttach(): void;
593
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
594
- addAssembly(configuration: any): void;
595
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
596
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
597
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
598
- }, {
599
- error: unknown;
600
- loadingP: Promise<void> | undefined;
601
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
602
- refNameAliases: {
603
- [x: string]: string;
604
- } | undefined;
605
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
606
- } & {
607
- getConf(arg: string): any;
608
- readonly lowerCaseRefNameAliases: {
609
- [k: string]: string;
610
- } | undefined;
611
- } & {
612
- readonly initialized: boolean;
613
- readonly name: string;
614
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
615
- readonly aliases: string[];
616
- readonly displayName: string;
617
- hasName(name: string): boolean;
618
- readonly allAliases: string[];
619
- readonly allRefNames: string[] | undefined;
620
- readonly lowerCaseRefNames: string[] | undefined;
621
- readonly allRefNamesWithLowerCase: string[] | undefined;
622
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
623
- readonly refNameColors: string[];
624
- } & {
625
- readonly refNames: string[] | undefined;
626
- } & {
627
- getCanonicalRefName(refName: string): string | undefined;
628
- getCanonicalRefName2(asmName: string): string;
629
- getRefNameColor(refName: string): string | undefined;
630
- isValidRefName(refName: string): boolean;
631
- } & {
632
- setLoaded({ regions, refNameAliases, cytobands, }: {
633
- regions: import("@jbrowse/core/util").Region[];
634
- refNameAliases: {
635
- [x: string]: string;
636
- };
637
- cytobands: import("@jbrowse/core/util").Feature[];
638
- }): void;
639
- setError(e: unknown): void;
640
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
641
- setRefNameAliases(aliases: {
642
- [x: string]: string;
643
- }): void;
644
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
645
- setLoadingP(p?: Promise<void>): void;
646
- load(): Promise<void>;
647
- loadPre(): Promise<void>;
648
- } & {
649
- getAdapterMapEntry(adapterConf: {
650
- [x: string]: unknown;
651
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
652
- getRefNameMapForAdapter(adapterConf: {
653
- [x: string]: unknown;
654
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
655
- [x: string]: string;
656
- }>;
657
- getReverseRefNameMapForAdapter(adapterConf: {
658
- [x: string]: unknown;
659
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
660
- [x: string]: string;
661
- }>;
662
- afterCreate(): void;
663
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
664
- }, {
665
- readonly assemblyNameMap: Record<string, {
666
- configuration: any;
667
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
668
- error: unknown;
669
- loadingP: Promise<void> | undefined;
670
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
671
- refNameAliases: {
672
- [x: string]: string;
673
- } | undefined;
674
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
675
- } & {
676
- getConf(arg: string): any;
677
- readonly lowerCaseRefNameAliases: {
678
- [k: string]: string;
679
- } | undefined;
680
- } & {
681
- readonly initialized: boolean;
682
- readonly name: string;
683
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
684
- readonly aliases: string[];
685
- readonly displayName: string;
686
- hasName(name: string): boolean;
687
- readonly allAliases: string[];
688
- readonly allRefNames: string[] | undefined;
689
- readonly lowerCaseRefNames: string[] | undefined;
690
- readonly allRefNamesWithLowerCase: string[] | undefined;
691
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
692
- readonly refNameColors: string[];
693
- } & {
694
- readonly refNames: string[] | undefined;
695
- } & {
696
- getCanonicalRefName(refName: string): string | undefined;
697
- getCanonicalRefName2(asmName: string): string;
698
- getRefNameColor(refName: string): string | undefined;
699
- isValidRefName(refName: string): boolean;
700
- } & {
701
- setLoaded({ regions, refNameAliases, cytobands, }: {
702
- regions: import("@jbrowse/core/util").Region[];
703
- refNameAliases: {
704
- [x: string]: string;
705
- };
706
- cytobands: import("@jbrowse/core/util").Feature[];
707
- }): void;
708
- setError(e: unknown): void;
709
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
710
- setRefNameAliases(aliases: {
711
- [x: string]: string;
712
- }): void;
713
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
714
- setLoadingP(p?: Promise<void>): void;
715
- load(): Promise<void>;
716
- loadPre(): Promise<void>;
717
- } & {
718
- getAdapterMapEntry(adapterConf: {
719
- [x: string]: unknown;
720
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
721
- getRefNameMapForAdapter(adapterConf: {
722
- [x: string]: unknown;
723
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
724
- [x: string]: string;
725
- }>;
726
- getReverseRefNameMapForAdapter(adapterConf: {
727
- [x: string]: unknown;
728
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
729
- [x: string]: string;
730
- }>;
731
- afterCreate(): void;
