@jbrowse/react-linear-genome-view2 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 (66) hide show
  1. package/esm/JBrowseLinearGenomeView/JBrowseLinearGenomeView.d.ts +1 -1
  2. package/esm/JBrowseLinearGenomeView/JBrowseLinearGenomeView.js +2 -2
  3. package/esm/JBrowseLinearGenomeView/index.d.ts +1 -1
  4. package/esm/JBrowseLinearGenomeView/index.js +1 -1
  5. package/esm/corePlugins.d.ts +2 -2
  6. package/esm/corePlugins.js +2 -2
  7. package/esm/createModel/createConfigModel.d.ts +23 -23
  8. package/esm/createModel/createConfigModel.js +1 -1
  9. package/esm/createModel/createModel.d.ts +1060 -1185
  10. package/esm/createModel/createModel.js +5 -5
  11. package/esm/createModel/createSessionModel.d.ts +547 -616
  12. package/esm/createModel/createSessionModel.js +5 -4
  13. package/esm/createModel/index.d.ts +3 -3
  14. package/esm/createModel/index.js +3 -3
  15. package/esm/createViewState.d.ts +2780 -3139
  16. package/esm/createViewState.js +3 -3
  17. package/esm/index.d.ts +5 -5
  18. package/esm/index.js +4 -4
  19. package/esm/loadPlugins.js +1 -1
  20. package/esm/rpcWorker.d.ts +1 -1
  21. package/esm/rpcWorker.js +2 -2
  22. package/esm/types.d.ts +1 -1
  23. package/esm/version.d.ts +1 -1
  24. package/esm/version.js +1 -1
  25. package/esm/webpack.d.ts +5 -5
  26. package/esm/webpack.js +4 -4
  27. package/package.json +48 -56
  28. package/dist/JBrowseLinearGenomeView/JBrowseLinearGenomeView.d.ts +0 -5
  29. package/dist/JBrowseLinearGenomeView/JBrowseLinearGenomeView.js +0 -19
  30. package/dist/JBrowseLinearGenomeView/JBrowseLinearGenomeView.test.d.ts +0 -1
  31. package/dist/JBrowseLinearGenomeView/JBrowseLinearGenomeView.test.js +0 -77
  32. package/dist/JBrowseLinearGenomeView/index.d.ts +0 -1
  33. package/dist/JBrowseLinearGenomeView/index.js +0 -8
  34. package/dist/corePlugins.d.ts +0 -3
  35. package/dist/corePlugins.js +0 -38
  36. package/dist/createModel/AboutDialog.d.ts +0 -1
  37. package/dist/createModel/AboutDialog.js +0 -5
  38. package/dist/createModel/createConfigModel.d.ts +0 -94
  39. package/dist/createModel/createConfigModel.js +0 -43
  40. package/dist/createModel/createModel.d.ts +0 -6390
  41. package/dist/createModel/createModel.js +0 -118
  42. package/dist/createModel/createSessionModel.d.ts +0 -2792
  43. package/dist/createModel/createSessionModel.js +0 -118
  44. package/dist/createModel/index.d.ts +0 -3
  45. package/dist/createModel/index.js +0 -12
  46. package/dist/createViewState.d.ts +0 -16739
  47. package/dist/createViewState.js +0 -75
  48. package/dist/index.d.ts +0 -5
  49. package/dist/index.js +0 -14
  50. package/dist/loadPlugins.d.ts +0 -13
  51. package/dist/loadPlugins.js +0 -12
  52. package/dist/react-linear-genome-view.umd.production.min.js +0 -229
  53. package/dist/react-linear-genome-view.umd.production.min.js.LICENSE.txt +0 -195
  54. package/dist/react-linear-genome-view.umd.production.min.js.map +0 -1
  55. package/dist/rpcWorker.d.ts +0 -2
  56. package/dist/rpcWorker.js +0 -57
  57. package/dist/types.d.ts +0 -5
  58. package/dist/types.js +0 -2
  59. package/dist/version.d.ts +0 -1
  60. package/dist/version.js +0 -4
  61. package/dist/webpack.d.ts +0 -8
  62. package/dist/webpack.js +0 -53
  63. package/dist/workerPolyfill.d.ts +0 -0
  64. package/dist/workerPolyfill.js +0 -34
  65. package/esm/workerPolyfill.d.ts +0 -0
  66. package/esm/workerPolyfill.js +0 -34
package/dist/createModel/createSessionModel.d.ts DELETED
@@ -1,2792 +0,0 @@
1
- import type PluginManager from '@jbrowse/core/PluginManager';
2
- import type { LinearGenomeViewStateModel } from '@jbrowse/plugin-linear-genome-view';
3
- import type { Instance } from 'mobx-state-tree';
4
- export default function sessionModelFactory(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
- connectionInstances: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
16
- name: import("mobx-state-tree").ISimpleType<string>;
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- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
18
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
19
- name: {
20
- type: string;
21
- defaultValue: string;
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- description: string;
23
- };
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- assemblyNames: {
25
- type: string;
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- defaultValue: never[];
27
- description: string;
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- };
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
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- }, {
31
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
32
- } & {
33
- afterAttach(): void;
34
- addTrackConf(trackConf: ({
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- [x: string]: any;
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- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
37
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
38
- [x: string]: any;
39
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
40
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
41
- [x: string]: any;
42
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
43
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
44
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
45
- addTrackConfs(trackConfs: (({
46
- [x: string]: any;
47
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
48
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
49
- [x: string]: any;
50
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
51
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
52
- [x: string]: any;
53
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
54
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
55
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
56
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
57
- clear(): void;
58
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
59
- } & {
60
- sessionTracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
61
- } & {
62
- view: LinearGenomeViewStateModel;
63
- sessionTracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
64
- }, {
65
- selection: unknown;
66
- hovered: unknown;
67
- } & {
68
- readonly root: {
69
- jbrowse: any;
70
- session: any;
71
- sessionPath: string;
72
- assemblyManager: {
73
- assemblies: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
74
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
75
- }, {
76
- error: unknown;
77
- loadingP: Promise<void> | undefined;
78
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
79
- refNameAliases: {
80
- [x: string]: string;
81
- } | undefined;
82
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
83
- } & {
84
- getConf(arg: string): any;
85
- readonly lowerCaseRefNameAliases: {
86
- [k: string]: string;
87
- } | undefined;
88
- } & {
89
- readonly initialized: boolean;
90
- readonly name: string;
91
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
92
- readonly aliases: string[];
93
- readonly displayName: string;
94
- hasName(name: string): boolean;
95
- readonly allAliases: string[];
96
- readonly allRefNames: string[] | undefined;
97
- readonly lowerCaseRefNames: string[] | undefined;
98
- readonly allRefNamesWithLowerCase: string[] | undefined;
99
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
100
- readonly refNameColors: string[];
101
- } & {
102
- readonly refNames: string[] | undefined;
103
- } & {
104
- getCanonicalRefName(refName: string): string | undefined;
105
- getCanonicalRefName2(asmName: string): string;
106
- getRefNameColor(refName: string): string | undefined;
107
- isValidRefName(refName: string): boolean;
108
- } & {
109
- setLoaded({ regions, refNameAliases, cytobands, }: {
110
- regions: import("@jbrowse/core/util/types").Region[];
111
- refNameAliases: {
112
- [x: string]: string;
113
- };
114
- cytobands: import("@jbrowse/core/util").Feature[];
115
- }): void;
116
- setError(e: unknown): void;
117
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
118
- setRefNameAliases(aliases: {
119
- [x: string]: string;
120
- }): void;
121
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
122
- setLoadingP(p?: Promise<void>): void;
123
- load(): Promise<void>;
124
- loadPre(): Promise<void>;
125
- } & {
126
- getAdapterMapEntry(adapterConf: {
127
- [x: string]: unknown;
128
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
129
- getRefNameMapForAdapter(adapterConf: {
130
- [x: string]: unknown;
131
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
132
- [x: string]: string;
133
- }>;
134
- getReverseRefNameMapForAdapter(adapterConf: {
135
- [x: string]: unknown;
136
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
137
- [x: string]: string;
138
- }>;
139
- afterCreate(): void;
140
- }, 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<{
141
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
142
- }, {
143
- error: unknown;
144
- loadingP: Promise<void> | undefined;
145
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
146
- refNameAliases: {
147
- [x: string]: string;
148
- } | undefined;
149
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
150
- } & {
151
- getConf(arg: string): any;
152
- readonly lowerCaseRefNameAliases: {
153
- [k: string]: string;
154
- } | undefined;
155
- } & {
156
- readonly initialized: boolean;
157
- readonly name: string;
158
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
159
- readonly aliases: string[];
160
- readonly displayName: string;
161
- hasName(name: string): boolean;
162
- readonly allAliases: string[];
163
- readonly allRefNames: string[] | undefined;
164
- readonly lowerCaseRefNames: string[] | undefined;
165
- readonly allRefNamesWithLowerCase: string[] | undefined;
166
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
167
- readonly refNameColors: string[];
168
- } & {
169
- readonly refNames: string[] | undefined;
170
- } & {
171
- getCanonicalRefName(refName: string): string | undefined;
172
- getCanonicalRefName2(asmName: string): string;
173
- getRefNameColor(refName: string): string | undefined;
174
- isValidRefName(refName: string): boolean;
175
- } & {
176
- setLoaded({ regions, refNameAliases, cytobands, }: {
177
- regions: import("@jbrowse/core/util/types").Region[];
178
- refNameAliases: {
179
- [x: string]: string;
180
- };
181
- cytobands: import("@jbrowse/core/util").Feature[];
182
- }): void;
183
- setError(e: unknown): void;
184
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
185
- setRefNameAliases(aliases: {
186
- [x: string]: string;
187
- }): void;
188
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
189
- setLoadingP(p?: Promise<void>): void;
190
- load(): Promise<void>;
191
- loadPre(): Promise<void>;
192
- } & {
193
- getAdapterMapEntry(adapterConf: {
194
- [x: string]: unknown;
195
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
196
- getRefNameMapForAdapter(adapterConf: {
197
- [x: string]: unknown;
198
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
199
- [x: string]: string;
200
- }>;
201
- getReverseRefNameMapForAdapter(adapterConf: {
202
- [x: string]: unknown;
203
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
204
- [x: string]: string;
205
- }>;
206
- afterCreate(): void;
207
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
208
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
209
- readonly assemblyNameMap: Record<string, {
210
- configuration: any;
211
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
212
- error: unknown;
213
- loadingP: Promise<void> | undefined;
214
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
215
- refNameAliases: {
216
- [x: string]: string;
217
- } | undefined;
218
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
219
- } & {
220
- getConf(arg: string): any;
221
- readonly lowerCaseRefNameAliases: {
222
- [k: string]: string;
223
- } | undefined;
224
- } & {
225
- readonly initialized: boolean;
226
- readonly name: string;
227
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
228
- readonly aliases: string[];
229
- readonly displayName: string;
230
- hasName(name: string): boolean;
231
- readonly allAliases: string[];
232
- readonly allRefNames: string[] | undefined;
233
- readonly lowerCaseRefNames: string[] | undefined;
234
- readonly allRefNamesWithLowerCase: string[] | undefined;
235
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
236
- readonly refNameColors: string[];
237
- } & {
238
- readonly refNames: string[] | undefined;
239
- } & {
240
- getCanonicalRefName(refName: string): string | undefined;
241
- getCanonicalRefName2(asmName: string): string;
242
- getRefNameColor(refName: string): string | undefined;
243
- isValidRefName(refName: string): boolean;
244
- } & {
245
- setLoaded({ regions, refNameAliases, cytobands, }: {
246
- regions: import("@jbrowse/core/util/types").Region[];
247
- refNameAliases: {
248
- [x: string]: string;
249
- };
250
- cytobands: import("@jbrowse/core/util").Feature[];
251
- }): void;
252
- setError(e: unknown): void;
253
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
254
- setRefNameAliases(aliases: {
255
- [x: string]: string;
256
- }): void;
257
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
258
- setLoadingP(p?: Promise<void>): void;
259
- load(): Promise<void>;
260
- loadPre(): Promise<void>;
261
- } & {
262
- getAdapterMapEntry(adapterConf: {
263
- [x: string]: unknown;
264
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
265
- getRefNameMapForAdapter(adapterConf: {
266
- [x: string]: unknown;
267
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
268
- [x: string]: string;
269
- }>;
270
- getReverseRefNameMapForAdapter(adapterConf: {
271
- [x: string]: unknown;
272
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
273
- [x: string]: string;
274
- }>;
275
- afterCreate(): void;
276
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
277
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
278
- }, {
279
- error: unknown;
280
- loadingP: Promise<void> | undefined;
281
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
282
- refNameAliases: {
283
- [x: string]: string;
284
- } | undefined;
285
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
286
