@jbrowse/react-linear-genome-view2 3.6.5 → 4.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (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 +1067 -1134
  10. package/esm/createModel/createModel.js +5 -5
  11. package/esm/createModel/createSessionModel.d.ts +550 -594
  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 +2798 -3007
  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 +11 -3
  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 -6332
  41. package/dist/createModel/createModel.js +0 -118
  42. package/dist/createModel/createSessionModel.d.ts +0 -2767
  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 -16589
  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 -192
  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 -49
  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
@@ -1,2767 +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>>>;
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- minimized: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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- } & {
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- connectionInstances: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
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- 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: {
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- type: string;
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- defaultValue: string;
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- description: string;
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- };
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- assemblyNames: {
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- type: string;
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- defaultValue: never[];
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- description: string;
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- };
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- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
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- }, {
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- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
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- } & {
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- afterAttach(): void;
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- 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> | ({
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- [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: (({
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- [x: string]: any;
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- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
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- [x: string]: any;
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- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
51
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
52
- [x: string]: any;
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- } & 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
- getRefNameColor(refName: string): string | undefined;
106
- isValidRefName(refName: string): boolean;
107
- } & {
108
- setLoaded({ regions, refNameAliases, cytobands, }: {
109
- regions: import("@jbrowse/core/util/types").Region[];
110
- refNameAliases: {
111
- [x: string]: string;
112
- };
113
- cytobands: import("@jbrowse/core/util").Feature[];
114
- }): void;
115
- setError(e: unknown): void;
116
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
117
- setRefNameAliases(aliases: {
118
- [x: string]: string;
119
- }): void;
120
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
121
- setLoadingP(p?: Promise<void>): void;
122
- load(): Promise<void>;
123
- loadPre(): Promise<void>;
124
- } & {
125
- getAdapterMapEntry(adapterConf: {
126
- [x: string]: unknown;
127
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
128
- getRefNameMapForAdapter(adapterConf: {
129
- [x: string]: unknown;
130
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
131
- [x: string]: string;
132
- }>;
133
- getReverseRefNameMapForAdapter(adapterConf: {
134
- [x: string]: unknown;
135
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
136
- [x: string]: string;
137
- }>;
138
- afterCreate(): void;
139
- }, 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<{
140
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
141
- }, {
142
- error: unknown;
143
- loadingP: Promise<void> | undefined;
144
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
145
- refNameAliases: {
146
- [x: string]: string;
147
- } | undefined;
148
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
149
- } & {
150
- getConf(arg: string): any;
151
- readonly lowerCaseRefNameAliases: {
152
- [k: string]: string;
153
- } | undefined;
154
- } & {
155
- readonly initialized: boolean;
156
- readonly name: string;
157
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
158
- readonly aliases: string[];
159
- readonly displayName: string;
160
- hasName(name: string): boolean;
161
- readonly allAliases: string[];
162
- readonly allRefNames: string[] | undefined;
163
- readonly lowerCaseRefNames: string[] | undefined;
164
- readonly allRefNamesWithLowerCase: string[] | undefined;
165
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
166
- readonly refNameColors: string[];
167
- } & {
168
- readonly refNames: string[] | undefined;
169
- } & {
170
- getCanonicalRefName(refName: string): string | undefined;
171
- getRefNameColor(refName: string): string | undefined;
172
- isValidRefName(refName: string): boolean;
173
- } & {
174
- setLoaded({ regions, refNameAliases, cytobands, }: {
175
- regions: import("@jbrowse/core/util/types").Region[];
176
- refNameAliases: {
177
- [x: string]: string;
178
- };
179
- cytobands: import("@jbrowse/core/util").Feature[];
180
- }): void;
181
- setError(e: unknown): void;
182
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
183
- setRefNameAliases(aliases: {
184
- [x: string]: string;
185
- }): void;
186
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
187
- setLoadingP(p?: Promise<void>): void;
188
- load(): Promise<void>;
189
- loadPre(): Promise<void>;
190
- } & {
191
- getAdapterMapEntry(adapterConf: {
192
- [x: string]: unknown;
193
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
194
- getRefNameMapForAdapter(adapterConf: {
195
- [x: string]: unknown;
196
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
197
- [x: string]: string;
198
- }>;
199
- getReverseRefNameMapForAdapter(adapterConf: {
200
- [x: string]: unknown;
201
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
202
- [x: string]: string;
203
- }>;
204
- afterCreate(): void;
205
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
206
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
207
- readonly assemblyNameMap: Record<string, {
208
- configuration: any;
209
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
210
- error: unknown;
211
- loadingP: Promise<void> | undefined;
212
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
213
- refNameAliases: {
214
- [x: string]: string;
215
- } | undefined;
216
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
217
- } & {
218
- getConf(arg: string): any;