732
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
733
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
734
- }, {
735
- error: unknown;
736
- loadingP: Promise<void> | undefined;
737
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
738
- refNameAliases: {
739
- [x: string]: string;
740
- } | undefined;
741
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
742
- } & {
743
- getConf(arg: string): any;
744
- readonly lowerCaseRefNameAliases: {
745
- [k: string]: string;
746
- } | undefined;
747
- } & {
748
- readonly initialized: boolean;
749
- readonly name: string;
750
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
751
- readonly aliases: string[];
752
- readonly displayName: string;
753
- hasName(name: string): boolean;
754
- readonly allAliases: string[];
755
- readonly allRefNames: string[] | undefined;
756
- readonly lowerCaseRefNames: string[] | undefined;
757
- readonly allRefNamesWithLowerCase: string[] | undefined;
758
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
759
- readonly refNameColors: string[];
760
- } & {
761
- readonly refNames: string[] | undefined;
762
- } & {
763
- getCanonicalRefName(refName: string): string | undefined;
764
- getCanonicalRefName2(asmName: string): string;
765
- getRefNameColor(refName: string): string | undefined;
766
- isValidRefName(refName: string): boolean;
767
- } & {
768
- setLoaded({ regions, refNameAliases, cytobands, }: {
769
- regions: import("@jbrowse/core/util").Region[];
770
- refNameAliases: {
771
- [x: string]: string;
772
- };
773
- cytobands: import("@jbrowse/core/util").Feature[];
774
- }): void;
775
- setError(e: unknown): void;
776
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
777
- setRefNameAliases(aliases: {
778
- [x: string]: string;
779
- }): void;
780
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
781
- setLoadingP(p?: Promise<void>): void;
782
- load(): Promise<void>;
783
- loadPre(): Promise<void>;
784
- } & {
785
- getAdapterMapEntry(adapterConf: {
786
- [x: string]: unknown;
787
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
788
- getRefNameMapForAdapter(adapterConf: {
789
- [x: string]: unknown;
790
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
791
- [x: string]: string;
792
- }>;
793
- getReverseRefNameMapForAdapter(adapterConf: {
794
- [x: string]: unknown;
795
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
796
- [x: string]: string;
797
- }>;
798
- afterCreate(): void;
799
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
800
- } & {
801
- getCanonicalAssemblyName(asmName: string): string | undefined;
802
- getCanonicalAssemblyName2(asmName: string): string;
803
- get(asmName: string): ({
804
- configuration: any;
805
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
806
- error: unknown;
807
- loadingP: Promise<void> | undefined;
808
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
809
- refNameAliases: {
810
- [x: string]: string;
811
- } | undefined;
812
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
813
- } & {
814
- getConf(arg: string): any;
815
- readonly lowerCaseRefNameAliases: {
816
- [k: string]: string;
817
- } | undefined;
818
- } & {
819
- readonly initialized: boolean;
820
- readonly name: string;
821
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
822
- readonly aliases: string[];
823
- readonly displayName: string;
824
- hasName(name: string): boolean;
825
- readonly allAliases: string[];
826
- readonly allRefNames: string[] | undefined;
827
- readonly lowerCaseRefNames: string[] | undefined;
828
- readonly allRefNamesWithLowerCase: string[] | undefined;
829
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
830
- readonly refNameColors: string[];
831
- } & {
832
- readonly refNames: string[] | undefined;
833
- } & {
834
- getCanonicalRefName(refName: string): string | undefined;
835
- getCanonicalRefName2(asmName: string): string;
836
- getRefNameColor(refName: string): string | undefined;
837
- isValidRefName(refName: string): boolean;
838
- } & {
839
- setLoaded({ regions, refNameAliases, cytobands, }: {
840
- regions: import("@jbrowse/core/util").Region[];
841
- refNameAliases: {
842
- [x: string]: string;
843
- };
844
- cytobands: import("@jbrowse/core/util").Feature[];
845
- }): void;
846
- setError(e: unknown): void;
847
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
848
- setRefNameAliases(aliases: {
849
- [x: string]: string;
850
- }): void;
851
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
852
- setLoadingP(p?: Promise<void>): void;
853
- load(): Promise<void>;
854
- loadPre(): Promise<void>;
855
- } & {
856
- getAdapterMapEntry(adapterConf: {
857
- [x: string]: unknown;
858
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
859
- getRefNameMapForAdapter(adapterConf: {
860
- [x: string]: unknown;
861
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
862
- [x: string]: string;
863
- }>;
864
- getReverseRefNameMapForAdapter(adapterConf: {
865
- [x: string]: unknown;
866
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
867
- [x: string]: string;
868
- }>;
869
- afterCreate(): void;
870
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
871