- } & {
287
- getConf(arg: string): any;
288
- readonly lowerCaseRefNameAliases: {
289
- [k: string]: string;
290
- } | undefined;
291
- } & {
292
- readonly initialized: boolean;
293
- readonly name: string;
294
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
295
- readonly aliases: string[];
296
- readonly displayName: string;
297
- hasName(name: string): boolean;
298
- readonly allAliases: string[];
299
- readonly allRefNames: string[] | undefined;
300
- readonly lowerCaseRefNames: string[] | undefined;
301
- readonly allRefNamesWithLowerCase: string[] | undefined;
302
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
303
- readonly refNameColors: string[];
304
- } & {
305
- readonly refNames: string[] | undefined;
306
- } & {
307
- getCanonicalRefName(refName: string): string | undefined;
308
- getCanonicalRefName2(asmName: string): string;
309
- getRefNameColor(refName: string): string | undefined;
310
- isValidRefName(refName: string): boolean;
311
- } & {
312
- setLoaded({ regions, refNameAliases, cytobands, }: {
313
- regions: import("@jbrowse/core/util/types").Region[];
314
- refNameAliases: {
315
- [x: string]: string;
316
- };
317
- cytobands: import("@jbrowse/core/util").Feature[];
318
- }): void;
319
- setError(e: unknown): void;
320
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
321
- setRefNameAliases(aliases: {
322
- [x: string]: string;
323
- }): void;
324
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
325
- setLoadingP(p?: Promise<void>): void;
326
- load(): Promise<void>;
327
- loadPre(): Promise<void>;
328
- } & {
329
- getAdapterMapEntry(adapterConf: {
330
- [x: string]: unknown;
331
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
332
- getRefNameMapForAdapter(adapterConf: {
333
- [x: string]: unknown;
334
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
335
- [x: string]: string;
336
- }>;
337
- getReverseRefNameMapForAdapter(adapterConf: {
338
- [x: string]: unknown;
339
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
340
- [x: string]: string;
341
- }>;
342
- afterCreate(): void;
343
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
344
- } & {
345
- getCanonicalAssemblyName(asmName: string): string | undefined;
346
- getCanonicalAssemblyName2(asmName: string): string;
347
- get(asmName: string): ({
348
- configuration: any;
349
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
350
- error: unknown;
351
- loadingP: Promise<void> | undefined;
352
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
353
- refNameAliases: {
354
- [x: string]: string;
355
- } | undefined;
356
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
357
- } & {
358
- getConf(arg: string): any;
359
- readonly lowerCaseRefNameAliases: {
360
- [k: string]: string;
361
- } | undefined;
362
- } & {
363
- readonly initialized: boolean;
364
- readonly name: string;
365
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
366
- readonly aliases: string[];
367
- readonly displayName: string;
368
- hasName(name: string): boolean;
369
- readonly allAliases: string[];
370
- readonly allRefNames: string[] | undefined;
371
- readonly lowerCaseRefNames: string[] | undefined;
372
- readonly allRefNamesWithLowerCase: string[] | undefined;
373
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
374
- readonly refNameColors: string[];
375
- } & {
376
- readonly refNames: string[] | undefined;
377
- } & {
378
- getCanonicalRefName(refName: string): string | undefined;
379
- getCanonicalRefName2(asmName: string): string;
380
- getRefNameColor(refName: string): string | undefined;
381
- isValidRefName(refName: string): boolean;
382
- } & {
383
- setLoaded({ regions, refNameAliases, cytobands, }: {
384
- regions: import("@jbrowse/core/util/types").Region[];
385
- refNameAliases: {
386
- [x: string]: string;
387
- };
388
- cytobands: import("@jbrowse/core/util").Feature[];
389
- }): void;
390
- setError(e: unknown): void;
391
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
392
- setRefNameAliases(aliases: {
393
- [x: string]: string;
394
- }): void;
395
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
396
- setLoadingP(p?: Promise<void>): void;
397
- load(): Promise<void>;
398
- loadPre(): Promise<void>;
399
- } & {
400
- getAdapterMapEntry(adapterConf: {
401
- [x: string]: unknown;
402
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
403
- getRefNameMapForAdapter(adapterConf: {
404
- [x: string]: unknown;
405
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
406
- [x: string]: string;
407
- }>;
408
- getReverseRefNameMapForAdapter(adapterConf: {
409
- [x: string]: unknown;
410
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
411
- [x: string]: string;
412
- }>;
413
- afterCreate(): void;
414
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
415
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
416
- }, {
417
- error: unknown;
418
- loadingP: Promise<void> | undefined;
419
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
420
- refNameAliases: {
421
- [x: string]: string;
422
- } | undefined;
423
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
424
- } & {
425
- getConf(arg: string): any;
426
- readonly lowerCaseRefNameAliases: {
427
- [k: string]: string;
428
- } | undefined;
429
- } & {
430
- readonly initialized: boolean;
431
- readonly name: string;
432
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
433
- readonly aliases: string[];
434
- readonly displayName: string;
435
- hasName(name: string): boolean;
436
- readonly allAliases: string[];
437
- readonly allRefNames: string[] | undefined;
438
- readonly lowerCaseRefNames: string[] | undefined;
439
- readonly allRefNamesWithLowerCase: string[] | undefined;
440
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
441
- readonly refNameColors: string[];
442
- } & {
443
- readonly refNames: string[] | undefined;
444
- } & {
445
- getCanonicalRefName(refName: string): string | undefined;
446
- getCanonicalRefName2(asmName: string): string;
447
- getRefNameColor(refName: string): string | undefined;
448
- isValidRefName(refName: string): boolean;
449
- } & {
450
- setLoaded({ regions, refNameAliases, cytobands, }: {
451
- regions: import("@jbrowse/core/util/types").Region[];
452
- refNameAliases: {
453
- [x: string]: string;
454
- };
455
- cytobands: import("@jbrowse/core/util").Feature[];
456
- }): void;
457
- setError(e: unknown): void;
458
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
459
- setRefNameAliases(aliases: {
460
- [x: string]: string;
461
- }): void;
462
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
463
- setLoadingP(p?: Promise<void>): void;
464
- load(): Promise<void>;
465
- loadPre(): Promise<void>;
466
- } & {
467
- getAdapterMapEntry(adapterConf: {
468
- [x: string]: unknown;
469
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
470
- getRefNameMapForAdapter(adapterConf: {
471
- [x: string]: unknown;
472
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
473
- [x: string]: string;
474
- }>;
475
- getReverseRefNameMapForAdapter(adapterConf: {
476
- [x: string]: unknown;
477
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
478
- [x: string]: string;
479
- }>;
480
- afterCreate(): void;
481
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
482
- readonly assemblyNamesList: any[];
483
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
484
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
485
- } & {
486
- waitForAssembly(assemblyName: string): Promise<({
487
- configuration: any;
488
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
489
- error: unknown;
490
- loadingP: Promise<void> | undefined;
491
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
492
- refNameAliases: {
493
- [x: string]: string;
494
- } | undefined;
495
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
496
- } & {
497
- getConf(arg: string): any;
498
- readonly lowerCaseRefNameAliases: {
499
- [k: string]: string;
500
- } | undefined;
501
- } & {
502
- readonly initialized: boolean;
503
- readonly name: string;
504
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
505
- readonly aliases: string[];
506
- readonly displayName: string;
507
- hasName(name: string): boolean;
508
- readonly allAliases: string[];
509
- readonly allRefNames: string[] | undefined;
510
- readonly lowerCaseRefNames: string[] | undefined;
511
- readonly allRefNamesWithLowerCase: string[] | undefined;
512
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
513
- readonly refNameColors: string[];
514
- } & {
515
- readonly refNames: string[] | undefined;
516
- } & {
517
- getCanonicalRefName(refName: string): string | undefined;
518
- getCanonicalRefName2(asmName: string): string;
519
- getRefNameColor(refName: string): string | undefined;
520
- isValidRefName(refName: string): boolean;
521
- } & {
522
- setLoaded({ regions, refNameAliases, cytobands, }: {
523
- regions: import("@jbrowse/core/util/types").Region[];
524
- refNameAliases: {
525
- [x: string]: string;
526
- };
527
- cytobands: import("@jbrowse/core/util").Feature[];
528
- }): void;
529
- setError(e: unknown): void;
530
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
531
- setRefNameAliases(aliases: {
532
- [x: string]: string;
533
- }): void;
534
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
535
- setLoadingP(p?: Promise<void>): void;
536
- load(): Promise<void>;
537
- loadPre(): Promise<void>;
538
- } & {
539
- getAdapterMapEntry(adapterConf: {
540
- [x: string]: unknown;
541
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
542
- getRefNameMapForAdapter(adapterConf: {
543
- [x: string]: unknown;
544
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
545
- [x: string]: string;
546
- }>;
547
- getReverseRefNameMapForAdapter(adapterConf: {
548
- [x: string]: unknown;
549
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
550
- [x: string]: string;
551
- }>;
552
- afterCreate(): void;
553
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
554
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
555
- }, {
556
- error: unknown;
557
- loadingP: Promise<void> | undefined;
558
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
559
- refNameAliases: {
560
- [x: string]: string;
561
- } | undefined;
562
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
563
- } & {
564
- getConf(arg: string): any;
565
- readonly lowerCaseRefNameAliases: {
566
- [k: string]: string;
567
- } | undefined;
568
- } & {
569
- readonly initialized: boolean;
570
- readonly name: string;
571
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
572
- readonly aliases: string[];
573
- readonly displayName: string;
574
- hasName(name: string): boolean;
575
- readonly allAliases: string[];
576
- readonly allRefNames: string[] | undefined;
577
- readonly lowerCaseRefNames: string[] | undefined;
578
- readonly allRefNamesWithLowerCase: string[] | undefined;
579
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
580
- readonly refNameColors: string[];
581
- } & {
582
- readonly refNames: string[] | undefined;
583
- } & {
584
- getCanonicalRefName(refName: string): string | undefined;
585
- getCanonicalRefName2(asmName: string): string;
586
- getRefNameColor(refName: string): string | undefined;
587
- isValidRefName(refName: string): boolean;
588
- } & {
589
- setLoaded({ regions, refNameAliases, cytobands, }: {
590
- regions: import("@jbrowse/core/util/types").Region[];
591
- refNameAliases: {
592
- [x: string]: string;
593
- };
594
- cytobands: import("@jbrowse/core/util").Feature[];
595
- }): void;
596
- setError(e: unknown): void;
597
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
598
- setRefNameAliases(aliases: {
599
- [x: string]: string;
600
- }): void;
601
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
602
- setLoadingP(p?: Promise<void>): void;
603
- load(): Promise<void>;
604
- loadPre(): Promise<void>;
605
- } & {
606
- getAdapterMapEntry(adapterConf: {
607
- [x: string]: unknown;
608
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
609
- getRefNameMapForAdapter(adapterConf: {
610
- [x: string]: unknown;
611
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
612
- [x: string]: string;
613
- }>;
614
- getReverseRefNameMapForAdapter(adapterConf: {
615
- [x: string]: unknown;
616
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
617
- [x: string]: string;
618
- }>;
619
- afterCreate(): void;
620
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
621
- getRefNameMapForAdapter(adapterConf: {
622
- [x: string]: unknown;
623
- }, assemblyName: string | undefined, opts: {
624
- stopToken?: string;
625
- sessionId: string;
626
- }): Promise<{
627
- [x: string]: string;
628
- } | undefined>;
629
- getReverseRefNameMapForAdapter(adapterConf: {
630
- [x: string]: unknown;
631
- }, assemblyName: string | undefined, opts: {
632
- stopToken?: string;
633
- sessionId: string;
634
- }): Promise<{
635
- [x: string]: string;
636
- } | undefined>;
637
- isValidRefName(refName: string, assemblyName: string): boolean;
638
- } & {
639
- afterAttach(): void;
640
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
641
- addAssembly(configuration: any): void;
642
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
643
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
644
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
645
- }, {
646
- error: unknown;
647
- loadingP: Promise<void> | undefined;
648
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
649
- refNameAliases: {
650
- [x: string]: string;
651
- } | undefined;
652
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
653
- } & {
654
- getConf(arg: string): any;
655
- readonly lowerCaseRefNameAliases: {
656
- [k: string]: string;
657
- } | undefined;
658
- } & {
659
- readonly initialized: boolean;
660
- readonly name: string;
661
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
662
- readonly aliases: string[];
663
- readonly displayName: string;
664
- hasName(name: string): boolean;
665
- readonly allAliases: string[];
666
- readonly allRefNames: string[] | undefined;
667
- readonly lowerCaseRefNames: string[] | undefined;
668
- readonly allRefNamesWithLowerCase: string[] | undefined;
669
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
670