219
- readonly lowerCaseRefNameAliases: {
220
- [k: string]: string;
221
- } | undefined;
222
- } & {
223
- readonly initialized: boolean;
224
- readonly name: string;
225
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
226
- readonly aliases: string[];
227
- readonly displayName: string;
228
- hasName(name: string): boolean;
229
- readonly allAliases: string[];
230
- readonly allRefNames: string[] | undefined;
231
- readonly lowerCaseRefNames: string[] | undefined;
232
- readonly allRefNamesWithLowerCase: string[] | undefined;
233
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
234
- readonly refNameColors: string[];
235
- } & {
236
- readonly refNames: string[] | undefined;
237
- } & {
238
- getCanonicalRefName(refName: string): string | undefined;
239
- getRefNameColor(refName: string): string | undefined;
240
- isValidRefName(refName: string): boolean;
241
- } & {
242
- setLoaded({ regions, refNameAliases, cytobands, }: {
243
- regions: import("@jbrowse/core/util/types").Region[];
244
- refNameAliases: {
245
- [x: string]: string;
246
- };
247
- cytobands: import("@jbrowse/core/util").Feature[];
248
- }): void;
249
- setError(e: unknown): void;
250
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
251
- setRefNameAliases(aliases: {
252
- [x: string]: string;
253
- }): void;
254
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
255
- setLoadingP(p?: Promise<void>): void;
256
- load(): Promise<void>;
257
- loadPre(): Promise<void>;
258
- } & {
259
- getAdapterMapEntry(adapterConf: {
260
- [x: string]: unknown;
261
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
262
- getRefNameMapForAdapter(adapterConf: {
263
- [x: string]: unknown;
264
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
265
- [x: string]: string;
266
- }>;
267
- getReverseRefNameMapForAdapter(adapterConf: {
268
- [x: string]: unknown;
269
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
270
- [x: string]: string;
271
- }>;
272
- afterCreate(): void;
273
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
274
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
275
- }, {
276
- error: unknown;
277
- loadingP: Promise<void> | undefined;
278
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
279
- refNameAliases: {
280
- [x: string]: string;
281
- } | undefined;
282
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
283
- } & {
284
- getConf(arg: string): any;
285
- readonly lowerCaseRefNameAliases: {
286
- [k: string]: string;
287
- } | undefined;
288
- } & {
289
- readonly initialized: boolean;
290
- readonly name: string;
291
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
292
- readonly aliases: string[];
293
- readonly displayName: string;
294
- hasName(name: string): boolean;
295
- readonly allAliases: string[];
296
- readonly allRefNames: string[] | undefined;
297
- readonly lowerCaseRefNames: string[] | undefined;
298
- readonly allRefNamesWithLowerCase: string[] | undefined;
299
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
300
- readonly refNameColors: string[];
301
- } & {
302
- readonly refNames: string[] | undefined;
303
- } & {
304
- getCanonicalRefName(refName: string): string | undefined;
305
- getRefNameColor(refName: string): string | undefined;
306
- isValidRefName(refName: string): boolean;
307
- } & {
308
- setLoaded({ regions, refNameAliases, cytobands, }: {
309
- regions: import("@jbrowse/core/util/types").Region[];
310
- refNameAliases: {
311
- [x: string]: string;
312
- };
313
- cytobands: import("@jbrowse/core/util").Feature[];
314
- }): void;
315
- setError(e: unknown): void;
316
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
317
- setRefNameAliases(aliases: {
318
- [x: string]: string;
319
- }): void;
320
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
321
- setLoadingP(p?: Promise<void>): void;
322
- load(): Promise<void>;
323
- loadPre(): Promise<void>;
324
- } & {
325
- getAdapterMapEntry(adapterConf: {
326
- [x: string]: unknown;
327
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
328
- getRefNameMapForAdapter(adapterConf: {
329
- [x: string]: unknown;
330
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
331
- [x: string]: string;
332
- }>;
333
- getReverseRefNameMapForAdapter(adapterConf: {
334
- [x: string]: unknown;
335
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
336
- [x: string]: string;
337
- }>;
338
- afterCreate(): void;
339
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
340
- } & {
341
- getCanonicalAssemblyName(asmName: string): string | undefined;
342
- get(asmName: string): ({
343
- configuration: any;
344
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
345
- error: unknown;
346
- loadingP: Promise<void> | undefined;
347
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
348
- refNameAliases: {
349
- [x: string]: string;
350
- } | undefined;
351
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
352
- } & {
353
- getConf(arg: string): any;
354
- readonly lowerCaseRefNameAliases: {
355
- [k: string]: string;
356
- } | undefined;
357
- } & {
358
- readonly initialized: boolean;
359
- readonly name: string;
360
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
361
- readonly aliases: string[];
362
- readonly displayName: string;
363
- hasName(name: string): boolean;
364
- readonly allAliases: string[];
365
- readonly allRefNames: string[] | undefined;
366
- readonly lowerCaseRefNames: string[] | undefined;
367
- readonly allRefNamesWithLowerCase: string[] | undefined;
368
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
369
- readonly refNameColors: string[];
370
- } & {
371
- readonly refNames: string[] | undefined;
372
- } & {
373
- getCanonicalRefName(refName: string): string | undefined;
374
- getRefNameColor(refName: string): string | undefined;
375
- isValidRefName(refName: string): boolean;
376
- } & {
377
- setLoaded({ regions, refNameAliases, cytobands, }: {
378
- regions: import("@jbrowse/core/util/types").Region[];
379
- refNameAliases: {
380
- [x: string]: string;
381
- };
382
- cytobands: import("@jbrowse/core/util").Feature[];
383
- }): void;
384
- setError(e: unknown): void;
385
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
386
- setRefNameAliases(aliases: {
387
- [x: string]: string;
388
- }): void;
389
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
390
- setLoadingP(p?: Promise<void>): void;
391
- load(): Promise<void>;
392
- loadPre(): Promise<void>;
393
- } & {
394
- getAdapterMapEntry(adapterConf: {
395
- [x: string]: unknown;
396
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
397
- getRefNameMapForAdapter(adapterConf: {
398
- [x: string]: unknown;
399
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
400
- [x: string]: string;
401
- }>;
402
- getReverseRefNameMapForAdapter(adapterConf: {
403
- [x: string]: unknown;
404
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
405
- [x: string]: string;
406
- }>;
407
- afterCreate(): void;
408
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
409
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
410
- }, {
411
- error: unknown;
412
- loadingP: Promise<void> | undefined;
413
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
414
- refNameAliases: {
415
- [x: string]: string;
416
- } | undefined;
417
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
418