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
872
- }, {
873
- error: unknown;
874
- loadingP: Promise<void> | undefined;
875
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
876
- refNameAliases: {
877
- [x: string]: string;
878
- } | undefined;
879
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
880
- } & {
881
- getConf(arg: string): any;
882
- readonly lowerCaseRefNameAliases: {
883
- [k: string]: string;
884
- } | undefined;
885
- } & {
886
- readonly initialized: boolean;
887
- readonly name: string;
888
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
889
- readonly aliases: string[];
890
- readonly displayName: string;
891
- hasName(name: string): boolean;
892
- readonly allAliases: string[];
893
- readonly allRefNames: string[] | undefined;
894
- readonly lowerCaseRefNames: string[] | undefined;
895
- readonly allRefNamesWithLowerCase: string[] | undefined;
896
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
897
- readonly refNameColors: string[];
898
- } & {
899
- readonly refNames: string[] | undefined;
900
- } & {
901
- getCanonicalRefName(refName: string): string | undefined;
902
- getCanonicalRefName2(asmName: string): string;
903
- getRefNameColor(refName: string): string | undefined;
904
- isValidRefName(refName: string): boolean;
905
- } & {
906
- setLoaded({ regions, refNameAliases, cytobands, }: {
907
- regions: import("@jbrowse/core/util").Region[];
908
- refNameAliases: {
909
- [x: string]: string;
910
- };
911
- cytobands: import("@jbrowse/core/util").Feature[];
912
- }): void;
913
- setError(e: unknown): void;
914
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
915
- setRefNameAliases(aliases: {
916
- [x: string]: string;
917
- }): void;
918
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
919
- setLoadingP(p?: Promise<void>): void;
920
- load(): Promise<void>;
921
- loadPre(): Promise<void>;
922
- } & {
923
- getAdapterMapEntry(adapterConf: {
924
- [x: string]: unknown;
925
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
926
- getRefNameMapForAdapter(adapterConf: {
927
- [x: string]: unknown;
928
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
929
- [x: string]: string;
930
- }>;
931
- getReverseRefNameMapForAdapter(adapterConf: {
932
- [x: string]: unknown;
933
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
934
- [x: string]: string;
935
- }>;
936
- afterCreate(): void;
937
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
938
- readonly assemblyNamesList: any[];
939
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
940
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
941
- } & {
942
- waitForAssembly(assemblyName: string): Promise<({
943
- configuration: any;
944
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
945
- error: unknown;
946
- loadingP: Promise<void> | undefined;
947
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
948
- refNameAliases: {
949
- [x: string]: string;
950
- } | undefined;
951
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
952
- } & {
953
- getConf(arg: string): any;
954
- readonly lowerCaseRefNameAliases: {
955
- [k: string]: string;
956
- } | undefined;
957
- } & {
958
- readonly initialized: boolean;
959
- readonly name: string;
960
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
961
- readonly aliases: string[];
962
- readonly displayName: string;
963
- hasName(name: string): boolean;
964
- readonly allAliases: string[];
965
- readonly allRefNames: string[] | undefined;
966
- readonly lowerCaseRefNames: string[] | undefined;
967
- readonly allRefNamesWithLowerCase: string[] | undefined;
968
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
969
- readonly refNameColors: string[];
970
- } & {
971
- readonly refNames: string[] | undefined;
972
- } & {
973
- getCanonicalRefName(refName: string): string | undefined;
974
- getCanonicalRefName2(asmName: string): string;
975
- getRefNameColor(refName: string): string | undefined;
976
- isValidRefName(refName: string): boolean;
977
- } & {
978
- setLoaded({ regions, refNameAliases, cytobands, }: {
979
- regions: import("@jbrowse/core/util").Region[];
980
- refNameAliases: {
981
- [x: string]: string;
982
- };
983
- cytobands: import("@jbrowse/core/util").Feature[];
984
- }): void;
985
- setError(e: unknown): void;
986
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
987
- setRefNameAliases(aliases: {
988
- [x: string]: string;
989
- }): void;
990
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
991
- setLoadingP(p?: Promise<void>): void;
992
- load(): Promise<void>;
993
- loadPre(): Promise<void>;
994
- } & {
995
- getAdapterMapEntry(adapterConf: {
996
- [x: string]: unknown;
997
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
998
- getRefNameMapForAdapter(adapterConf: {
999
- [x: string]: unknown;
1000
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1001
- [x: string]: string;
1002
- }>;
1003
- getReverseRefNameMapForAdapter(adapterConf: {
1004
- [x: string]: unknown;
1005
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1006
- [x: string]: string;
1007
- }>;
1008
- afterCreate(): void;
1009
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1010