- readonly refNameColors: string[];
671
- } & {
672
- readonly refNames: string[] | undefined;
673
- } & {
674
- getCanonicalRefName(refName: string): string | undefined;
675
- getCanonicalRefName2(asmName: string): string;
676
- getRefNameColor(refName: string): string | undefined;
677
- isValidRefName(refName: string): boolean;
678
- } & {
679
- setLoaded({ regions, refNameAliases, cytobands, }: {
680
- regions: import("@jbrowse/core/util/types").Region[];
681
- refNameAliases: {
682
- [x: string]: string;
683
- };
684
- cytobands: import("@jbrowse/core/util").Feature[];
685
- }): void;
686
- setError(e: unknown): void;
687
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
688
- setRefNameAliases(aliases: {
689
- [x: string]: string;
690
- }): void;
691
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
692
- setLoadingP(p?: Promise<void>): void;
693
- load(): Promise<void>;
694
- loadPre(): Promise<void>;
695
- } & {
696
- getAdapterMapEntry(adapterConf: {
697
- [x: string]: unknown;
698
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
699
- getRefNameMapForAdapter(adapterConf: {
700
- [x: string]: unknown;
701
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
702
- [x: string]: string;
703
- }>;
704
- getReverseRefNameMapForAdapter(adapterConf: {
705
- [x: string]: unknown;
706
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
707
- [x: string]: string;
708
- }>;
709
- afterCreate(): void;
710
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
711
- }, {
712
- readonly assemblyNameMap: Record<string, {
713
- configuration: any;
714
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
715
- error: unknown;
716
- loadingP: Promise<void> | undefined;
717
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
718
- refNameAliases: {
719
- [x: string]: string;
720
- } | undefined;
721
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
722
- } & {
723
- getConf(arg: string): any;
724
- readonly lowerCaseRefNameAliases: {
725
- [k: string]: string;
726
- } | undefined;
727
- } & {
728
- readonly initialized: boolean;
729
- readonly name: string;
730
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
731
- readonly aliases: string[];
732
- readonly displayName: string;
733
- hasName(name: string): boolean;
734
- readonly allAliases: string[];
735
- readonly allRefNames: string[] | undefined;
736
- readonly lowerCaseRefNames: string[] | undefined;
737
- readonly allRefNamesWithLowerCase: string[] | undefined;
738
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
739
- readonly refNameColors: string[];
740
- } & {
741
- readonly refNames: string[] | undefined;
742
- } & {
743
- getCanonicalRefName(refName: string): string | undefined;
744
- getCanonicalRefName2(asmName: string): string;
745
- getRefNameColor(refName: string): string | undefined;
746
- isValidRefName(refName: string): boolean;
747
- } & {
748
- setLoaded({ regions, refNameAliases, cytobands, }: {
749
- regions: import("@jbrowse/core/util/types").Region[];
750
- refNameAliases: {
751
- [x: string]: string;
752
- };
753
- cytobands: import("@jbrowse/core/util").Feature[];
754
- }): void;
755
- setError(e: unknown): void;
756
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
757
- setRefNameAliases(aliases: {
758
- [x: string]: string;
759
- }): void;
760
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
761
- setLoadingP(p?: Promise<void>): void;
762
- load(): Promise<void>;
763
- loadPre(): Promise<void>;
764
- } & {
765
- getAdapterMapEntry(adapterConf: {
766
- [x: string]: unknown;
767
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
768
- getRefNameMapForAdapter(adapterConf: {
769
- [x: string]: unknown;
770
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
771
- [x: string]: string;
772
- }>;
773
- getReverseRefNameMapForAdapter(adapterConf: {
774
- [x: string]: unknown;
775
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
776
- [x: string]: string;
777
- }>;
778
- afterCreate(): void;
779
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
780
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
781
- }, {
782
- error: unknown;
783
- loadingP: Promise<void> | undefined;
784
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
785
- refNameAliases: {
786
- [x: string]: string;
787
- } | undefined;
788
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
789
- } & {
790
- getConf(arg: string): any;
791
- readonly lowerCaseRefNameAliases: {
792
- [k: string]: string;
793
- } | undefined;
794
- } & {
795
- readonly initialized: boolean;
796
- readonly name: string;
797
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
798
- readonly aliases: string[];
799
- readonly displayName: string;
800
- hasName(name: string): boolean;
801
- readonly allAliases: string[];
802
- readonly allRefNames: string[] | undefined;
803
- readonly lowerCaseRefNames: string[] | undefined;
804
- readonly allRefNamesWithLowerCase: string[] | undefined;
805
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
806
- readonly refNameColors: string[];
807
- } & {
808
- readonly refNames: string[] | undefined;
809
- } & {
810
- getCanonicalRefName(refName: string): string | undefined;
811
- getCanonicalRefName2(asmName: string): string;
812
- getRefNameColor(refName: string): string | undefined;
813
- isValidRefName(refName: string): boolean;
814
- } & {
815
- setLoaded({ regions, refNameAliases, cytobands, }: {
816
- regions: import("@jbrowse/core/util/types").Region[];
817
- refNameAliases: {
818
- [x: string]: string;
819
- };
820
- cytobands: import("@jbrowse/core/util").Feature[];
821
- }): void;
822
- setError(e: unknown): void;
823
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
824
- setRefNameAliases(aliases: {
825
- [x: string]: string;
826
- }): void;
827
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
828
- setLoadingP(p?: Promise<void>): void;
829
- load(): Promise<void>;
830
- loadPre(): Promise<void>;
831
- } & {
832
- getAdapterMapEntry(adapterConf: {
833
- [x: string]: unknown;
834
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
835
- getRefNameMapForAdapter(adapterConf: {
836
- [x: string]: unknown;
837
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
838
- [x: string]: string;
839
- }>;
840
- getReverseRefNameMapForAdapter(adapterConf: {
841
- [x: string]: unknown;
842
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
843
- [x: string]: string;
844
- }>;
845
- afterCreate(): void;
846
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
847
- } & {
848
- getCanonicalAssemblyName(asmName: string): string | undefined;
849
- getCanonicalAssemblyName2(asmName: string): string;
850
- get(asmName: string): ({
851
- configuration: any;
852
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
853
- error: unknown;
854
- loadingP: Promise<void> | undefined;
855
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
856
- refNameAliases: {
857
- [x: string]: string;
858
- } | undefined;
859
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
860
- } & {
861
- getConf(arg: string): any;
862
- readonly lowerCaseRefNameAliases: {
863
- [k: string]: string;
864
- } | undefined;
865
- } & {
866
- readonly initialized: boolean;
867
- readonly name: string;
868
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
869
- readonly aliases: string[];
870
- readonly displayName: string;
871
- hasName(name: string): boolean;
872
- readonly allAliases: string[];
873
- readonly allRefNames: string[] | undefined;
874
- readonly lowerCaseRefNames: string[] | undefined;
875
- readonly allRefNamesWithLowerCase: string[] | undefined;
876
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
877
- readonly refNameColors: string[];
878
- } & {
879
- readonly refNames: string[] | undefined;
880
- } & {
881
- getCanonicalRefName(refName: string): string | undefined;
882
- getCanonicalRefName2(asmName: string): string;
883
- getRefNameColor(refName: string): string | undefined;
884
- isValidRefName(refName: string): boolean;
885
- } & {
886
- setLoaded({ regions, refNameAliases, cytobands, }: {
887
- regions: import("@jbrowse/core/util/types").Region[];
888
- refNameAliases: {
889
- [x: string]: string;
890
- };
891
- cytobands: import("@jbrowse/core/util").Feature[];
892
- }): void;
893
- setError(e: unknown): void;
894
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
895
- setRefNameAliases(aliases: {
896
- [x: string]: string;
897
- }): void;
898
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
899
- setLoadingP(p?: Promise<void>): void;
900
- load(): Promise<void>;
901
- loadPre(): Promise<void>;
902
- } & {
903
- getAdapterMapEntry(adapterConf: {
904
- [x: string]: unknown;
905
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
906
- getRefNameMapForAdapter(adapterConf: {
907
- [x: string]: unknown;
908
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
909
- [x: string]: string;
910
- }>;
911
- getReverseRefNameMapForAdapter(adapterConf: {
912
- [x: string]: unknown;
913
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
914
- [x: string]: string;
915
- }>;
916
- afterCreate(): void;
917
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
918
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
919
- }, {
920
- error: unknown;
921
- loadingP: Promise<void> | undefined;
922
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
923
- refNameAliases: {
924
- [x: string]: string;
925
- } | undefined;
926
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
927
- } & {
928
- getConf(arg: string): any;
929
- readonly lowerCaseRefNameAliases: {
930
- [k: string]: string;
931
- } | undefined;
932
- } & {
933
- readonly initialized: boolean;
934
- readonly name: string;
935
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
936
- readonly aliases: string[];
937
- readonly displayName: string;
938
- hasName(name: string): boolean;
939
- readonly allAliases: string[];
940
- readonly allRefNames: string[] | undefined;
941
- readonly lowerCaseRefNames: string[] | undefined;
942
- readonly allRefNamesWithLowerCase: string[] | undefined;
943
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
944
- readonly refNameColors: string[];
945
- } & {
946
- readonly refNames: string[] | undefined;
947
- } & {
948
- getCanonicalRefName(refName: string): string | undefined;
949
- getCanonicalRefName2(asmName: string): string;
950
- getRefNameColor(refName: string): string | undefined;
951
- isValidRefName(refName: string): boolean;
952
- } & {
953
- setLoaded({ regions, refNameAliases, cytobands, }: {
954
- regions: import("@jbrowse/core/util/types").Region[];
955
- refNameAliases: {
956
- [x: string]: string;
957
- };
958
- cytobands: import("@jbrowse/core/util").Feature[];
959
- }): void;
960
- setError(e: unknown): void;
961
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
962
- setRefNameAliases(aliases: {
963
- [x: string]: string;
964
- }): void;
965
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
966
- setLoadingP(p?: Promise<void>): void;
967
- load(): Promise<void>;
968
- loadPre(): Promise<void>;
969
- } & {
970
- getAdapterMapEntry(adapterConf: {
971
- [x: string]: unknown;
972
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
973
- getRefNameMapForAdapter(adapterConf: {
974
- [x: string]: unknown;
975
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
976
- [x: string]: string;
977
- }>;
978
- getReverseRefNameMapForAdapter(adapterConf: {
979
- [x: string]: unknown;
980
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
981
- [x: string]: string;
982
- }>;
983
- afterCreate(): void;
984
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
985
- readonly assemblyNamesList: any[];
986
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
987
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
988
- } & {
989
- waitForAssembly(assemblyName: string): Promise<({
990
- configuration: any;
991
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
992
- error: unknown;
993
- loadingP: Promise<void> | undefined;
994
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
995
- refNameAliases: {
996
- [x: string]: string;
997
- } | undefined;
998
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
999
- } & {
1000
- getConf(arg: string): any;
1001
- readonly lowerCaseRefNameAliases: {
1002
- [k: string]: string;
1003
- } | undefined;
1004
- } & {
1005
- readonly initialized: boolean;
1006
- readonly name: string;
1007
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1008
- readonly aliases: string[];
1009
- readonly displayName: string;
1010
- hasName(name: string): boolean;
1011
- readonly allAliases: string[];
1012
- readonly allRefNames: string[] | undefined;
1013
- readonly lowerCaseRefNames: string[] | undefined;
1014
- readonly allRefNamesWithLowerCase: string[] | undefined;
1015
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1016
- readonly refNameColors: string[];
1017
- } & {
1018
- readonly refNames: string[] | undefined;
1019
- } & {
1020
- getCanonicalRefName(refName: string): string | undefined;
1021
- getCanonicalRefName2(asmName: string): string;
1022
- getRefNameColor(refName: string): string | undefined;
1023
- isValidRefName(refName: string): boolean;
1024
- } & {
1025
- setLoaded({ regions, refNameAliases, cytobands, }: {
1026
- regions: import("@jbrowse/core/util/types").Region[];
1027
- refNameAliases: {
1028
- [x: string]: string;
1029
- };
1030
- cytobands: import("@jbrowse/core/util").Feature[];
1031
- }): void;
1032
- setError(e: unknown): void;
1033
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1034
- setRefNameAliases(aliases: {
1035
- [x: string]: string;
1036
- }): void;
1037
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1038
- setLoadingP(p?: Promise<void>): void;
1039
- load(): Promise<void>;
1040
- loadPre(): Promise<void>;
1041
- } & {
1042
- getAdapterMapEntry(adapterConf: {
1043
- [x: string]: unknown;
1044
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1045
- getRefNameMapForAdapter(adapterConf: {
1046
- [x: string]: unknown;
1047
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1048
- [x: string]: string;
1049
- }>;
1050
- getReverseRefNameMapForAdapter(adapterConf: {
1051
- [x: string]: unknown;
1052
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1053