- } & {
419
- getConf(arg: string): any;
420
- readonly lowerCaseRefNameAliases: {
421
- [k: string]: string;
422
- } | undefined;
423
- } & {
424
- readonly initialized: boolean;
425
- readonly name: string;
426
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
427
- readonly aliases: string[];
428
- readonly displayName: string;
429
- hasName(name: string): boolean;
430
- readonly allAliases: string[];
431
- readonly allRefNames: string[] | undefined;
432
- readonly lowerCaseRefNames: string[] | undefined;
433
- readonly allRefNamesWithLowerCase: string[] | undefined;
434
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
435
- readonly refNameColors: string[];
436
- } & {
437
- readonly refNames: string[] | undefined;
438
- } & {
439
- getCanonicalRefName(refName: string): string | undefined;
440
- getRefNameColor(refName: string): string | undefined;
441
- isValidRefName(refName: string): boolean;
442
- } & {
443
- setLoaded({ regions, refNameAliases, cytobands, }: {
444
- regions: import("@jbrowse/core/util/types").Region[];
445
- refNameAliases: {
446
- [x: string]: string;
447
- };
448
- cytobands: import("@jbrowse/core/util").Feature[];
449
- }): void;
450
- setError(e: unknown): void;
451
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
452
- setRefNameAliases(aliases: {
453
- [x: string]: string;
454
- }): void;
455
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
456
- setLoadingP(p?: Promise<void>): void;
457
- load(): Promise<void>;
458
- loadPre(): Promise<void>;
459
- } & {
460
- getAdapterMapEntry(adapterConf: {
461
- [x: string]: unknown;
462
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
463
- getRefNameMapForAdapter(adapterConf: {
464
- [x: string]: unknown;
465
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
466
- [x: string]: string;
467
- }>;
468
- getReverseRefNameMapForAdapter(adapterConf: {
469
- [x: string]: unknown;
470
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
471
- [x: string]: string;
472
- }>;
473
- afterCreate(): void;
474
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
475
- readonly assemblyNamesList: any[];
476
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
477
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
478
- } & {
479
- waitForAssembly(assemblyName: string): Promise<({
480
- configuration: any;
481
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
482
- error: unknown;
483
- loadingP: Promise<void> | undefined;
484
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
485
- refNameAliases: {
486
- [x: string]: string;
487
- } | undefined;
488
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
489
- } & {
490
- getConf(arg: string): any;
491
- readonly lowerCaseRefNameAliases: {
492
- [k: string]: string;
493
- } | undefined;
494
- } & {
495
- readonly initialized: boolean;
496
- readonly name: string;
497
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
498
- readonly aliases: string[];
499
- readonly displayName: string;
500
- hasName(name: string): boolean;
501
- readonly allAliases: string[];
502
- readonly allRefNames: string[] | undefined;
503
- readonly lowerCaseRefNames: string[] | undefined;
504
- readonly allRefNamesWithLowerCase: string[] | undefined;
505
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
506
- readonly refNameColors: string[];
507
- } & {
508
- readonly refNames: string[] | undefined;
509
- } & {
510
- getCanonicalRefName(refName: string): string | undefined;
511
- getRefNameColor(refName: string): string | undefined;
512
- isValidRefName(refName: string): boolean;
513
- } & {
514
- setLoaded({ regions, refNameAliases, cytobands, }: {
515
- regions: import("@jbrowse/core/util/types").Region[];
516
- refNameAliases: {
517
- [x: string]: string;
518
- };
519
- cytobands: import("@jbrowse/core/util").Feature[];
520
- }): void;
521
- setError(e: unknown): void;
522
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
523
- setRefNameAliases(aliases: {
524
- [x: string]: string;
525
- }): void;
526
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
527
- setLoadingP(p?: Promise<void>): void;
528
- load(): Promise<void>;
529
- loadPre(): Promise<void>;
530
- } & {
531
- getAdapterMapEntry(adapterConf: {
532
- [x: string]: unknown;
533
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
534
- getRefNameMapForAdapter(adapterConf: {
535
- [x: string]: unknown;
536
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
537
- [x: string]: string;
538
- }>;
539
- getReverseRefNameMapForAdapter(adapterConf: {
540
- [x: string]: unknown;
541
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
542
- [x: string]: string;
543
- }>;
544
- afterCreate(): void;
545
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
546
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
547
- }, {
548
- error: unknown;
549
- loadingP: Promise<void> | undefined;
550
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
551
- refNameAliases: {
552
- [x: string]: string;
553
- } | undefined;
554
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
555
- } & {
556
- getConf(arg: string): any;
557
- readonly lowerCaseRefNameAliases: {
558
- [k: string]: string;
559
- } | undefined;
560
- } & {
561
- readonly initialized: boolean;
562
- readonly name: string;
563
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
564
- readonly aliases: string[];
565
- readonly displayName: string;
566
- hasName(name: string): boolean;
567
- readonly allAliases: string[];
568
- readonly allRefNames: string[] | undefined;
569
- readonly lowerCaseRefNames: string[] | undefined;
570
- readonly allRefNamesWithLowerCase: string[] | undefined;
571
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
572
- readonly refNameColors: string[];
573
- } & {
574
- readonly refNames: string[] | undefined;
575
- } & {
576
- getCanonicalRefName(refName: string): string | undefined;
577
- getRefNameColor(refName: string): string | undefined;
578
- isValidRefName(refName: string): boolean;
579
- } & {
580
- setLoaded({ regions, refNameAliases, cytobands, }: {
581
- regions: import("@jbrowse/core/util/types").Region[];
582
- refNameAliases: {
583
- [x: string]: string;
584
- };
585
- cytobands: import("@jbrowse/core/util").Feature[];
586
- }): void;
587
- setError(e: unknown): void;
588
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
589
- setRefNameAliases(aliases: {
590
- [x: string]: string;
591
- }): void;
592
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
593
- setLoadingP(p?: Promise<void>): void;
594
- load(): Promise<void>;
595
- loadPre(): Promise<void>;
596
- } & {
597
- getAdapterMapEntry(adapterConf: {
598
- [x: string]: unknown;
599
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
600
- getRefNameMapForAdapter(adapterConf: {
601
- [x: string]: unknown;
602
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
603
- [x: string]: string;
604
- }>;
605
- getReverseRefNameMapForAdapter(adapterConf: {
606
- [x: string]: unknown;
607
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
608
- [x: string]: string;
609
- }>;
610
- afterCreate(): void;
611
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
612
- getRefNameMapForAdapter(adapterConf: {
613
- [x: string]: unknown;
614
- }, assemblyName: string | undefined, opts: {
615
- stopToken?: string;
616
- sessionId: string;
617