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1011
- }, {
1012
- error: unknown;
1013
- loadingP: Promise<void> | undefined;
1014
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1015
- refNameAliases: {
1016
- [x: string]: string;
1017
- } | undefined;
1018
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1019
- } & {
1020
- getConf(arg: string): any;
1021
- readonly lowerCaseRefNameAliases: {
1022
- [k: string]: string;
1023
- } | undefined;
1024
- } & {
1025
- readonly initialized: boolean;
1026
- readonly name: string;
1027
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1028
- readonly aliases: string[];
1029
- readonly displayName: string;
1030
- hasName(name: string): boolean;
1031
- readonly allAliases: string[];
1032
- readonly allRefNames: string[] | undefined;
1033
- readonly lowerCaseRefNames: string[] | undefined;
1034
- readonly allRefNamesWithLowerCase: string[] | undefined;
1035
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1036
- readonly refNameColors: string[];
1037
- } & {
1038
- readonly refNames: string[] | undefined;
1039
- } & {
1040
- getCanonicalRefName(refName: string): string | undefined;
1041
- getCanonicalRefName2(asmName: string): string;
1042
- getRefNameColor(refName: string): string | undefined;
1043
- isValidRefName(refName: string): boolean;
1044
- } & {
1045
- setLoaded({ regions, refNameAliases, cytobands, }: {
1046
- regions: import("@jbrowse/core/util").Region[];
1047
- refNameAliases: {
1048
- [x: string]: string;
1049
- };
1050
- cytobands: import("@jbrowse/core/util").Feature[];
1051
- }): void;
1052
- setError(e: unknown): void;
1053
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1054
- setRefNameAliases(aliases: {
1055
- [x: string]: string;
1056
- }): void;
1057
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1058
- setLoadingP(p?: Promise<void>): void;
1059
- load(): Promise<void>;
1060
- loadPre(): Promise<void>;
1061
- } & {
1062
- getAdapterMapEntry(adapterConf: {
1063
- [x: string]: unknown;
1064
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1065
- getRefNameMapForAdapter(adapterConf: {
1066
- [x: string]: unknown;
1067
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1068
- [x: string]: string;
1069
- }>;
1070
- getReverseRefNameMapForAdapter(adapterConf: {
1071
- [x: string]: unknown;
1072
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1073
- [x: string]: string;
1074
- }>;
1075
- afterCreate(): void;
1076
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1077
- getRefNameMapForAdapter(adapterConf: {
1078
- [x: string]: unknown;
1079
- }, assemblyName: string | undefined, opts: {
1080
- stopToken?: string;
1081
- sessionId: string;
1082
- }): Promise<{
1083
- [x: string]: string;
1084
- } | undefined>;
1085
- getReverseRefNameMapForAdapter(adapterConf: {
1086
- [x: string]: unknown;
1087
- }, assemblyName: string | undefined, opts: {
1088
- stopToken?: string;
1089
- sessionId: string;
1090
- }): Promise<{
1091
- [x: string]: string;
1092
- } | undefined>;
1093
- isValidRefName(refName: string, assemblyName: string): boolean;
1094
- } & {
1095
- afterAttach(): void;
1096
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1097
- addAssembly(configuration: any): void;
1098
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
1099
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1100
- rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1101
- adminMode: boolean;
1102
- error: unknown;
1103
- textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1104
- pluginManager: PluginManager;
1105
- } & {
1106
- setError(error: unknown): void;
1107
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1108
- setDefaultSession(): void;
1109
- setSessionPath(path: string): void;
1110
- renameCurrentSession(newName: string): void;
1111
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1112
- jbrowse: import("mobx-state-tree").IAnyType;
1113
- session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
1114
- sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1115
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1116
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1117
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1118
- }, {
1119
- error: unknown;
1120
- loadingP: Promise<void> | undefined;
1121
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1122
- refNameAliases: {
1123
- [x: string]: string;
1124
- } | undefined;
1125
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1126
- } & {
1127
- getConf(arg: string): any;
1128
- readonly lowerCaseRefNameAliases: {
1129
- [k: string]: string;
1130
- } | undefined;
1131
- } & {
1132
- readonly initialized: boolean;
1133
- readonly name: string;
1134
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1135
- readonly aliases: string[];
1136
- readonly displayName: string;
1137
- hasName(name: string): boolean;
1138
- readonly allAliases: string[];
1139
- readonly allRefNames: string[] | undefined;
1140
- readonly lowerCaseRefNames: string[] | undefined;
1141
- readonly allRefNamesWithLowerCase: string[] | undefined;
1142
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1143
- readonly refNameColors: string[];