- [x: string]: string;
1054
- }>;
1055
- afterCreate(): void;
1056
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1057
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1058
- }, {
1059
- error: unknown;
1060
- loadingP: Promise<void> | undefined;
1061
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1062
- refNameAliases: {
1063
- [x: string]: string;
1064
- } | undefined;
1065
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1066
- } & {
1067
- getConf(arg: string): any;
1068
- readonly lowerCaseRefNameAliases: {
1069
- [k: string]: string;
1070
- } | undefined;
1071
- } & {
1072
- readonly initialized: boolean;
1073
- readonly name: string;
1074
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1075
- readonly aliases: string[];
1076
- readonly displayName: string;
1077
- hasName(name: string): boolean;
1078
- readonly allAliases: string[];
1079
- readonly allRefNames: string[] | undefined;
1080
- readonly lowerCaseRefNames: string[] | undefined;
1081
- readonly allRefNamesWithLowerCase: string[] | undefined;
1082
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1083
- readonly refNameColors: string[];
1084
- } & {
1085
- readonly refNames: string[] | undefined;
1086
- } & {
1087
- getCanonicalRefName(refName: string): string | undefined;
1088
- getCanonicalRefName2(asmName: string): string;
1089
- getRefNameColor(refName: string): string | undefined;
1090
- isValidRefName(refName: string): boolean;
1091
- } & {
1092
- setLoaded({ regions, refNameAliases, cytobands, }: {
1093
- regions: import("@jbrowse/core/util/types").Region[];
1094
- refNameAliases: {
1095
- [x: string]: string;
1096
- };
1097
- cytobands: import("@jbrowse/core/util").Feature[];
1098
- }): void;
1099
- setError(e: unknown): void;
1100
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1101
- setRefNameAliases(aliases: {
1102
- [x: string]: string;
1103
- }): void;
1104
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1105
- setLoadingP(p?: Promise<void>): void;
1106
- load(): Promise<void>;
1107
- loadPre(): Promise<void>;
1108
- } & {
1109
- getAdapterMapEntry(adapterConf: {
1110
- [x: string]: unknown;
1111
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1112
- getRefNameMapForAdapter(adapterConf: {
1113
- [x: string]: unknown;
1114
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1115
- [x: string]: string;
1116
- }>;
1117
- getReverseRefNameMapForAdapter(adapterConf: {
1118
- [x: string]: unknown;
1119
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1120
- [x: string]: string;
1121
- }>;
1122
- afterCreate(): void;
1123
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1124
- getRefNameMapForAdapter(adapterConf: {
1125
- [x: string]: unknown;
1126
- }, assemblyName: string | undefined, opts: {
1127
- stopToken?: string;
1128
- sessionId: string;
1129
- }): Promise<{
1130
- [x: string]: string;
1131
- } | undefined>;
1132
- getReverseRefNameMapForAdapter(adapterConf: {
1133
- [x: string]: unknown;
1134
- }, assemblyName: string | undefined, opts: {
1135
- stopToken?: string;
1136
- sessionId: string;
1137
- }): Promise<{
1138
- [x: string]: string;
1139
- } | undefined>;
1140
- isValidRefName(refName: string, assemblyName: string): boolean;
1141
- } & {
1142
- afterAttach(): void;
1143
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1144
- addAssembly(configuration: any): void;
1145
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
1146
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1147
- rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1148
- adminMode: boolean;
1149
- error: unknown;
1150
- textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1151
- pluginManager: PluginManager;
1152
- } & {
1153
- setError(error: unknown): void;
1154
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1155
- setDefaultSession(): void;
1156
- setSessionPath(path: string): void;
1157
- renameCurrentSession(newName: string): void;
1158
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1159
- jbrowse: import("mobx-state-tree").IAnyType;
1160
- session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
1161
- sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1162
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1163
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1164
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1165
- }, {
1166
- error: unknown;
1167
- loadingP: Promise<void> | undefined;
1168
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1169
- refNameAliases: {
1170
- [x: string]: string;
1171
- } | undefined;
1172
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1173
- } & {
1174
- getConf(arg: string): any;
1175
- readonly lowerCaseRefNameAliases: {
1176
- [k: string]: string;
1177
- } | undefined;
1178
- } & {
1179
- readonly initialized: boolean;
1180
- readonly name: string;
1181
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1182
- readonly aliases: string[];
1183
- readonly displayName: string;
1184
- hasName(name: string): boolean;
1185
- readonly allAliases: string[];
1186
- readonly allRefNames: string[] | undefined;
1187
- readonly lowerCaseRefNames: string[] | undefined;
1188
- readonly allRefNamesWithLowerCase: string[] | undefined;
1189
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1190
- readonly refNameColors: string[];
1191
- } & {
1192
- readonly refNames: string[] | undefined;
1193
- } & {
1194
- getCanonicalRefName(refName: string): string | undefined;
1195
- getCanonicalRefName2(asmName: string): string;
1196
- getRefNameColor(refName: string): string | undefined;
1197
- isValidRefName(refName: string): boolean;
1198
- } & {
1199
- setLoaded({ regions, refNameAliases, cytobands, }: {
1200
- regions: import("@jbrowse/core/util/types").Region[];
1201
- refNameAliases: {
1202
- [x: string]: string;
1203
- };
1204
- cytobands: import("@jbrowse/core/util").Feature[];
1205
- }): void;
1206
- setError(e: unknown): void;
1207
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1208
- setRefNameAliases(aliases: {
1209
- [x: string]: string;
1210
- }): void;
1211
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1212
- setLoadingP(p?: Promise<void>): void;
1213
- load(): Promise<void>;
1214
- loadPre(): Promise<void>;
1215
- } & {
1216
- getAdapterMapEntry(adapterConf: {
1217
- [x: string]: unknown;
1218
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1219
- getRefNameMapForAdapter(adapterConf: {
1220
- [x: string]: unknown;
1221
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1222
- [x: string]: string;
1223
- }>;
1224
- getReverseRefNameMapForAdapter(adapterConf: {
1225
- [x: string]: unknown;
1226
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1227
- [x: string]: string;
1228
- }>;
1229
- afterCreate(): void;
1230
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1231
- }, {
1232
- readonly assemblyNameMap: Record<string, {
1233
- configuration: any;
1234
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1235
- error: unknown;
1236
- loadingP: Promise<void> | undefined;
1237
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1238
- refNameAliases: {
1239
- [x: string]: string;
1240
- } | undefined;
1241
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1242
- } & {
1243
- getConf(arg: string): any;
1244
- readonly lowerCaseRefNameAliases: {
1245
- [k: string]: string;
1246
- } | undefined;
1247
- } & {
1248
- readonly initialized: boolean;
1249
- readonly name: string;
1250
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1251
- readonly aliases: string[];
1252
- readonly displayName: string;
1253
- hasName(name: string): boolean;
1254
- readonly allAliases: string[];
1255
- readonly allRefNames: string[] | undefined;
1256
- readonly lowerCaseRefNames: string[] | undefined;
1257
- readonly allRefNamesWithLowerCase: string[] | undefined;
1258
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1259
- readonly refNameColors: string[];
1260
- } & {
1261
- readonly refNames: string[] | undefined;
1262
- } & {
1263
- getCanonicalRefName(refName: string): string | undefined;
1264
- getCanonicalRefName2(asmName: string): string;
1265
- getRefNameColor(refName: string): string | undefined;
1266
- isValidRefName(refName: string): boolean;
1267
- } & {
1268
- setLoaded({ regions, refNameAliases, cytobands, }: {
1269
- regions: import("@jbrowse/core/util/types").Region[];
1270
- refNameAliases: {
1271
- [x: string]: string;
1272
- };
1273
- cytobands: import("@jbrowse/core/util").Feature[];
1274
- }): void;
1275
- setError(e: unknown): void;
1276
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1277
- setRefNameAliases(aliases: {
1278
- [x: string]: string;
1279
- }): void;
1280
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1281
- setLoadingP(p?: Promise<void>): void;
1282
- load(): Promise<void>;
1283
- loadPre(): Promise<void>;
1284
- } & {
1285
- getAdapterMapEntry(adapterConf: {
1286
- [x: string]: unknown;
1287
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1288
- getRefNameMapForAdapter(adapterConf: {
1289
- [x: string]: unknown;
1290
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1291
- [x: string]: string;
1292
- }>;
1293
- getReverseRefNameMapForAdapter(adapterConf: {
1294
- [x: string]: unknown;
1295
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1296
- [x: string]: string;
1297
- }>;
1298
- afterCreate(): void;
1299
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1300
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1301
- }, {
1302
- error: unknown;
1303
- loadingP: Promise<void> | undefined;
1304
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1305
- refNameAliases: {
1306
- [x: string]: string;
1307
- } | undefined;
1308
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1309
- } & {
1310
- getConf(arg: string): any;
1311
- readonly lowerCaseRefNameAliases: {
1312
- [k: string]: string;
1313
- } | undefined;
1314
- } & {
1315
- readonly initialized: boolean;
1316
- readonly name: string;
1317
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1318
- readonly aliases: string[];
1319
- readonly displayName: string;
1320
- hasName(name: string): boolean;
1321
- readonly allAliases: string[];
1322
- readonly allRefNames: string[] | undefined;
1323
- readonly lowerCaseRefNames: string[] | undefined;
1324
- readonly allRefNamesWithLowerCase: string[] | undefined;
1325
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1326
- readonly refNameColors: string[];
1327
- } & {
1328
- readonly refNames: string[] | undefined;
1329
- } & {
1330
- getCanonicalRefName(refName: string): string | undefined;
1331
- getCanonicalRefName2(asmName: string): string;
1332
- getRefNameColor(refName: string): string | undefined;
1333
- isValidRefName(refName: string): boolean;
1334
- } & {
1335
- setLoaded({ regions, refNameAliases, cytobands, }: {
1336
- regions: import("@jbrowse/core/util/types").Region[];
1337
- refNameAliases: {
1338
- [x: string]: string;
1339
- };
1340
- cytobands: import("@jbrowse/core/util").Feature[];
1341
- }): void;
1342
- setError(e: unknown): void;
1343
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1344
- setRefNameAliases(aliases: {
1345
- [x: string]: string;
1346
- }): void;
1347
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1348
- setLoadingP(p?: Promise<void>): void;
1349
- load(): Promise<void>;
1350
- loadPre(): Promise<void>;
1351
- } & {
1352
- getAdapterMapEntry(adapterConf: {
1353
- [x: string]: unknown;
1354
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1355
- getRefNameMapForAdapter(adapterConf: {
1356
- [x: string]: unknown;
1357
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1358
- [x: string]: string;
1359
- }>;
1360
- getReverseRefNameMapForAdapter(adapterConf: {
1361
- [x: string]: unknown;
1362
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1363
- [x: string]: string;
1364
- }>;
1365
- afterCreate(): void;
1366
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
1367
- } & {
1368
- getCanonicalAssemblyName(asmName: string): string | undefined;
1369
- getCanonicalAssemblyName2(asmName: string): string;
1370
- get(asmName: string): ({
1371
- configuration: any;
1372
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1373
- error: unknown;
1374
- loadingP: Promise<void> | undefined;
1375
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1376
- refNameAliases: {
1377
- [x: string]: string;
1378
- } | undefined;
1379
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1380
- } & {
1381
- getConf(arg: string): any;
1382
- readonly lowerCaseRefNameAliases: {
1383
- [k: string]: string;
1384
- } | undefined;
1385
- } & {
1386
- readonly initialized: boolean;
1387
- readonly name: string;
1388
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1389
- readonly aliases: string[];
1390
- readonly displayName: string;
1391
- hasName(name: string): boolean;
1392
- readonly allAliases: string[];
1393
- readonly allRefNames: string[] | undefined;
1394
- readonly lowerCaseRefNames: string[] | undefined;
1395
- readonly allRefNamesWithLowerCase: string[] | undefined;
1396
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1397
- readonly refNameColors: string[];
1398
- } & {
1399
- readonly refNames: string[] | undefined;
1400
- } & {
1401
- getCanonicalRefName(refName: string): string | undefined;
1402
- getCanonicalRefName2(asmName: string): string;
1403
- getRefNameColor(refName: string): string | undefined;
1404
- isValidRefName(refName: string): boolean;
1405
- } & {
1406
- setLoaded({ regions, refNameAliases, cytobands, }: {
1407
- regions: import("@jbrowse/core/util/types").Region[];
1408
- refNameAliases: {
1409
- [x: string]: string;
1410
- };
1411
- cytobands: import("@jbrowse/core/util").Feature[];
1412
- }): void;
1413
- setError(e: unknown): void;
1414
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1415
- setRefNameAliases(aliases: {
1416
- [x: string]: string;
1417
- }): void;
1418
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1419
- setLoadingP(p?: Promise<void>): void;
1420
- load(): Promise<void>;
1421
- loadPre(): Promise<void>;
1422
- } & {
1423
- getAdapterMapEntry(adapterConf: {
1424
- [x: string]: unknown;
1425
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1426