- }): Promise<{
618
- [x: string]: string;
619
- } | undefined>;
620
- getReverseRefNameMapForAdapter(adapterConf: {
621
- [x: string]: unknown;
622
- }, assemblyName: string | undefined, opts: {
623
- stopToken?: string;
624
- sessionId: string;
625
- }): Promise<{
626
- [x: string]: string;
627
- } | undefined>;
628
- isValidRefName(refName: string, assemblyName: string): boolean;
629
- } & {
630
- afterAttach(): void;
631
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
632
- addAssembly(configuration: any): void;
633
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
634
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
635
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
636
- }, {
637
- error: unknown;
638
- loadingP: Promise<void> | undefined;
639
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
640
- refNameAliases: {
641
- [x: string]: string;
642
- } | undefined;
643
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
644
- } & {
645
- getConf(arg: string): any;
646
- readonly lowerCaseRefNameAliases: {
647
- [k: string]: string;
648
- } | undefined;
649
- } & {
650
- readonly initialized: boolean;
651
- readonly name: string;
652
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
653
- readonly aliases: string[];
654
- readonly displayName: string;
655
- hasName(name: string): boolean;
656
- readonly allAliases: string[];
657
- readonly allRefNames: string[] | undefined;
658
- readonly lowerCaseRefNames: string[] | undefined;
659
- readonly allRefNamesWithLowerCase: string[] | undefined;
660
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
661
- readonly refNameColors: string[];
662
- } & {
663
- readonly refNames: string[] | undefined;
664
- } & {
665
- getCanonicalRefName(refName: string): string | undefined;
666
- getRefNameColor(refName: string): string | undefined;
667
- isValidRefName(refName: string): boolean;
668
- } & {
669
- setLoaded({ regions, refNameAliases, cytobands, }: {
670
- regions: import("@jbrowse/core/util/types").Region[];
671
- refNameAliases: {
672
- [x: string]: string;
673
- };
674
- cytobands: import("@jbrowse/core/util").Feature[];
675
- }): void;
676
- setError(e: unknown): void;
677
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
678
- setRefNameAliases(aliases: {
679
- [x: string]: string;
680
- }): void;
681
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
682
- setLoadingP(p?: Promise<void>): void;
683
- load(): Promise<void>;
684
- loadPre(): Promise<void>;
685
- } & {
686
- getAdapterMapEntry(adapterConf: {
687
- [x: string]: unknown;
688
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
689
- getRefNameMapForAdapter(adapterConf: {
690
- [x: string]: unknown;
691
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
692
- [x: string]: string;
693
- }>;
694
- getReverseRefNameMapForAdapter(adapterConf: {
695
- [x: string]: unknown;
696
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
697
- [x: string]: string;
698
- }>;
699
- afterCreate(): void;
700
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
701
- }, {
702
- readonly assemblyNameMap: Record<string, {
703
- configuration: any;
704
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
705
- error: unknown;
706
- loadingP: Promise<void> | undefined;
707
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
708
- refNameAliases: {
709
- [x: string]: string;
710
- } | undefined;
711
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
712
- } & {
713
- getConf(arg: string): any;
714
- readonly lowerCaseRefNameAliases: {
715
- [k: string]: string;
716
- } | undefined;
717
- } & {
718
- readonly initialized: boolean;
719
- readonly name: string;
720
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
721
- readonly aliases: string[];
722
- readonly displayName: string;
723
- hasName(name: string): boolean;
724
- readonly allAliases: string[];
725
- readonly allRefNames: string[] | undefined;
726
- readonly lowerCaseRefNames: string[] | undefined;
727
- readonly allRefNamesWithLowerCase: string[] | undefined;
728
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
729
- readonly refNameColors: string[];
730
- } & {
731
- readonly refNames: string[] | undefined;
732
- } & {
733
- getCanonicalRefName(refName: string): string | undefined;
734
- getRefNameColor(refName: string): string | undefined;
735
- isValidRefName(refName: string): boolean;
736
- } & {
737
- setLoaded({ regions, refNameAliases, cytobands, }: {
738
- regions: import("@jbrowse/core/util/types").Region[];
739
- refNameAliases: {
740
- [x: string]: string;
741
- };
742
- cytobands: import("@jbrowse/core/util").Feature[];
743
- }): void;
744
- setError(e: unknown): void;
745
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
746
- setRefNameAliases(aliases: {
747
- [x: string]: string;
748
- }): void;
749
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
750
- setLoadingP(p?: Promise<void>): void;
751
- load(): Promise<void>;
752
- loadPre(): Promise<void>;
753
- } & {
754
- getAdapterMapEntry(adapterConf: {
755
- [x: string]: unknown;
756
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
757
- getRefNameMapForAdapter(adapterConf: {
758
- [x: string]: unknown;
759
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
760
- [x: string]: string;
761
- }>;
762
- getReverseRefNameMapForAdapter(adapterConf: {
763
- [x: string]: unknown;
764
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
765
- [x: string]: string;
766
- }>;
767
- afterCreate(): void;
768
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
769
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
770
- }, {
771
- error: unknown;
772
- loadingP: Promise<void> | undefined;
773
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
774
- refNameAliases: {
775
- [x: string]: string;
776
- } | undefined;
777
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
778
- } & {
779
- getConf(arg: string): any;
780
- readonly lowerCaseRefNameAliases: {
781
- [k: string]: string;
782
- } | undefined;
783
- } & {
784
- readonly initialized: boolean;
785
- readonly name: string;
786
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
787
- readonly aliases: string[];
788
- readonly displayName: string;
789
- hasName(name: string): boolean;
790
- readonly allAliases: string[];
791
- readonly allRefNames: string[] | undefined;
792
- readonly lowerCaseRefNames: string[] | undefined;
793
- readonly allRefNamesWithLowerCase: string[] | undefined;
794
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
795
- readonly refNameColors: string[];
796
- } & {
797
- readonly refNames: string[] | undefined;
798
- } & {
799
- getCanonicalRefName(refName: string): string | undefined;
800
- getRefNameColor(refName: string): string | undefined;
801
- isValidRefName(refName: string): boolean;
802
- } & {
803
- setLoaded({ regions, refNameAliases, cytobands, }: {
804
- regions: import("@jbrowse/core/util/types").Region[];
805
- refNameAliases: {
806
- [x: string]: string;
807
- };
808
- cytobands: import("@jbrowse/core/util").Feature[];
809
- }): void;
810
- setError(e: unknown): void;
811
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
812
- setRefNameAliases(aliases: {
813
- [x: string]: string;
814
- }): void;
815
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
816
- setLoadingP(p?: Promise<void>): void;