1144
- } & {
1145
- readonly refNames: string[] | undefined;
1146
- } & {
1147
- getCanonicalRefName(refName: string): string | undefined;
1148
- getCanonicalRefName2(asmName: string): string;
1149
- getRefNameColor(refName: string): string | undefined;
1150
- isValidRefName(refName: string): boolean;
1151
- } & {
1152
- setLoaded({ regions, refNameAliases, cytobands, }: {
1153
- regions: import("@jbrowse/core/util").Region[];
1154
- refNameAliases: {
1155
- [x: string]: string;
1156
- };
1157
- cytobands: import("@jbrowse/core/util").Feature[];
1158
- }): void;
1159
- setError(e: unknown): void;
1160
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1161
- setRefNameAliases(aliases: {
1162
- [x: string]: string;
1163
- }): void;
1164
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1165
- setLoadingP(p?: Promise<void>): void;
1166
- load(): Promise<void>;
1167
- loadPre(): Promise<void>;
1168
- } & {
1169
- getAdapterMapEntry(adapterConf: {
1170
- [x: string]: unknown;
1171
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1172
- getRefNameMapForAdapter(adapterConf: {
1173
- [x: string]: unknown;
1174
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1175
- [x: string]: string;
1176
- }>;
1177
- getReverseRefNameMapForAdapter(adapterConf: {
1178
- [x: string]: unknown;
1179
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1180
- [x: string]: string;
1181
- }>;
1182
- afterCreate(): void;
1183
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1184
- }, {
1185
- readonly assemblyNameMap: Record<string, {
1186
- configuration: any;
1187
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1188
- error: unknown;
1189
- loadingP: Promise<void> | undefined;
1190
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1191
- refNameAliases: {
1192
- [x: string]: string;
1193
- } | undefined;
1194
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1195
- } & {
1196
- getConf(arg: string): any;
1197
- readonly lowerCaseRefNameAliases: {
1198
- [k: string]: string;
1199
- } | undefined;
1200
- } & {
1201
- readonly initialized: boolean;
1202
- readonly name: string;
1203
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1204
- readonly aliases: string[];
1205
- readonly displayName: string;
1206
- hasName(name: string): boolean;
1207
- readonly allAliases: string[];
1208
- readonly allRefNames: string[] | undefined;
1209
- readonly lowerCaseRefNames: string[] | undefined;
1210
- readonly allRefNamesWithLowerCase: string[] | undefined;
1211
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1212
- readonly refNameColors: string[];
1213
- } & {
1214
- readonly refNames: string[] | undefined;
1215
- } & {
1216
- getCanonicalRefName(refName: string): string | undefined;
1217
- getCanonicalRefName2(asmName: string): string;
1218
- getRefNameColor(refName: string): string | undefined;
1219
- isValidRefName(refName: string): boolean;
1220
- } & {
1221
- setLoaded({ regions, refNameAliases, cytobands, }: {
1222
- regions: import("@jbrowse/core/util").Region[];
1223
- refNameAliases: {
1224
- [x: string]: string;
1225
- };
1226
- cytobands: import("@jbrowse/core/util").Feature[];
1227
- }): void;
1228
- setError(e: unknown): void;
1229
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1230
- setRefNameAliases(aliases: {
1231
- [x: string]: string;
1232
- }): void;
1233
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1234
- setLoadingP(p?: Promise<void>): void;
1235
- load(): Promise<void>;
1236
- loadPre(): Promise<void>;
1237
- } & {
1238
- getAdapterMapEntry(adapterConf: {
1239
- [x: string]: unknown;
1240
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1241
- getRefNameMapForAdapter(adapterConf: {
1242
- [x: string]: unknown;
1243
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1244
- [x: string]: string;
1245
- }>;
1246
- getReverseRefNameMapForAdapter(adapterConf: {
1247
- [x: string]: unknown;
1248
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1249
- [x: string]: string;
1250
- }>;
1251
- afterCreate(): void;
1252
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1253
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1254
- }, {
1255
- error: unknown;
1256
- loadingP: Promise<void> | undefined;
1257
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1258
- refNameAliases: {
1259
- [x: string]: string;
1260
- } | undefined;
1261
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1262
- } & {
1263
- getConf(arg: string): any;
1264
- readonly lowerCaseRefNameAliases: {
1265
- [k: string]: string;
1266
- } | undefined;
1267
- } & {
1268
- readonly initialized: boolean;
1269
- readonly name: string;
1270
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1271
- readonly aliases: string[];
1272
- readonly displayName: string;
1273
- hasName(name: string): boolean;
1274
- readonly allAliases: string[];
1275
- readonly allRefNames: string[] | undefined;
1276
- readonly lowerCaseRefNames: string[] | undefined;
1277
- readonly allRefNamesWithLowerCase: string[] | undefined;
1278
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1279
- readonly refNameColors: string[];
1280
- } & {
1281
- readonly refNames: string[] | undefined;