- getRefNameMapForAdapter(adapterConf: {
1427
- [x: string]: unknown;
1428
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1429
- [x: string]: string;
1430
- }>;
1431
- getReverseRefNameMapForAdapter(adapterConf: {
1432
- [x: string]: unknown;
1433
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1434
- [x: string]: string;
1435
- }>;
1436
- afterCreate(): void;
1437
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1438
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1439
- }, {
1440
- error: unknown;
1441
- loadingP: Promise<void> | undefined;
1442
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1443
- refNameAliases: {
1444
- [x: string]: string;
1445
- } | undefined;
1446
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1447
- } & {
1448
- getConf(arg: string): any;
1449
- readonly lowerCaseRefNameAliases: {
1450
- [k: string]: string;
1451
- } | undefined;
1452
- } & {
1453
- readonly initialized: boolean;
1454
- readonly name: string;
1455
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1456
- readonly aliases: string[];
1457
- readonly displayName: string;
1458
- hasName(name: string): boolean;
1459
- readonly allAliases: string[];
1460
- readonly allRefNames: string[] | undefined;
1461
- readonly lowerCaseRefNames: string[] | undefined;
1462
- readonly allRefNamesWithLowerCase: string[] | undefined;
1463
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1464
- readonly refNameColors: string[];
1465
- } & {
1466
- readonly refNames: string[] | undefined;
1467
- } & {
1468
- getCanonicalRefName(refName: string): string | undefined;
1469
- getCanonicalRefName2(asmName: string): string;
1470
- getRefNameColor(refName: string): string | undefined;
1471
- isValidRefName(refName: string): boolean;
1472
- } & {
1473
- setLoaded({ regions, refNameAliases, cytobands, }: {
1474
- regions: import("@jbrowse/core/util/types").Region[];
1475
- refNameAliases: {
1476
- [x: string]: string;
1477
- };
1478
- cytobands: import("@jbrowse/core/util").Feature[];
1479
- }): void;
1480
- setError(e: unknown): void;
1481
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1482
- setRefNameAliases(aliases: {
1483
- [x: string]: string;
1484
- }): void;
1485
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1486
- setLoadingP(p?: Promise<void>): void;
1487
- load(): Promise<void>;
1488
- loadPre(): Promise<void>;
1489
- } & {
1490
- getAdapterMapEntry(adapterConf: {
1491
- [x: string]: unknown;
1492
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1493
- getRefNameMapForAdapter(adapterConf: {
1494
- [x: string]: unknown;
1495
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1496
- [x: string]: string;
1497
- }>;
1498
- getReverseRefNameMapForAdapter(adapterConf: {
1499
- [x: string]: unknown;
1500
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1501
- [x: string]: string;
1502
- }>;
1503
- afterCreate(): void;
1504
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1505
- readonly assemblyNamesList: any[];
1506
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1507
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1508
- } & {
1509
- waitForAssembly(assemblyName: string): Promise<({
1510
- configuration: any;
1511
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1512
- error: unknown;
1513
- loadingP: Promise<void> | undefined;
1514
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1515
- refNameAliases: {
1516
- [x: string]: string;
1517
- } | undefined;
1518
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1519
- } & {
1520
- getConf(arg: string): any;
1521
- readonly lowerCaseRefNameAliases: {
1522
- [k: string]: string;
1523
- } | undefined;
1524
- } & {
1525
- readonly initialized: boolean;
1526
- readonly name: string;
1527
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1528
- readonly aliases: string[];
1529
- readonly displayName: string;
1530
- hasName(name: string): boolean;
1531
- readonly allAliases: string[];
1532
- readonly allRefNames: string[] | undefined;
1533
- readonly lowerCaseRefNames: string[] | undefined;
1534
- readonly allRefNamesWithLowerCase: string[] | undefined;
1535
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1536
- readonly refNameColors: string[];
1537
- } & {
1538
- readonly refNames: string[] | undefined;
1539
- } & {
1540
- getCanonicalRefName(refName: string): string | undefined;
1541
- getCanonicalRefName2(asmName: string): string;
1542
- getRefNameColor(refName: string): string | undefined;
1543
- isValidRefName(refName: string): boolean;
1544
- } & {
1545
- setLoaded({ regions, refNameAliases, cytobands, }: {
1546
- regions: import("@jbrowse/core/util/types").Region[];
1547
- refNameAliases: {
1548
- [x: string]: string;
1549
- };
1550
- cytobands: import("@jbrowse/core/util").Feature[];
1551
- }): void;
1552
- setError(e: unknown): void;
1553
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1554
- setRefNameAliases(aliases: {
1555
- [x: string]: string;
1556
- }): void;
1557
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1558
- setLoadingP(p?: Promise<void>): void;
1559
- load(): Promise<void>;
1560
- loadPre(): Promise<void>;
1561
- } & {
1562
- getAdapterMapEntry(adapterConf: {
1563
- [x: string]: unknown;
1564
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1565
- getRefNameMapForAdapter(adapterConf: {
1566
- [x: string]: unknown;
1567
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1568
- [x: string]: string;
1569
- }>;
1570
- getReverseRefNameMapForAdapter(adapterConf: {
1571
- [x: string]: unknown;
1572
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1573
- [x: string]: string;
1574
- }>;
1575
- afterCreate(): void;
1576
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1577
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1578
- }, {
1579
- error: unknown;
1580
- loadingP: Promise<void> | undefined;
1581
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1582
- refNameAliases: {
1583
- [x: string]: string;
1584
- } | undefined;
1585
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1586
- } & {
1587
- getConf(arg: string): any;
1588
- readonly lowerCaseRefNameAliases: {
1589
- [k: string]: string;
1590
- } | undefined;
1591
- } & {
1592
- readonly initialized: boolean;
1593
- readonly name: string;
1594
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1595
- readonly aliases: string[];
1596
- readonly displayName: string;
1597
- hasName(name: string): boolean;
1598
- readonly allAliases: string[];
1599
- readonly allRefNames: string[] | undefined;
1600
- readonly lowerCaseRefNames: string[] | undefined;
1601
- readonly allRefNamesWithLowerCase: string[] | undefined;
1602
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1603
- readonly refNameColors: string[];
1604
- } & {
1605
- readonly refNames: string[] | undefined;
1606
- } & {
1607
- getCanonicalRefName(refName: string): string | undefined;
1608
- getCanonicalRefName2(asmName: string): string;
1609
- getRefNameColor(refName: string): string | undefined;
1610
- isValidRefName(refName: string): boolean;
1611
- } & {
1612
- setLoaded({ regions, refNameAliases, cytobands, }: {
1613
- regions: import("@jbrowse/core/util/types").Region[];
1614
- refNameAliases: {
1615
- [x: string]: string;
1616
- };
1617
- cytobands: import("@jbrowse/core/util").Feature[];
1618
- }): void;
1619
- setError(e: unknown): void;
1620
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1621
- setRefNameAliases(aliases: {
1622
- [x: string]: string;
1623
- }): void;
1624
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1625
- setLoadingP(p?: Promise<void>): void;
1626
- load(): Promise<void>;
1627
- loadPre(): Promise<void>;
1628
- } & {
1629
- getAdapterMapEntry(adapterConf: {
1630
- [x: string]: unknown;
1631
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1632
- getRefNameMapForAdapter(adapterConf: {
1633
- [x: string]: unknown;
1634
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1635
- [x: string]: string;
1636
- }>;
1637
- getReverseRefNameMapForAdapter(adapterConf: {
1638
- [x: string]: unknown;
1639
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1640
- [x: string]: string;
1641
- }>;
1642
- afterCreate(): void;
1643
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1644
- getRefNameMapForAdapter(adapterConf: {
1645
- [x: string]: unknown;
1646
- }, assemblyName: string | undefined, opts: {
1647
- stopToken?: string;
1648
- sessionId: string;
1649
- }): Promise<{
1650
- [x: string]: string;
1651
- } | undefined>;
1652
- getReverseRefNameMapForAdapter(adapterConf: {
1653
- [x: string]: unknown;
1654
- }, assemblyName: string | undefined, opts: {
1655
- stopToken?: string;
1656
- sessionId: string;
1657
- }): Promise<{
1658
- [x: string]: string;
1659
- } | undefined>;
1660
- isValidRefName(refName: string, assemblyName: string): boolean;
1661
- } & {
1662
- afterAttach(): void;
1663
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1664
- addAssembly(configuration: any): void;
1665
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
1666
- }, {
1667
- rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1668
- adminMode: boolean;
1669
- error: unknown;
1670
- textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1671
- pluginManager: PluginManager;
1672
- } & {
1673
- setError(error: unknown): void;
1674
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1675
- setDefaultSession(): void;
1676
- setSessionPath(path: string): void;
1677
- renameCurrentSession(newName: string): void;
1678
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1679
- } & {
1680
- readonly jbrowse: any;
1681
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1682
- readonly configuration: {
1683
- [x: string]: any;
1684
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1685
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1686
- [x: string]: any;
1687
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1688
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1689
- [x: string]: any;
1690
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1691
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1692
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1693
- readonly adminMode: boolean;
1694
- readonly textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1695
- } & {
1696
- readonly assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
1697
- } & {
1698
- setSelection(thing: unknown): void;
1699
- clearSelection(): void;
1700
- setHovered(thing: unknown): void;
1701
- } & {
1702
- readonly visibleWidget: any;
1703
- } & {
1704
- setDrawerPosition(arg: string): void;
1705
- updateDrawerWidth(drawerWidth: number): number;
1706
- resizeDrawer(distance: number): number;
1707
- addWidget(typeName: string, id: string, initialState?: {}, conf?: unknown): any;
1708
- showWidget(widget: any): void;
1709
- hasWidget(widget: any): boolean;
1710
- hideWidget(widget: any): void;
1711
- minimizeWidgetDrawer(): void;
1712
- showWidgetDrawer(): void;
1713
- hideAllWidgets(): void;
1714
- editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1715
- afterAttach(): void;
1716
- } & {
1717
- readonly connections: import("@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig").BaseConnectionConfigModel[];
1718
- } & {
1719
- makeConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: {}): ({
1720
- name: string;
1721
- tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
1722
- configuration: {
1723
- [x: string]: any;
1724
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1725
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1726
- [x: string]: any;
1727
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1728
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1729
- [x: string]: any;
1730
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1731
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1732
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1733
- name: {
1734
- type: string;
1735
- defaultValue: string;
1736
- description: string;
1737
- };
1738
- assemblyNames: {
1739
- type: string;
1740
- defaultValue: never[];
1741
- description: string;
1742
- };
1743
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>;
1744
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1745
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1746
- } & {
1747
- afterAttach(): void;
1748
- addTrackConf(trackConf: ({
1749
- [x: string]: any;
1750
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1751
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1752
- [x: string]: any;
1753
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1754
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1755
- [x: string]: any;
1756
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1757
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1758
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
1759
- addTrackConfs(trackConfs: (({
1760
- [x: string]: any;
1761
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1762
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1763
- [x: string]: any;
1764
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1765
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1766
- [x: string]: any;
1767
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1768
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1769
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
1770
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
1771
- clear(): void;
1772
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1773
- name: import("mobx-state-tree").ISimpleType<string>;
1774
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
1775
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1776
- name: {
1777
- type: string;
1778
- defaultValue: string;
1779
- description: string;
1780
- };
1781
- assemblyNames: {
1782
- type: string;
1783
- defaultValue: never[];
1784
- description: string;
1785
- };
1786
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
1787
- }, {
1788
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1789
- } & {
1790
- afterAttach(): void;
1791
- addTrackConf(trackConf: ({
1792
- [x: string]: any;
1793
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1794