817
- load(): Promise<void>;
818
- loadPre(): Promise<void>;
819
- } & {
820
- getAdapterMapEntry(adapterConf: {
821
- [x: string]: unknown;
822
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
823
- getRefNameMapForAdapter(adapterConf: {
824
- [x: string]: unknown;
825
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
826
- [x: string]: string;
827
- }>;
828
- getReverseRefNameMapForAdapter(adapterConf: {
829
- [x: string]: unknown;
830
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
831
- [x: string]: string;
832
- }>;
833
- afterCreate(): void;
834
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
835
- } & {
836
- getCanonicalAssemblyName(asmName: string): string | undefined;
837
- get(asmName: string): ({
838
- configuration: any;
839
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
840
- error: unknown;
841
- loadingP: Promise<void> | undefined;
842
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
843
- refNameAliases: {
844
- [x: string]: string;
845
- } | undefined;
846
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
847
- } & {
848
- getConf(arg: string): any;
849
- readonly lowerCaseRefNameAliases: {
850
- [k: string]: string;
851
- } | undefined;
852
- } & {
853
- readonly initialized: boolean;
854
- readonly name: string;
855
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
856
- readonly aliases: string[];
857
- readonly displayName: string;
858
- hasName(name: string): boolean;
859
- readonly allAliases: string[];
860
- readonly allRefNames: string[] | undefined;
861
- readonly lowerCaseRefNames: string[] | undefined;
862
- readonly allRefNamesWithLowerCase: string[] | undefined;
863
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
864
- readonly refNameColors: string[];
865
- } & {
866
- readonly refNames: string[] | undefined;
867
- } & {
868
- getCanonicalRefName(refName: string): string | undefined;
869
- getRefNameColor(refName: string): string | undefined;
870
- isValidRefName(refName: string): boolean;
871
- } & {
872
- setLoaded({ regions, refNameAliases, cytobands, }: {
873
- regions: import("@jbrowse/core/util/types").Region[];
874
- refNameAliases: {
875
- [x: string]: string;
876
- };
877
- cytobands: import("@jbrowse/core/util").Feature[];
878
- }): void;
879
- setError(e: unknown): void;
880
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
881
- setRefNameAliases(aliases: {
882
- [x: string]: string;
883
- }): void;
884
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
885
- setLoadingP(p?: Promise<void>): void;
886
- load(): Promise<void>;
887
- loadPre(): Promise<void>;
888
- } & {
889
- getAdapterMapEntry(adapterConf: {
890
- [x: string]: unknown;
891
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
892
- getRefNameMapForAdapter(adapterConf: {
893
- [x: string]: unknown;
894
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
895
- [x: string]: string;
896
- }>;
897
- getReverseRefNameMapForAdapter(adapterConf: {
898
- [x: string]: unknown;
899
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
900
- [x: string]: string;
901
- }>;
902
- afterCreate(): void;
903
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
904
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
905
- }, {
906
- error: unknown;
907
- loadingP: Promise<void> | undefined;
908
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
909
- refNameAliases: {
910
- [x: string]: string;
911
- } | undefined;
912
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
913
- } & {
914
- getConf(arg: string): any;
915
- readonly lowerCaseRefNameAliases: {
916
- [k: string]: string;
917
- } | undefined;
918
- } & {
919
- readonly initialized: boolean;
920
- readonly name: string;
921
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
922
- readonly aliases: string[];
923
- readonly displayName: string;
924
- hasName(name: string): boolean;
925
- readonly allAliases: string[];
926
- readonly allRefNames: string[] | undefined;
927
- readonly lowerCaseRefNames: string[] | undefined;
928
- readonly allRefNamesWithLowerCase: string[] | undefined;
929
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
930
- readonly refNameColors: string[];
931
- } & {
932
- readonly refNames: string[] | undefined;
933
- } & {
934
- getCanonicalRefName(refName: string): string | undefined;
935
- getRefNameColor(refName: string): string | undefined;
936
- isValidRefName(refName: string): boolean;
937
- } & {
938
- setLoaded({ regions, refNameAliases, cytobands, }: {
939
- regions: import("@jbrowse/core/util/types").Region[];
940
- refNameAliases: {
941
- [x: string]: string;
942
- };
943
- cytobands: import("@jbrowse/core/util").Feature[];
944
- }): void;
945
- setError(e: unknown): void;
946
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
947
- setRefNameAliases(aliases: {
948
- [x: string]: string;
949
- }): void;
950
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
951
- setLoadingP(p?: Promise<void>): void;
952
- load(): Promise<void>;
953
- loadPre(): Promise<void>;
954
- } & {
955
- getAdapterMapEntry(adapterConf: {
956
- [x: string]: unknown;
957
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
958
- getRefNameMapForAdapter(adapterConf: {
959
- [x: string]: unknown;
960
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
961
- [x: string]: string;
962
- }>;
963
- getReverseRefNameMapForAdapter(adapterConf: {
964
- [x: string]: unknown;
965
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
966
- [x: string]: string;
967
- }>;
968
- afterCreate(): void;
969
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
970
- readonly assemblyNamesList: any[];
971
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
972
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
973
- } & {
974
- waitForAssembly(assemblyName: string): Promise<({
975
- configuration: any;
976
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
977
- error: unknown;
978
- loadingP: Promise<void> | undefined;
979
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
980
- refNameAliases: {
981
- [x: string]: string;
982
- } | undefined;
983
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
984
- } & {
985
- getConf(arg: string): any;
986
- readonly lowerCaseRefNameAliases: {
987
- [k: string]: string;
988
- } | undefined;
989
- } & {
990
- readonly initialized: boolean;
991
- readonly name: string;
992
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
993
- readonly aliases: string[];
994
- readonly displayName: string;
995
- hasName(name: string): boolean;
996
- readonly allAliases: string[];
997
- readonly allRefNames: string[] | undefined;
998
- readonly lowerCaseRefNames: string[] | undefined;
999
- readonly allRefNamesWithLowerCase: string[] | undefined;
1000
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1001
- readonly refNameColors: string[];
1002
- } & {
1003
- readonly refNames: string[] | undefined;
1004
- } & {
1005
- getCanonicalRefName(refName: string): string | undefined;
1006
- getRefNameColor(refName: string): string | undefined;
1007
- isValidRefName(refName: string): boolean;
1008
- } & {
1009
- setLoaded({ regions, refNameAliases, cytobands, }: {
1010
- regions: import("@jbrowse/core/util/types").Region[];
1011
- refNameAliases: {
1012
- [x: string]: string;
1013
- };
1014
- cytobands: import("@jbrowse/core/util").Feature[];