1282
- } & {
1283
- getCanonicalRefName(refName: string): string | undefined;
1284
- getCanonicalRefName2(asmName: string): string;
1285
- getRefNameColor(refName: string): string | undefined;
1286
- isValidRefName(refName: string): boolean;
1287
- } & {
1288
- setLoaded({ regions, refNameAliases, cytobands, }: {
1289
- regions: import("@jbrowse/core/util").Region[];
1290
- refNameAliases: {
1291
- [x: string]: string;
1292
- };
1293
- cytobands: import("@jbrowse/core/util").Feature[];
1294
- }): void;
1295
- setError(e: unknown): void;
1296
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1297
- setRefNameAliases(aliases: {
1298
- [x: string]: string;
1299
- }): void;
1300
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1301
- setLoadingP(p?: Promise<void>): void;
1302
- load(): Promise<void>;
1303
- loadPre(): Promise<void>;
1304
- } & {
1305
- getAdapterMapEntry(adapterConf: {
1306
- [x: string]: unknown;
1307
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1308
- getRefNameMapForAdapter(adapterConf: {
1309
- [x: string]: unknown;
1310
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1311
- [x: string]: string;
1312
- }>;
1313
- getReverseRefNameMapForAdapter(adapterConf: {
1314
- [x: string]: unknown;
1315
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1316
- [x: string]: string;
1317
- }>;
1318
- afterCreate(): void;
1319
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
1320
- } & {
1321
- getCanonicalAssemblyName(asmName: string): string | undefined;
1322
- getCanonicalAssemblyName2(asmName: string): string;
1323
- get(asmName: string): ({
1324
- configuration: any;
1325
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1326
- error: unknown;
1327
- loadingP: Promise<void> | undefined;
1328
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1329
- refNameAliases: {
1330
- [x: string]: string;
1331
- } | undefined;
1332
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1333
- } & {
1334
- getConf(arg: string): any;
1335
- readonly lowerCaseRefNameAliases: {
1336
- [k: string]: string;
1337
- } | undefined;
1338
- } & {
1339
- readonly initialized: boolean;
1340
- readonly name: string;
1341
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1342
- readonly aliases: string[];
1343
- readonly displayName: string;
1344
- hasName(name: string): boolean;
1345
- readonly allAliases: string[];
1346
- readonly allRefNames: string[] | undefined;
1347
- readonly lowerCaseRefNames: string[] | undefined;
1348
- readonly allRefNamesWithLowerCase: string[] | undefined;
1349
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1350
- readonly refNameColors: string[];
1351
- } & {
1352
- readonly refNames: string[] | undefined;
1353
- } & {
1354
- getCanonicalRefName(refName: string): string | undefined;
1355
- getCanonicalRefName2(asmName: string): string;
1356
- getRefNameColor(refName: string): string | undefined;
1357
- isValidRefName(refName: string): boolean;
1358
- } & {
1359
- setLoaded({ regions, refNameAliases, cytobands, }: {
1360
- regions: import("@jbrowse/core/util").Region[];
1361
- refNameAliases: {
1362
- [x: string]: string;
1363
- };
1364
- cytobands: import("@jbrowse/core/util").Feature[];
1365
- }): void;
1366
- setError(e: unknown): void;
1367
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1368
- setRefNameAliases(aliases: {
1369
- [x: string]: string;
1370
- }): void;
1371
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1372
- setLoadingP(p?: Promise<void>): void;
1373
- load(): Promise<void>;
1374
- loadPre(): Promise<void>;
1375
- } & {
1376
- getAdapterMapEntry(adapterConf: {
1377
- [x: string]: unknown;
1378
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1379
- getRefNameMapForAdapter(adapterConf: {
1380
- [x: string]: unknown;
1381
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1382
- [x: string]: string;
1383
- }>;
1384
- getReverseRefNameMapForAdapter(adapterConf: {
1385
- [x: string]: unknown;
1386
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1387
- [x: string]: string;
1388
- }>;
1389
- afterCreate(): void;
1390
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1391
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1392
- }, {
1393
- error: unknown;
1394
- loadingP: Promise<void> | undefined;
1395
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1396
- refNameAliases: {
1397
- [x: string]: string;
1398
- } | undefined;
1399
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1400
- } & {
1401
- getConf(arg: string): any;
1402
- readonly lowerCaseRefNameAliases: {
1403
- [k: string]: string;
1404
- } | undefined;
1405
- } & {
1406
- readonly initialized: boolean;
1407
- readonly name: string;
1408
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1409
- readonly aliases: string[];
1410
- readonly displayName: string;
1411
- hasName(name: string): boolean;
1412
- readonly allAliases: string[];
1413
- readonly allRefNames: string[] | undefined;
1414
- readonly lowerCaseRefNames: string[] | undefined;
1415
- readonly allRefNamesWithLowerCase: string[] | undefined;
1416
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1417
- readonly refNameColors: string[];