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1795
- [x: string]: any;
1796
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1797
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1798
- [x: string]: any;
1799
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1800
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1801
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
1802
- addTrackConfs(trackConfs: (({
1803
- [x: string]: any;
1804
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1805
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1806
- [x: string]: any;
1807
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1808
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1809
- [x: string]: any;
1810
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1811
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1812
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
1813
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
1814
- clear(): void;
1815
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1816
- prepareToBreakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): (Record<string, number> | (() => void))[] | undefined;
1817
- breakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1818
- deleteConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1819
- addConnectionConf(connectionConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1820
- clearConnections(): void;
1821
- } & {
1822
- queueOfDialogs: [import("@jbrowse/core/util/types").DialogComponentType, unknown][];
1823
- } & {
1824
- readonly DialogComponent: import("@jbrowse/core/util/types").DialogComponentType | undefined;
1825
- readonly DialogProps: unknown;
1826
- } & {
1827
- removeActiveDialog(): void;
1828
- queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util/types").DialogComponentType, unknown]): void;
1829
- } & {
1830
- getReferring(object: import("mobx-state-tree").IAnyStateTreeNode): import("@jbrowse/product-core").ReferringNode[];
1831
- } & {
1832
- removeReferring(referring: import("@jbrowse/product-core").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
1833
- } & {
1834
- readonly tracks: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1835
- } & {
1836
- addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfiguration): any;
1837
- deleteTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1838
- } & {
1839
- readonly tracks: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1840
- } & {
1841
- addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfiguration): any;
1842
- deleteTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1843
- } & {
1844
- snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1845
- } & {
1846
- readonly snackbarMessageSet: Map<string, import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1847
- } & {
1848
- notify(message: string, level?: import("@jbrowse/core/util/types").NotificationLevel, action?: import("@jbrowse/core/util/types").SnackAction): void;
1849
- notifyError(errorMessage: string, error?: unknown, extra?: unknown): void;
1850
- pushSnackbarMessage(message: string, level?: import("@jbrowse/core/util/types").NotificationLevel, action?: import("@jbrowse/core/util/types").SnackAction): void;
1851
- popSnackbarMessage(): import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage | undefined;
1852
- removeSnackbarMessage(message: string): void;
1853
- } & {
1854
- readonly version: any;
1855
- readonly disableAddTracks: any;
1856
- readonly assemblies: any[];
1857
- readonly assemblyNames: any[];
1858
- readonly connections: any;
1859
- readonly assemblyManager: any;
1860
- readonly views: ({
1861
- id: string;
1862
- displayName: string | undefined;
1863
- minimized: boolean;
1864
- type: string;
1865
- offsetPx: number;
1866
- bpPerPx: number;
1867
- displayedRegions: import("@jbrowse/core/util/types").Region[] & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util/types").Region[], import("@jbrowse/core/util/types").Region[], import("@jbrowse/core/util/types").Region[]>, [undefined]>>;
1868
- tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
1869
- hideHeader: boolean;
1870
- hideHeaderOverview: boolean;
1871
- hideNoTracksActive: boolean;
1872
- trackSelectorType: string;
1873
- showCenterLine: boolean;
1874
- showCytobandsSetting: boolean;
1875
- trackLabels: string;
1876
- showGridlines: boolean;
1877
- highlight: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>>;
1878
- colorByCDS: boolean;
1879
- showTrackOutlines: boolean;
1880
- init: (import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined>>) | undefined;
1881
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1882
- width: number;
1883
- } & {
1884
- menuItems(): import("@jbrowse/core/ui").MenuItem[];
1885
- } & {
1886
- setDisplayName(name: string): void;
1887
- setWidth(newWidth: number): void;
1888
- setMinimized(flag: boolean): void;
1889
- } & {
1890
- volatileWidth: number | undefined;
1891
- minimumBlockWidth: number;
1892
- draggingTrackId: undefined | string;
1893
- volatileError: unknown;
1894
- afterDisplayedRegionsSetCallbacks: (() => void)[];
1895
- scaleFactor: number;
1896
- trackRefs: Record<string, HTMLDivElement>;
1897
- coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
1898
- coarseTotalBp: number;
1899
- leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
1900
- rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
1901
- } & {
1902
- readonly pinnedTracks: any[];
1903
- readonly unpinnedTracks: any[];
1904
- readonly trackLabelsSetting: any;
1905
- readonly width: number;
1906
- readonly interRegionPaddingWidth: number;
1907
- readonly assemblyNames: string[];
1908
- readonly assemblyDisplayNames: string[];
1909
- readonly isTopLevelView: boolean;
1910
- readonly stickyViewHeaders: boolean;
1911
- readonly rubberbandTop: number;
1912
- readonly pinnedTracksTop: number;
1913
- } & {
1914
- scaleBarDisplayPrefix(): string | undefined;
1915
- MiniControlsComponent(): React.FC<any>;
1916
- HeaderComponent(): React.FC<any>;
1917
- readonly assembliesNotFound: string | undefined;
1918
- readonly assemblyErrors: string;
1919
- readonly assembliesInitialized: boolean;
1920
- readonly initialized: boolean;
1921
- readonly hasDisplayedRegions: boolean;
1922
- readonly scaleBarHeight: number;
1923
- readonly headerHeight: number;
1924
- readonly trackHeights: number;
1925
- readonly trackHeightsWithResizeHandles: number;
1926
- readonly height: number;
1927
- readonly totalBp: number;
1928
- readonly maxBpPerPx: number;
1929
- readonly minBpPerPx: number;
1930
- readonly error: unknown;
1931
- readonly maxOffset: number;
1932
- readonly minOffset: number;
1933
- readonly displayedRegionsTotalPx: number;
1934
- renderProps(): any;
1935
- searchScope(assemblyName: string): {
1936
- assemblyName: string;
1937
- includeAggregateIndexes: boolean;
1938
- tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
1939
- };
1940
- getTrack(id: string): any;
1941
- rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
1942
- rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
1943
- readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
1944
- } & {
1945
- setShowTrackOutlines(arg: boolean): void;
1946
- setColorByCDS(flag: boolean): void;
1947
- setShowCytobands(flag: boolean): void;
1948
- setWidth(newWidth: number): void;
1949
- setError(error: unknown): void;
1950
- setHideHeader(b: boolean): void;
1951
- setHideHeaderOverview(b: boolean): void;
1952
- setHideNoTracksActive(b: boolean): void;
1953
- setShowGridlines(b: boolean): void;
1954
- addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
1955
- setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
1956
- removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
1957
- scrollTo(offsetPx: number): number;
1958
- zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
1959
- setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
1960
- setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
1961
- setNewView(bpPerPx: number, offsetPx: number): void;
1962
- horizontallyFlip(): void;
1963
- showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
1964
- hideTrack(trackId: string): number;
1965
- } & {
1966
- moveTrackDown(id: string): void;
1967
- moveTrackUp(id: string): void;
1968
- moveTrackToTop(id: string): void;
1969
- moveTrackToBottom(id: string): void;
1970
- moveTrack(movingId: string, targetId: string): void;
1971
- toggleTrack(trackId: string): boolean;
1972
- setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
1973
- setShowCenterLine(b: boolean): void;
1974
- setDisplayedRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1975
- activateTrackSelector(): import("@jbrowse/core/util/types").Widget;
1976
- getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
1977
- start: number;
1978
- end: number;
1979
- type: string;
1980
- regionNumber?: number;
1981
- reversed?: boolean;
1982
- refName: string;
1983
- assemblyName: string;
1984
- key: string;
1985
- offsetPx: number;
1986
- widthPx: number;
1987
- variant?: string;
1988
- isLeftEndOfDisplayedRegion?: boolean;
1989
- }[];
1990
- afterDisplayedRegionsSet(cb: () => void): void;
1991
- horizontalScroll(distance: number): number;
1992
- center(): void;
1993
- showAllRegions(): void;
1994
- showAllRegionsInAssembly(assemblyName?: string): void;
1995
- setDraggingTrackId(idx?: string): void;
1996
- setScaleFactor(factor: number): void;
1997
- clearView(): void;
1998
- setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
1999
- exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
2000
- } & {
2001
- slide: (viewWidths: number) => void;
2002
- } & {
2003
- zoom: (targetBpPerPx: number) => void;
2004
- } & {
2005
- readonly canShowCytobands: boolean;
2006
- readonly showCytobands: boolean;
2007
- readonly anyCytobandsExist: boolean;
2008
- readonly cytobandOffset: number;
2009
- } & {
2010
- menuItems(): import("@jbrowse/core/ui").MenuItem[];
2011
- } & {
2012
- readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2013
- readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2014
- readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2015
- readonly visibleLocStrings: string;
2016
- readonly coarseVisibleLocStrings: string;
2017
- } & {
2018
- setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
2019
- } & {
2020
- moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2021
- navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
2022
- navToSearchString({ input, assembly, }: {
2023
- input: string;
2024
- assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
2025
- }): Promise<void>;
2026
- navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
2027
- navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
2028
- navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
2029
- navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
2030
- } & {
2031
- rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
2032
- bpToPx({ refName, coord, regionNumber, }: {
2033
- refName: string;
2034
- coord: number;
2035
- regionNumber?: number;
2036
- }): {
2037
- index: number;
2038
- offsetPx: number;
2039
- } | undefined;
2040
- centerAt(coord: number, refName: string, regionNumber?: number): void;
2041
- pxToBp(px: number): {
2042
- coord: number;
2043
- index: number;
2044
- refName: string;
2045
- oob: boolean;
2046
- assemblyName: string;
2047
- offset: number;
2048
- start: number;
2049
- end: number;
2050
- reversed?: boolean;
2051
- };
2052
- readonly centerLineInfo: {
2053
- coord: number;
2054
- index: number;
2055
- refName: string;
2056
- oob: boolean;
2057
- assemblyName: string;
2058
- offset: number;
2059
- start: number;
2060
- end: number;
2061
- reversed?: boolean;
2062
- } | undefined;
2063
- } & {
2064
- afterCreate(): void;
2065
- afterAttach(): void;
2066
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2067
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2068
- displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
2069
- minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2070
- } & {
2071
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2072
- type: import("mobx-state-tree").IType<string | undefined, string, string>;
2073
- offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2074
- bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2075
- displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util/types").Region[], import("@jbrowse/core/util/types").Region[], import("@jbrowse/core/util/types").Region[]>, [undefined]>;
2076
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
2077
- hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2078
- hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2079
- hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2080
- trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2081
- showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2082
- showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2083
- trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2084
- showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2085
- highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
2086
- colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2087
- showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2088
- init: import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined>;
2089
- }, {
2090
- width: number;
2091
- } & {
2092
- menuItems(): import("@jbrowse/core/ui").MenuItem[];
2093
- } & {
2094
- setDisplayName(name: string): void;
2095
- setWidth(newWidth: number): void;
2096
- setMinimized(flag: boolean): void;
2097
- } & {
2098
- volatileWidth: number | undefined;
2099
- minimumBlockWidth: number;
2100
- draggingTrackId: undefined | string;
2101
- volatileError: unknown;
2102
- afterDisplayedRegionsSetCallbacks: (() => void)[];
2103
- scaleFactor: number;
2104
- trackRefs: Record<string, HTMLDivElement>;
2105
- coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2106
- coarseTotalBp: number;
2107
- leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
2108
- rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
2109
- } & {
2110
- readonly pinnedTracks: any[];
2111