1015
- }): void;
1016
- setError(e: unknown): void;
1017
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1018
- setRefNameAliases(aliases: {
1019
- [x: string]: string;
1020
- }): void;
1021
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1022
- setLoadingP(p?: Promise<void>): void;
1023
- load(): Promise<void>;
1024
- loadPre(): Promise<void>;
1025
- } & {
1026
- getAdapterMapEntry(adapterConf: {
1027
- [x: string]: unknown;
1028
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1029
- getRefNameMapForAdapter(adapterConf: {
1030
- [x: string]: unknown;
1031
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1032
- [x: string]: string;
1033
- }>;
1034
- getReverseRefNameMapForAdapter(adapterConf: {
1035
- [x: string]: unknown;
1036
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1037
- [x: string]: string;
1038
- }>;
1039
- afterCreate(): void;
1040
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1041
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1042
- }, {
1043
- error: unknown;
1044
- loadingP: Promise<void> | undefined;
1045
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1046
- refNameAliases: {
1047
- [x: string]: string;
1048
- } | undefined;
1049
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1050
- } & {
1051
- getConf(arg: string): any;
1052
- readonly lowerCaseRefNameAliases: {
1053
- [k: string]: string;
1054
- } | undefined;
1055
- } & {
1056
- readonly initialized: boolean;
1057
- readonly name: string;
1058
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1059
- readonly aliases: string[];
1060
- readonly displayName: string;
1061
- hasName(name: string): boolean;
1062
- readonly allAliases: string[];
1063
- readonly allRefNames: string[] | undefined;
1064
- readonly lowerCaseRefNames: string[] | undefined;
1065
- readonly allRefNamesWithLowerCase: string[] | undefined;
1066
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1067
- readonly refNameColors: string[];
1068
- } & {
1069
- readonly refNames: string[] | undefined;
1070
- } & {
1071
- getCanonicalRefName(refName: string): string | undefined;
1072
- getRefNameColor(refName: string): string | undefined;
1073
- isValidRefName(refName: string): boolean;
1074
- } & {
1075
- setLoaded({ regions, refNameAliases, cytobands, }: {
1076
- regions: import("@jbrowse/core/util/types").Region[];
1077
- refNameAliases: {
1078
- [x: string]: string;
1079
- };
1080
- cytobands: import("@jbrowse/core/util").Feature[];
1081
- }): void;
1082
- setError(e: unknown): void;
1083
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1084
- setRefNameAliases(aliases: {
1085
- [x: string]: string;
1086
- }): void;
1087
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1088
- setLoadingP(p?: Promise<void>): void;
1089
- load(): Promise<void>;
1090
- loadPre(): Promise<void>;
1091
- } & {
1092
- getAdapterMapEntry(adapterConf: {
1093
- [x: string]: unknown;
1094
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1095
- getRefNameMapForAdapter(adapterConf: {
1096
- [x: string]: unknown;
1097
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1098
- [x: string]: string;
1099
- }>;
1100
- getReverseRefNameMapForAdapter(adapterConf: {
1101
- [x: string]: unknown;
1102
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1103
- [x: string]: string;
1104
- }>;
1105
- afterCreate(): void;
1106
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1107
- getRefNameMapForAdapter(adapterConf: {
1108
- [x: string]: unknown;
1109
- }, assemblyName: string | undefined, opts: {
1110
- stopToken?: string;
1111
- sessionId: string;
1112
- }): Promise<{
1113
- [x: string]: string;
1114
- } | undefined>;
1115
- getReverseRefNameMapForAdapter(adapterConf: {
1116
- [x: string]: unknown;
1117
- }, assemblyName: string | undefined, opts: {
1118
- stopToken?: string;
1119
- sessionId: string;
1120
- }): Promise<{
1121
- [x: string]: string;
1122
- } | undefined>;
1123
- isValidRefName(refName: string, assemblyName: string): boolean;
1124
- } & {
1125
- afterAttach(): void;
1126
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1127
- addAssembly(configuration: any): void;
1128
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
1129
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1130
- rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1131
- adminMode: boolean;
1132
- error: unknown;
1133
- textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1134
- pluginManager: PluginManager;
1135
- } & {
1136
- setError(error: unknown): void;
1137
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1138
- setDefaultSession(): void;
1139
- setSessionPath(path: string): void;
1140
- renameCurrentSession(newName: string): void;
1141
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1142
- jbrowse: import("mobx-state-tree").IAnyType;
1143
- session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
1144
- sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1145
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1146
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1147
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1148
- }, {
1149
- error: unknown;
1150
- loadingP: Promise<void> | undefined;
1151
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1152
- refNameAliases: {
1153
- [x: string]: string;
1154
- } | undefined;
1155
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1156
- } & {
1157
- getConf(arg: string): any;
1158
- readonly lowerCaseRefNameAliases: {
1159
- [k: string]: string;
1160
- } | undefined;
1161
- } & {
1162
- readonly initialized: boolean;
1163
- readonly name: string;
1164
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1165
- readonly aliases: string[];
1166
- readonly displayName: string;
1167
- hasName(name: string): boolean;
1168
- readonly allAliases: string[];
1169
- readonly allRefNames: string[] | undefined;
1170
- readonly lowerCaseRefNames: string[] | undefined;
1171
- readonly allRefNamesWithLowerCase: string[] | undefined;
1172
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1173
- readonly refNameColors: string[];
1174
- } & {
1175
- readonly refNames: string[] | undefined;
1176
- } & {
1177
- getCanonicalRefName(refName: string): string | undefined;
1178
- getRefNameColor(refName: string): string | undefined;
1179
- isValidRefName(refName: string): boolean;
1180
- } & {
1181
- setLoaded({ regions, refNameAliases, cytobands, }: {
1182
- regions: import("@jbrowse/core/util/types").Region[];
1183
- refNameAliases: {
1184
- [x: string]: string;
1185
- };
1186
- cytobands: import("@jbrowse/core/util").Feature[];
1187
- }): void;
1188
- setError(e: unknown): void;
1189
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1190
- setRefNameAliases(aliases: {
1191
- [x: string]: string;
1192
- }): void;
1193
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1194
- setLoadingP(p?: Promise<void>): void;
1195
- load(): Promise<void>;
1196
- loadPre(): Promise<void>;
1197
- } & {
1198
- getAdapterMapEntry(adapterConf: {
1199
- [x: string]: unknown;
1200
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1201
- getRefNameMapForAdapter(adapterConf: {
1202
- [x: string]: unknown;
1203
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1204
- [x: string]: string;
1205
- }>;
1206
- getReverseRefNameMapForAdapter(adapterConf: {
1207