1418
- } & {
1419
- readonly refNames: string[] | undefined;
1420
- } & {
1421
- getCanonicalRefName(refName: string): string | undefined;
1422
- getCanonicalRefName2(asmName: string): string;
1423
- getRefNameColor(refName: string): string | undefined;
1424
- isValidRefName(refName: string): boolean;
1425
- } & {
1426
- setLoaded({ regions, refNameAliases, cytobands, }: {
1427
- regions: import("@jbrowse/core/util").Region[];
1428
- refNameAliases: {
1429
- [x: string]: string;
1430
- };
1431
- cytobands: import("@jbrowse/core/util").Feature[];
1432
- }): void;
1433
- setError(e: unknown): void;
1434
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1435
- setRefNameAliases(aliases: {
1436
- [x: string]: string;
1437
- }): void;
1438
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1439
- setLoadingP(p?: Promise<void>): void;
1440
- load(): Promise<void>;
1441
- loadPre(): Promise<void>;
1442
- } & {
1443
- getAdapterMapEntry(adapterConf: {
1444
- [x: string]: unknown;
1445
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1446
- getRefNameMapForAdapter(adapterConf: {
1447
- [x: string]: unknown;
1448
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1449
- [x: string]: string;
1450
- }>;
1451
- getReverseRefNameMapForAdapter(adapterConf: {
1452
- [x: string]: unknown;
1453
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1454
- [x: string]: string;
1455
- }>;
1456
- afterCreate(): void;
1457
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1458
- readonly assemblyNamesList: any[];
1459
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1460
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1461
- } & {
1462
- waitForAssembly(assemblyName: string): Promise<({
1463
- configuration: any;
1464
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1465
- error: unknown;
1466
- loadingP: Promise<void> | undefined;
1467
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1468
- refNameAliases: {
1469
- [x: string]: string;
1470
- } | undefined;
1471
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1472
- } & {
1473
- getConf(arg: string): any;
1474
- readonly lowerCaseRefNameAliases: {
1475
- [k: string]: string;
1476
- } | undefined;
1477
- } & {
1478
- readonly initialized: boolean;
1479
- readonly name: string;
1480
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1481
- readonly aliases: string[];
1482
- readonly displayName: string;
1483
- hasName(name: string): boolean;
1484
- readonly allAliases: string[];
1485
- readonly allRefNames: string[] | undefined;
1486
- readonly lowerCaseRefNames: string[] | undefined;
1487
- readonly allRefNamesWithLowerCase: string[] | undefined;
1488
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1489
- readonly refNameColors: string[];
1490
- } & {
1491
- readonly refNames: string[] | undefined;
1492
- } & {
1493
- getCanonicalRefName(refName: string): string | undefined;
1494
- getCanonicalRefName2(asmName: string): string;
1495
- getRefNameColor(refName: string): string | undefined;
1496
- isValidRefName(refName: string): boolean;
1497
- } & {
1498
- setLoaded({ regions, refNameAliases, cytobands, }: {
1499
- regions: import("@jbrowse/core/util").Region[];
1500
- refNameAliases: {
1501
- [x: string]: string;
1502
- };
1503
- cytobands: import("@jbrowse/core/util").Feature[];
1504
- }): void;
1505
- setError(e: unknown): void;
1506
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1507
- setRefNameAliases(aliases: {
1508
- [x: string]: string;
1509
- }): void;
1510
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1511
- setLoadingP(p?: Promise<void>): void;
1512
- load(): Promise<void>;
1513
- loadPre(): Promise<void>;
1514
- } & {
1515
- getAdapterMapEntry(adapterConf: {
1516
- [x: string]: unknown;
1517
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1518
- getRefNameMapForAdapter(adapterConf: {
1519
- [x: string]: unknown;
1520
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1521
- [x: string]: string;
1522
- }>;
1523
- getReverseRefNameMapForAdapter(adapterConf: {
1524
- [x: string]: unknown;
1525
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1526
- [x: string]: string;
1527
- }>;
1528
- afterCreate(): void;
1529
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1530
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1531
- }, {
1532
- error: unknown;
1533
- loadingP: Promise<void> | undefined;
1534
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1535
- refNameAliases: {
1536
- [x: string]: string;
1537
- } | undefined;
1538
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1539
- } & {
1540
- getConf(arg: string): any;
1541
- readonly lowerCaseRefNameAliases: {
1542
- [k: string]: string;
1543
- } | undefined;
1544
- } & {
1545
- readonly initialized: boolean;
1546
- readonly name: string;
1547
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1548
- readonly aliases: string[];
1549
- readonly displayName: string;
1550
- hasName(name: string): boolean;
1551
- readonly allAliases: string[];
1552
- readonly allRefNames: string[] | undefined;
1553
- readonly lowerCaseRefNames: string[] | undefined;
1554
- readonly allRefNamesWithLowerCase: string[] | undefined;