- readonly unpinnedTracks: any[];
2112
- readonly trackLabelsSetting: any;
2113
- readonly width: number;
2114
- readonly interRegionPaddingWidth: number;
2115
- readonly assemblyNames: string[];
2116
- readonly assemblyDisplayNames: string[];
2117
- readonly isTopLevelView: boolean;
2118
- readonly stickyViewHeaders: boolean;
2119
- readonly rubberbandTop: number;
2120
- readonly pinnedTracksTop: number;
2121
- } & {
2122
- scaleBarDisplayPrefix(): string | undefined;
2123
- MiniControlsComponent(): React.FC<any>;
2124
- HeaderComponent(): React.FC<any>;
2125
- readonly assembliesNotFound: string | undefined;
2126
- readonly assemblyErrors: string;
2127
- readonly assembliesInitialized: boolean;
2128
- readonly initialized: boolean;
2129
- readonly hasDisplayedRegions: boolean;
2130
- readonly scaleBarHeight: number;
2131
- readonly headerHeight: number;
2132
- readonly trackHeights: number;
2133
- readonly trackHeightsWithResizeHandles: number;
2134
- readonly height: number;
2135
- readonly totalBp: number;
2136
- readonly maxBpPerPx: number;
2137
- readonly minBpPerPx: number;
2138
- readonly error: unknown;
2139
- readonly maxOffset: number;
2140
- readonly minOffset: number;
2141
- readonly displayedRegionsTotalPx: number;
2142
- renderProps(): any;
2143
- searchScope(assemblyName: string): {
2144
- assemblyName: string;
2145
- includeAggregateIndexes: boolean;
2146
- tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
2147
- };
2148
- getTrack(id: string): any;
2149
- rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
2150
- rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
2151
- readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
2152
- } & {
2153
- setShowTrackOutlines(arg: boolean): void;
2154
- setColorByCDS(flag: boolean): void;
2155
- setShowCytobands(flag: boolean): void;
2156
- setWidth(newWidth: number): void;
2157
- setError(error: unknown): void;
2158
- setHideHeader(b: boolean): void;
2159
- setHideHeaderOverview(b: boolean): void;
2160
- setHideNoTracksActive(b: boolean): void;
2161
- setShowGridlines(b: boolean): void;
2162
- addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
2163
- setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
2164
- removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
2165
- scrollTo(offsetPx: number): number;
2166
- zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
2167
- setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2168
- setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
2169
- setNewView(bpPerPx: number, offsetPx: number): void;
2170
- horizontallyFlip(): void;
2171
- showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
2172
- hideTrack(trackId: string): number;
2173
- } & {
2174
- moveTrackDown(id: string): void;
2175
- moveTrackUp(id: string): void;
2176
- moveTrackToTop(id: string): void;
2177
- moveTrackToBottom(id: string): void;
2178
- moveTrack(movingId: string, targetId: string): void;
2179
- toggleTrack(trackId: string): boolean;
2180
- setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
2181
- setShowCenterLine(b: boolean): void;
2182
- setDisplayedRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
2183
- activateTrackSelector(): import("@jbrowse/core/util/types").Widget;
2184
- getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
2185
- start: number;
2186
- end: number;
2187
- type: string;
2188
- regionNumber?: number;
2189
- reversed?: boolean;
2190
- refName: string;
2191
- assemblyName: string;
2192
- key: string;
2193
- offsetPx: number;
2194
- widthPx: number;
2195
- variant?: string;
2196
- isLeftEndOfDisplayedRegion?: boolean;
2197
- }[];
2198
- afterDisplayedRegionsSet(cb: () => void): void;
2199
- horizontalScroll(distance: number): number;
2200
- center(): void;
2201
- showAllRegions(): void;
2202
- showAllRegionsInAssembly(assemblyName?: string): void;
2203
- setDraggingTrackId(idx?: string): void;
2204
- setScaleFactor(factor: number): void;
2205
- clearView(): void;
2206
- setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
2207
- exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
2208
- } & {
2209
- slide: (viewWidths: number) => void;
2210
- } & {
2211
- zoom: (targetBpPerPx: number) => void;
2212
- } & {
2213
- readonly canShowCytobands: boolean;
2214
- readonly showCytobands: boolean;
2215
- readonly anyCytobandsExist: boolean;
2216
- readonly cytobandOffset: number;
2217
- } & {
2218
- menuItems(): import("@jbrowse/core/ui").MenuItem[];
2219
- } & {
2220
- readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2221
- readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2222
- readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2223
- readonly visibleLocStrings: string;
2224
- readonly coarseVisibleLocStrings: string;
2225
- } & {
2226
- setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
2227
- } & {
2228
- moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2229
- navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
2230
- navToSearchString({ input, assembly, }: {
2231
- input: string;
2232
- assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
2233
- }): Promise<void>;
2234
- navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
2235
- navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
2236
- navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
2237
- navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
2238
- } & {
2239
- rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
2240
- bpToPx({ refName, coord, regionNumber, }: {
2241
- refName: string;
2242
- coord: number;
2243
- regionNumber?: number;
2244
- }): {
2245
- index: number;
2246
- offsetPx: number;
2247
- } | undefined;
2248
- centerAt(coord: number, refName: string, regionNumber?: number): void;
2249
- pxToBp(px: number): {
2250
- coord: number;
2251
- index: number;
2252
- refName: string;
2253
- oob: boolean;
2254
- assemblyName: string;
2255
- offset: number;
2256
- start: number;
2257
- end: number;
2258
- reversed?: boolean;
2259
- };
2260
- readonly centerLineInfo: {
2261
- coord: number;
2262
- index: number;
2263
- refName: string;
2264
- oob: boolean;
2265
- assemblyName: string;
2266
- offset: number;
2267
- start: number;
2268
- end: number;
2269
- reversed?: boolean;
2270
- } | undefined;
2271
- } & {
2272
- afterCreate(): void;
2273
- afterAttach(): void;
2274
- }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
2275
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2276
- displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
2277
- minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2278
- } & {
2279
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2280
- type: import("mobx-state-tree").IType<string | undefined, string, string>;
2281
- offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2282
- bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2283
- displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util/types").Region[], import("@jbrowse/core/util/types").Region[], import("@jbrowse/core/util/types").Region[]>, [undefined]>;
2284
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
2285
- hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2286
- hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2287
- hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2288
- trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2289
- showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2290
- showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2291
- trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2292
- showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2293
- highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
2294
- colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2295
- showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2296
- init: import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined>;
2297
- }>>, {
2298
- type: string;
2299
- id: string;
2300
- displayName: string | undefined;
2301
- tracks: any[];
2302
- minimized: boolean;
2303
- offsetPx: number;
2304
- bpPerPx: number;
2305
- displayedRegions: import("@jbrowse/core/util/types").Region[];
2306
- hideHeader: boolean;
2307
- hideHeaderOverview: boolean;
2308
- hideNoTracksActive: boolean;
2309
- trackSelectorType: string;
2310
- showCenterLine: boolean;
2311
- showCytobandsSetting: boolean;
2312
- trackLabels: string;
2313
- showGridlines: boolean;
2314
- highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[];
2315
- colorByCDS: boolean;
2316
- showTrackOutlines: boolean;
2317
- }>>)[];
2318
- renderProps(): {
2319
- theme: any;
2320
- highResolutionScaling: any;
2321
- };
2322
- } & {
2323
- addView(typeName: string, initialState?: {}): {
2324
- id: string;
2325
- displayName: string | undefined;
2326
- minimized: boolean;
2327
- type: string;
2328
- offsetPx: number;
2329
- bpPerPx: number;
2330
- displayedRegions: import("@jbrowse/core/util/types").Region[] & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util/types").Region[], import("@jbrowse/core/util/types").Region[], import("@jbrowse/core/util/types").Region[]>, [undefined]>>;
2331
- tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
2332
- hideHeader: boolean;
2333
- hideHeaderOverview: boolean;
2334
- hideNoTracksActive: boolean;
2335
- trackSelectorType: string;
2336
- showCenterLine: boolean;
2337
- showCytobandsSetting: boolean;
2338
- trackLabels: string;
2339
- showGridlines: boolean;
2340
- highlight: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>>;
2341
- colorByCDS: boolean;
2342
- showTrackOutlines: boolean;
2343
- init: (import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined>>) | undefined;
2344
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2345
- width: number;
2346
- } & {
2347
- menuItems(): import("@jbrowse/core/ui").MenuItem[];
2348
- } & {
2349
- setDisplayName(name: string): void;
2350
- setWidth(newWidth: number): void;
2351
- setMinimized(flag: boolean): void;
2352
- } & {
2353
- volatileWidth: number | undefined;
2354
- minimumBlockWidth: number;
2355
- draggingTrackId: undefined | string;
2356
- volatileError: unknown;
2357
- afterDisplayedRegionsSetCallbacks: (() => void)[];
2358
- scaleFactor: number;
2359
- trackRefs: Record<string, HTMLDivElement>;
2360
- coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2361
- coarseTotalBp: number;
2362
- leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
2363
- rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
2364
- } & {
2365
- readonly pinnedTracks: any[];
2366
- readonly unpinnedTracks: any[];
2367
- readonly trackLabelsSetting: any;
2368
- readonly width: number;
2369
- readonly interRegionPaddingWidth: number;
2370
- readonly assemblyNames: string[];
2371
- readonly assemblyDisplayNames: string[];
2372
- readonly isTopLevelView: boolean;
2373
- readonly stickyViewHeaders: boolean;
2374
- readonly rubberbandTop: number;
2375
- readonly pinnedTracksTop: number;
2376
- } & {
2377
- scaleBarDisplayPrefix(): string | undefined;
2378
- MiniControlsComponent(): React.FC<any>;
2379
- HeaderComponent(): React.FC<any>;
2380
- readonly assembliesNotFound: string | undefined;
2381
- readonly assemblyErrors: string;
2382
- readonly assembliesInitialized: boolean;
2383
- readonly initialized: boolean;
2384
- readonly hasDisplayedRegions: boolean;
2385
- readonly scaleBarHeight: number;
2386
- readonly headerHeight: number;
2387
- readonly trackHeights: number;
2388
- readonly trackHeightsWithResizeHandles: number;
2389
- readonly height: number;
2390
- readonly totalBp: number;
2391
- readonly maxBpPerPx: number;
2392
- readonly minBpPerPx: number;
2393
- readonly error: unknown;
2394
- readonly maxOffset: number;
2395
- readonly minOffset: number;
2396
- readonly displayedRegionsTotalPx: number;
2397
- renderProps(): any;
2398
- searchScope(assemblyName: string): {
2399
- assemblyName: string;
2400
- includeAggregateIndexes: boolean;
2401
- tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
2402
- };
2403
- getTrack(id: string): any;
2404
- rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
2405
- rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
2406
- readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
2407
- } & {
2408
- setShowTrackOutlines(arg: boolean): void;
2409
- setColorByCDS(flag: boolean): void;
2410
- setShowCytobands(flag: boolean): void;
2411
- setWidth(newWidth: number): void;
2412
- setError(error: unknown): void;
2413
- setHideHeader(b: boolean): void;
2414
- setHideHeaderOverview(b: boolean): void;
2415
- setHideNoTracksActive(b: boolean): void;
2416
- setShowGridlines(b: boolean): void;
2417
- addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
2418
- setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
2419
- removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
2420
- scrollTo(offsetPx: number): number;
2421
- zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
2422
- setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2423
- setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
2424
- setNewView(bpPerPx: number, offsetPx: number): void;
2425
- horizontallyFlip(): void;
2426
- showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
2427
- hideTrack(trackId: string): number;
2428
- } & {
2429
- moveTrackDown(id: string): void;
2430
- moveTrackUp(id: string): void;
2431
- moveTrackToTop(id: string): void;
2432
- moveTrackToBottom(id: string): void;
2433
- moveTrack(movingId: string, targetId: string): void;
2434
- toggleTrack(trackId: string): boolean;
2435
- setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
2436
- setShowCenterLine(b: boolean): void;
2437
- setDisplayedRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
2438
- activateTrackSelector(): import("@jbrowse/core/util/types").Widget;
2439
- getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
2440
- start: number;
2441
- end: number;
2442
- type: string;
2443
- regionNumber?: number;
2444
- reversed?: boolean;
2445
- refName: string;
2446
- assemblyName: string;
2447
- key: string;
2448
- offsetPx: number;
2449
- widthPx: number;
2450
- variant?: string;
2451
- isLeftEndOfDisplayedRegion?: boolean;
2452
- }[];
2453