- [x: string]: unknown;
1208
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1209
- [x: string]: string;
1210
- }>;
1211
- afterCreate(): void;
1212
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1213
- }, {
1214
- readonly assemblyNameMap: Record<string, {
1215
- configuration: any;
1216
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1217
- error: unknown;
1218
- loadingP: Promise<void> | undefined;
1219
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1220
- refNameAliases: {
1221
- [x: string]: string;
1222
- } | undefined;
1223
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1224
- } & {
1225
- getConf(arg: string): any;
1226
- readonly lowerCaseRefNameAliases: {
1227
- [k: string]: string;
1228
- } | undefined;
1229
- } & {
1230
- readonly initialized: boolean;
1231
- readonly name: string;
1232
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1233
- readonly aliases: string[];
1234
- readonly displayName: string;
1235
- hasName(name: string): boolean;
1236
- readonly allAliases: string[];
1237
- readonly allRefNames: string[] | undefined;
1238
- readonly lowerCaseRefNames: string[] | undefined;
1239
- readonly allRefNamesWithLowerCase: string[] | undefined;
1240
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1241
- readonly refNameColors: string[];
1242
- } & {
1243
- readonly refNames: string[] | undefined;
1244
- } & {
1245
- getCanonicalRefName(refName: string): string | undefined;
1246
- getRefNameColor(refName: string): string | undefined;
1247
- isValidRefName(refName: string): boolean;
1248
- } & {
1249
- setLoaded({ regions, refNameAliases, cytobands, }: {
1250
- regions: import("@jbrowse/core/util/types").Region[];
1251
- refNameAliases: {
1252
- [x: string]: string;
1253
- };
1254
- cytobands: import("@jbrowse/core/util").Feature[];
1255
- }): void;
1256
- setError(e: unknown): void;
1257
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1258
- setRefNameAliases(aliases: {
1259
- [x: string]: string;
1260
- }): void;
1261
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1262
- setLoadingP(p?: Promise<void>): void;
1263
- load(): Promise<void>;
1264
- loadPre(): Promise<void>;
1265
- } & {
1266
- getAdapterMapEntry(adapterConf: {
1267
- [x: string]: unknown;
1268
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1269
- getRefNameMapForAdapter(adapterConf: {
1270
- [x: string]: unknown;
1271
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1272
- [x: string]: string;
1273
- }>;
1274
- getReverseRefNameMapForAdapter(adapterConf: {
1275
- [x: string]: unknown;
1276
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1277
- [x: string]: string;
1278
- }>;
1279
- afterCreate(): void;
1280
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1281
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1282
- }, {
1283
- error: unknown;
1284
- loadingP: Promise<void> | undefined;
1285
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1286
- refNameAliases: {
1287
- [x: string]: string;
1288
- } | undefined;
1289
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1290
- } & {
1291
- getConf(arg: string): any;
1292
- readonly lowerCaseRefNameAliases: {
1293
- [k: string]: string;
1294
- } | undefined;
1295
- } & {
1296
- readonly initialized: boolean;
1297
- readonly name: string;
1298
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1299
- readonly aliases: string[];
1300
- readonly displayName: string;
1301
- hasName(name: string): boolean;
1302
- readonly allAliases: string[];
1303
- readonly allRefNames: string[] | undefined;
1304
- readonly lowerCaseRefNames: string[] | undefined;
1305
- readonly allRefNamesWithLowerCase: string[] | undefined;
1306
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1307
- readonly refNameColors: string[];
1308
- } & {
1309
- readonly refNames: string[] | undefined;
1310
- } & {
1311
- getCanonicalRefName(refName: string): string | undefined;
1312
- getRefNameColor(refName: string): string | undefined;
1313
- isValidRefName(refName: string): boolean;
1314
- } & {
1315
- setLoaded({ regions, refNameAliases, cytobands, }: {
1316
- regions: import("@jbrowse/core/util/types").Region[];
1317
- refNameAliases: {
1318
- [x: string]: string;
1319
- };
1320
- cytobands: import("@jbrowse/core/util").Feature[];
1321
- }): void;
1322
- setError(e: unknown): void;
1323
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1324
- setRefNameAliases(aliases: {
1325
- [x: string]: string;
1326
- }): void;
1327
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1328
- setLoadingP(p?: Promise<void>): void;
1329
- load(): Promise<void>;
1330
- loadPre(): Promise<void>;
1331
- } & {
1332
- getAdapterMapEntry(adapterConf: {
1333
- [x: string]: unknown;
1334
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1335
- getRefNameMapForAdapter(adapterConf: {
1336
- [x: string]: unknown;
1337
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1338
- [x: string]: string;
1339
- }>;
1340
- getReverseRefNameMapForAdapter(adapterConf: {
1341
- [x: string]: unknown;
1342
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1343
- [x: string]: string;
1344
- }>;
1345
- afterCreate(): void;
1346
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
1347
- } & {
1348
- getCanonicalAssemblyName(asmName: string): string | undefined;
1349
- get(asmName: string): ({
1350
- configuration: any;
1351
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1352
- error: unknown;
1353
- loadingP: Promise<void> | undefined;
1354
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1355
- refNameAliases: {
1356
- [x: string]: string;
1357
- } | undefined;
1358
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1359
- } & {
1360
- getConf(arg: string): any;
1361
- readonly lowerCaseRefNameAliases: {
1362
- [k: string]: string;
1363
- } | undefined;
1364
- } & {
1365
- readonly initialized: boolean;
1366
- readonly name: string;
1367
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1368
- readonly aliases: string[];
1369
- readonly displayName: string;
1370
- hasName(name: string): boolean;
1371
- readonly allAliases: string[];
1372
- readonly allRefNames: string[] | undefined;
1373
- readonly lowerCaseRefNames: string[] | undefined;
1374
- readonly allRefNamesWithLowerCase: string[] | undefined;
1375
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1376
- readonly refNameColors: string[];
1377
- } & {
1378
- readonly refNames: string[] | undefined;
1379
- } & {
1380
- getCanonicalRefName(refName: string): string | undefined;
1381
- getRefNameColor(refName: string): string | undefined;
1382
- isValidRefName(refName: string): boolean;
1383
- } & {
1384
- setLoaded({ regions, refNameAliases, cytobands, }: {
1385
- regions: import("@jbrowse/core/util/types").Region[];
1386
- refNameAliases: {
1387
- [x: string]: string;
1388
- };
1389
- cytobands: import("@jbrowse/core/util").Feature[];
1390
- }): void;
1391
- setError(e: unknown): void;
1392
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1393
- setRefNameAliases(aliases: {
1394
- [x: string]: string;
1395
- }): void;
1396
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1397
- setLoadingP(p?: Promise<void>): void;
1398
- load(): Promise<void>;
1399
- loadPre(): Promise<void>;
1400
- } & {
1401
- getAdapterMapEntry(adapterConf: {
1402
- [x: string]: unknown;
1403