1555
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1556
- readonly refNameColors: string[];
1557
- } & {
1558
- readonly refNames: string[] | undefined;
1559
- } & {
1560
- getCanonicalRefName(refName: string): string | undefined;
1561
- getCanonicalRefName2(asmName: string): string;
1562
- getRefNameColor(refName: string): string | undefined;
1563
- isValidRefName(refName: string): boolean;
1564
- } & {
1565
- setLoaded({ regions, refNameAliases, cytobands, }: {
1566
- regions: import("@jbrowse/core/util").Region[];
1567
- refNameAliases: {
1568
- [x: string]: string;
1569
- };
1570
- cytobands: import("@jbrowse/core/util").Feature[];
1571
- }): void;
1572
- setError(e: unknown): void;
1573
- setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1574
- setRefNameAliases(aliases: {
1575
- [x: string]: string;
1576
- }): void;
1577
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1578
- setLoadingP(p?: Promise<void>): void;
1579
- load(): Promise<void>;
1580
- loadPre(): Promise<void>;
1581
- } & {
1582
- getAdapterMapEntry(adapterConf: {
1583
- [x: string]: unknown;
1584
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1585
- getRefNameMapForAdapter(adapterConf: {
1586
- [x: string]: unknown;
1587
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1588
- [x: string]: string;
1589
- }>;
1590
- getReverseRefNameMapForAdapter(adapterConf: {
1591
- [x: string]: unknown;
1592
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1593
- [x: string]: string;
1594
- }>;
1595
- afterCreate(): void;
1596
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1597
- getRefNameMapForAdapter(adapterConf: {
1598
- [x: string]: unknown;
1599
- }, assemblyName: string | undefined, opts: {
1600
- stopToken?: string;
1601
- sessionId: string;
1602
- }): Promise<{
1603
- [x: string]: string;
1604
- } | undefined>;
1605
- getReverseRefNameMapForAdapter(adapterConf: {
1606
- [x: string]: unknown;
1607
- }, assemblyName: string | undefined, opts: {
1608
- stopToken?: string;
1609
- sessionId: string;
1610
- }): Promise<{
1611
- [x: string]: string;
1612
- } | undefined>;
1613
- isValidRefName(refName: string, assemblyName: string): boolean;
1614
- } & {
1615
- afterAttach(): void;
1616
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1617
- addAssembly(configuration: any): void;
1618
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
1619
- }, {
1620
- rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1621
- adminMode: boolean;
1622
- error: unknown;
1623
- textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1624
- pluginManager: PluginManager;
1625
- } & {
1626
- setError(error: unknown): void;
1627
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1628
- setDefaultSession(): void;
1629
- setSessionPath(path: string): void;
1630
- renameCurrentSession(newName: string): void;
1631
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1632
- } & {
1633
- readonly jbrowse: any;
1634
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1635
- readonly configuration: {
1636
- [x: string]: any;
1637
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1638
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1639
- [x: string]: any;
1640
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1641
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1642
- [x: string]: any;
1643
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1644
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1645
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1646
- readonly adminMode: boolean;
1647
- readonly textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1648
- } & {
1649
- readonly assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
1650
- } & {
1651
- setSelection(thing: unknown): void;
1652
- clearSelection(): void;
1653
- setHovered(thing: unknown): void;
1654
- } & {
1655
- readonly visibleWidget: any;
1656
- } & {
1657
- setDrawerPosition(arg: string): void;
1658
- updateDrawerWidth(drawerWidth: number): number;
1659
- resizeDrawer(distance: number): number;
1660
- addWidget(typeName: string, id: string, initialState?: {}, conf?: unknown): any;
1661
- showWidget(widget: any): void;
1662
- hasWidget(widget: any): boolean;
1663
- hideWidget(widget: any): void;
1664
- minimizeWidgetDrawer(): void;
1665
- showWidgetDrawer(): void;
1666
- hideAllWidgets(): void;
1667
- editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1668
- afterAttach(): void;
1669
- } & {
1670
- moveViewDown(id: string): void;
1671
- moveViewUp(id: string): void;
1672
- moveViewToTop(id: string): void;
1673
- moveViewToBottom(id: string): void;
1674
- addView(typeName: string, initialState?: {}): any;
1675
- removeView(view: IBaseViewModel): void;
1676
- setStickyViewHeaders(sticky: boolean): void;
1677
- afterAttach(): void;
1678
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
1679
- export type SessionWithMultipleViewsType = ReturnType<typeof MultipleViewsSessionMixin>;
1680
- export type SessionWithMultipleViews = Instance<SessionWithMultipleViewsType>;
1681
- export declare function isSessionWithMultipleViews(session: IAnyStateTreeNode): session is SessionWithMultipleViews;