- afterDisplayedRegionsSet(cb: () => void): void;
2454
- horizontalScroll(distance: number): number;
2455
- center(): void;
2456
- showAllRegions(): void;
2457
- showAllRegionsInAssembly(assemblyName?: string): void;
2458
- setDraggingTrackId(idx?: string): void;
2459
- setScaleFactor(factor: number): void;
2460
- clearView(): void;
2461
- setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
2462
- exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
2463
- } & {
2464
- slide: (viewWidths: number) => void;
2465
- } & {
2466
- zoom: (targetBpPerPx: number) => void;
2467
- } & {
2468
- readonly canShowCytobands: boolean;
2469
- readonly showCytobands: boolean;
2470
- readonly anyCytobandsExist: boolean;
2471
- readonly cytobandOffset: number;
2472
- } & {
2473
- menuItems(): import("@jbrowse/core/ui").MenuItem[];
2474
- } & {
2475
- readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2476
- readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2477
- readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2478
- readonly visibleLocStrings: string;
2479
- readonly coarseVisibleLocStrings: string;
2480
- } & {
2481
- setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
2482
- } & {
2483
- moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2484
- navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
2485
- navToSearchString({ input, assembly, }: {
2486
- input: string;
2487
- assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
2488
- }): Promise<void>;
2489
- navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
2490
- navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
2491
- navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
2492
- navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
2493
- } & {
2494
- rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
2495
- bpToPx({ refName, coord, regionNumber, }: {
2496
- refName: string;
2497
- coord: number;
2498
- regionNumber?: number;
2499
- }): {
2500
- index: number;
2501
- offsetPx: number;
2502
- } | undefined;
2503
- centerAt(coord: number, refName: string, regionNumber?: number): void;
2504
- pxToBp(px: number): {
2505
- coord: number;
2506
- index: number;
2507
- refName: string;
2508
- oob: boolean;
2509
- assemblyName: string;
2510
- offset: number;
2511
- start: number;
2512
- end: number;
2513
- reversed?: boolean;
2514
- };
2515
- readonly centerLineInfo: {
2516
- coord: number;
2517
- index: number;
2518
- refName: string;
2519
- oob: boolean;
2520
- assemblyName: string;
2521
- offset: number;
2522
- start: number;
2523
- end: number;
2524
- reversed?: boolean;
2525
- } | undefined;
2526
- } & {
2527
- afterCreate(): void;
2528
- afterAttach(): void;
2529
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2530
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2531
- displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
2532
- minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2533
- } & {
2534
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2535
- type: import("mobx-state-tree").IType<string | undefined, string, string>;
2536
- offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2537
- bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2538
- displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util/types").Region[], import("@jbrowse/core/util/types").Region[], import("@jbrowse/core/util/types").Region[]>, [undefined]>;
2539
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
2540
- hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2541
- hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2542
- hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2543
- trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2544
- showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2545
- showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2546
- trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2547
- showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2548
- highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
2549
- colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2550
- showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2551
- init: import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined>;
2552
- }, {
2553
- width: number;
2554
- } & {
2555
- menuItems(): import("@jbrowse/core/ui").MenuItem[];
2556
- } & {
2557
- setDisplayName(name: string): void;
2558
- setWidth(newWidth: number): void;
2559
- setMinimized(flag: boolean): void;
2560
- } & {
2561
- volatileWidth: number | undefined;
2562
- minimumBlockWidth: number;
2563
- draggingTrackId: undefined | string;
2564
- volatileError: unknown;
2565
- afterDisplayedRegionsSetCallbacks: (() => void)[];
2566
- scaleFactor: number;
2567
- trackRefs: Record<string, HTMLDivElement>;
2568
- coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2569
- coarseTotalBp: number;
2570
- leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
2571
- rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
2572
- } & {
2573
- readonly pinnedTracks: any[];
2574
- readonly unpinnedTracks: any[];
2575
- readonly trackLabelsSetting: any;
2576
- readonly width: number;
2577
- readonly interRegionPaddingWidth: number;
2578
- readonly assemblyNames: string[];
2579
- readonly assemblyDisplayNames: string[];
2580
- readonly isTopLevelView: boolean;
2581
- readonly stickyViewHeaders: boolean;
2582
- readonly rubberbandTop: number;
2583
- readonly pinnedTracksTop: number;
2584
- } & {
2585
- scaleBarDisplayPrefix(): string | undefined;
2586
- MiniControlsComponent(): React.FC<any>;
2587
- HeaderComponent(): React.FC<any>;
2588
- readonly assembliesNotFound: string | undefined;
2589
- readonly assemblyErrors: string;
2590
- readonly assembliesInitialized: boolean;
2591
- readonly initialized: boolean;
2592
- readonly hasDisplayedRegions: boolean;
2593
- readonly scaleBarHeight: number;
2594
- readonly headerHeight: number;
2595
- readonly trackHeights: number;
2596
- readonly trackHeightsWithResizeHandles: number;
2597
- readonly height: number;
2598
- readonly totalBp: number;
2599
- readonly maxBpPerPx: number;
2600
- readonly minBpPerPx: number;
2601
- readonly error: unknown;
2602
- readonly maxOffset: number;
2603
- readonly minOffset: number;
2604
- readonly displayedRegionsTotalPx: number;
2605
- renderProps(): any;
2606
- searchScope(assemblyName: string): {
2607
- assemblyName: string;
2608
- includeAggregateIndexes: boolean;
2609
- tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
2610
- };
2611
- getTrack(id: string): any;
2612
- rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
2613
- rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
2614
- readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
2615
- } & {
2616
- setShowTrackOutlines(arg: boolean): void;
2617
- setColorByCDS(flag: boolean): void;
2618
- setShowCytobands(flag: boolean): void;
2619
- setWidth(newWidth: number): void;
2620
- setError(error: unknown): void;
2621
- setHideHeader(b: boolean): void;
2622
- setHideHeaderOverview(b: boolean): void;
2623
- setHideNoTracksActive(b: boolean): void;
2624
- setShowGridlines(b: boolean): void;
2625
- addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
2626
- setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
2627
- removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
2628
- scrollTo(offsetPx: number): number;
2629
- zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
2630
- setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2631
- setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
2632
- setNewView(bpPerPx: number, offsetPx: number): void;
2633
- horizontallyFlip(): void;
2634
- showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
2635
- hideTrack(trackId: string): number;
2636
- } & {
2637
- moveTrackDown(id: string): void;
2638
- moveTrackUp(id: string): void;
2639
- moveTrackToTop(id: string): void;
2640
- moveTrackToBottom(id: string): void;
2641
- moveTrack(movingId: string, targetId: string): void;
2642
- toggleTrack(trackId: string): boolean;
2643
- setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
2644
- setShowCenterLine(b: boolean): void;
2645
- setDisplayedRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
2646
- activateTrackSelector(): import("@jbrowse/core/util/types").Widget;
2647
- getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
2648
- start: number;
2649
- end: number;
2650
- type: string;
2651
- regionNumber?: number;
2652
- reversed?: boolean;
2653
- refName: string;
2654
- assemblyName: string;
2655
- key: string;
2656
- offsetPx: number;
2657
- widthPx: number;
2658
- variant?: string;
2659
- isLeftEndOfDisplayedRegion?: boolean;
2660
- }[];
2661
- afterDisplayedRegionsSet(cb: () => void): void;
2662
- horizontalScroll(distance: number): number;
2663
- center(): void;
2664
- showAllRegions(): void;
2665
- showAllRegionsInAssembly(assemblyName?: string): void;
2666
- setDraggingTrackId(idx?: string): void;
2667
- setScaleFactor(factor: number): void;
2668
- clearView(): void;
2669
- setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
2670
- exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
2671
- } & {
2672
- slide: (viewWidths: number) => void;
2673
- } & {
2674
- zoom: (targetBpPerPx: number) => void;
2675
- } & {
2676
- readonly canShowCytobands: boolean;
2677
- readonly showCytobands: boolean;
2678
- readonly anyCytobandsExist: boolean;
2679
- readonly cytobandOffset: number;
2680
- } & {
2681
- menuItems(): import("@jbrowse/core/ui").MenuItem[];
2682
- } & {
2683
- readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2684
- readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2685
- readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2686
- readonly visibleLocStrings: string;
2687
- readonly coarseVisibleLocStrings: string;
2688
- } & {
2689
- setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
2690
- } & {
2691
- moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2692
- navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
2693
- navToSearchString({ input, assembly, }: {
2694
- input: string;
2695
- assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
2696
- }): Promise<void>;
2697
- navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
2698
- navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
2699
- navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
2700
- navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
2701
- } & {
2702
- rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
2703
- bpToPx({ refName, coord, regionNumber, }: {
2704
- refName: string;
2705
- coord: number;
2706
- regionNumber?: number;
2707
- }): {
2708
- index: number;
2709
- offsetPx: number;
2710
- } | undefined;
2711
- centerAt(coord: number, refName: string, regionNumber?: number): void;
2712
- pxToBp(px: number): {
2713
- coord: number;
2714
- index: number;
2715
- refName: string;
2716
- oob: boolean;
2717
- assemblyName: string;
2718
- offset: number;
2719
- start: number;
2720
- end: number;
2721
- reversed?: boolean;
2722
- };
2723
- readonly centerLineInfo: {
2724
- coord: number;
2725
- index: number;
2726
- refName: string;
2727
- oob: boolean;
2728
- assemblyName: string;
2729
- offset: number;
2730
- start: number;
2731
- end: number;
2732
- reversed?: boolean;
2733
- } | undefined;
2734
- } & {
2735
- afterCreate(): void;
2736
- afterAttach(): void;
2737
- }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
2738
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2739
- displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
2740
- minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2741
- } & {
2742
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2743
- type: import("mobx-state-tree").IType<string | undefined, string, string>;
2744
- offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2745
- bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2746
- displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util/types").Region[], import("@jbrowse/core/util/types").Region[], import("@jbrowse/core/util/types").Region[]>, [undefined]>;
2747
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
2748
- hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2749
- hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2750
- hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2751
- trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2752
- showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2753
- showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2754
- trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2755
- showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2756
- highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType>>, [undefined]>;
2757
- colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2758
- showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2759
- init: import("mobx-state-tree").IType<import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined, import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState | undefined>;
2760
- }>>, {
2761
- type: string;
2762
- id: string;
2763
- displayName: string | undefined;
2764
- tracks: any[];
2765
- minimized: boolean;
2766
- offsetPx: number;
2767
- bpPerPx: number;
2768
- displayedRegions: import("@jbrowse/core/util/types").Region[];
2769
- hideHeader: boolean;
2770
- hideHeaderOverview: boolean;
2771
- hideNoTracksActive: boolean;
2772
- trackSelectorType: string;
2773
- showCenterLine: boolean;
2774
- showCytobandsSetting: boolean;
2775
- trackLabels: string;
2776
- showGridlines: boolean;
2777
- highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[];
2778
- colorByCDS: boolean;
2779
- showTrackOutlines: boolean;
2780
- }>>;
2781
- removeView(): void;
2782
- } & {
2783
- getTrackActionMenuItems(config: any): {
2784
- label: string;
2785
- onClick: () => void;
2786
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
2787
- muiName: string;
2788
- };
2789
- }[];
2790
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
2791
- export type SessionStateModel = ReturnType<typeof sessionModelFactory>;
2792
- export type SessionModel = Instance<SessionStateModel>;