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1404
- getRefNameMapForAdapter(adapterConf: {
1405
- [x: string]: unknown;
1406
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1407
- [x: string]: string;
1408
- }>;
1409
- getReverseRefNameMapForAdapter(adapterConf: {
1410
- [x: string]: unknown;
1411
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1412
- [x: string]: string;
1413
- }>;
1414
- afterCreate(): void;
1415
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1416
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1417
- }, {
1418
- error: unknown;
1419
- loadingP: Promise<void> | undefined;
1420
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1421
- refNameAliases: {
1422
- [x: string]: string;
1423
- } | undefined;
1424
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1425
- } & {
1426
- getConf(arg: string): any;
1427
- readonly lowerCaseRefNameAliases: {
1428
- [k: string]: string;
1429
- } | undefined;
1430
- } & {
1431
- readonly initialized: boolean;
1432
- readonly name: string;
1433
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1434
- readonly aliases: string[];
1435
- readonly displayName: string;
1436
- hasName(name: string): boolean;
1437
- readonly allAliases: string[];
1438
- readonly allRefNames: string[] | undefined;
1439
- readonly lowerCaseRefNames: string[] | undefined;
1440
- readonly allRefNamesWithLowerCase: string[] | undefined;
1441
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1442
- readonly refNameColors: string[];
1443
- } & {
1444
- readonly refNames: string[] | undefined;
1445
- } & {
1446
- getCanonicalRefName(refName: string): string | undefined;
1447
- getRefNameColor(refName: string): string | undefined;
1448
- isValidRefName(refName: string): boolean;
1449
- } & {
1450
- setLoaded({ regions, refNameAliases, cytobands, }: {
1451
- regions: import("@jbrowse/core/util/types").Region[];
1452
- refNameAliases: {
1453
- [x: string]: string;
1454
- };
1455
- cytobands: import("@jbrowse/core/util").Feature[];
1456
- }): void;
1457
- setError(e: unknown): void;
1458
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1459
- setRefNameAliases(aliases: {
1460
- [x: string]: string;
1461
- }): void;
1462
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1463
- setLoadingP(p?: Promise<void>): void;
1464
- load(): Promise<void>;
1465
- loadPre(): Promise<void>;
1466
- } & {
1467
- getAdapterMapEntry(adapterConf: {
1468
- [x: string]: unknown;
1469
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1470
- getRefNameMapForAdapter(adapterConf: {
1471
- [x: string]: unknown;
1472
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1473
- [x: string]: string;
1474
- }>;
1475
- getReverseRefNameMapForAdapter(adapterConf: {
1476
- [x: string]: unknown;
1477
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1478
- [x: string]: string;
1479
- }>;
1480
- afterCreate(): void;
1481
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1482
- readonly assemblyNamesList: any[];
1483
- readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1484
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1485
- } & {
1486
- waitForAssembly(assemblyName: string): Promise<({
1487
- configuration: any;
1488
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1489
- error: unknown;
1490
- loadingP: Promise<void> | undefined;
1491
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1492
- refNameAliases: {
1493
- [x: string]: string;
1494
- } | undefined;
1495
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1496
- } & {
1497
- getConf(arg: string): any;
1498
- readonly lowerCaseRefNameAliases: {
1499
- [k: string]: string;
1500
- } | undefined;
1501
- } & {
1502
- readonly initialized: boolean;
1503
- readonly name: string;
1504
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1505
- readonly aliases: string[];
1506
- readonly displayName: string;
1507
- hasName(name: string): boolean;
1508
- readonly allAliases: string[];
1509
- readonly allRefNames: string[] | undefined;
1510
- readonly lowerCaseRefNames: string[] | undefined;
1511
- readonly allRefNamesWithLowerCase: string[] | undefined;
1512
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1513
- readonly refNameColors: string[];
1514
- } & {
1515
- readonly refNames: string[] | undefined;
1516
- } & {
1517
- getCanonicalRefName(refName: string): string | undefined;
1518
- getRefNameColor(refName: string): string | undefined;
1519
- isValidRefName(refName: string): boolean;
1520
- } & {
1521
- setLoaded({ regions, refNameAliases, cytobands, }: {
1522
- regions: import("@jbrowse/core/util/types").Region[];
1523
- refNameAliases: {
1524
- [x: string]: string;
1525
- };
1526
- cytobands: import("@jbrowse/core/util").Feature[];
1527
- }): void;
1528
- setError(e: unknown): void;
1529
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1530
- setRefNameAliases(aliases: {
1531
- [x: string]: string;
1532
- }): void;
1533
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1534
- setLoadingP(p?: Promise<void>): void;
1535
- load(): Promise<void>;
1536
- loadPre(): Promise<void>;
1537
- } & {
1538
- getAdapterMapEntry(adapterConf: {
1539
- [x: string]: unknown;
1540
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1541
- getRefNameMapForAdapter(adapterConf: {
1542
- [x: string]: unknown;
1543
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1544
- [x: string]: string;
1545
- }>;
1546
- getReverseRefNameMapForAdapter(adapterConf: {
1547
- [x: string]: unknown;
1548
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1549
- [x: string]: string;
1550
- }>;
1551
- afterCreate(): void;
1552
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1553
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1554
- }, {
1555
- error: unknown;
1556
- loadingP: Promise<void> | undefined;
1557
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1558
- refNameAliases: {
1559
- [x: string]: string;
1560
- } | undefined;
1561
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1562
- } & {
1563
- getConf(arg: string): any;
1564
- readonly lowerCaseRefNameAliases: {
1565
- [k: string]: string;
1566
- } | undefined;
1567
- } & {
1568
- readonly initialized: boolean;
1569
- readonly name: string;
1570
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1571
- readonly aliases: string[];
1572
- readonly displayName: string;
1573
- hasName(name: string): boolean;
1574
- readonly allAliases: string[];
1575
- readonly allRefNames: string[] | undefined;
1576
- readonly lowerCaseRefNames: string[] | undefined;
1577
- readonly allRefNamesWithLowerCase: string[] | undefined;
1578
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1579
- readonly refNameColors: string[];
1580
- } & {
1581
- readonly refNames: string[] | undefined;
1582
- } & {
1583
- getCanonicalRefName(refName: string): string | undefined;
1584
- getRefNameColor(refName: string): string | undefined;
1585
- isValidRefName(refName: string): boolean;
1586
- } & {
1587
- setLoaded({ regions, refNameAliases, cytobands, }: {
1588
- regions: import("@jbrowse/core/util/types").Region[];
1589
- refNameAliases: {
1590
- [x: string]: string;
1591
- };
1592
- cytobands: import("@jbrowse/core/util").Feature[];
1593
- }): void;
1594
- setError(e: unknown): void;
1595
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1596
- setRefNameAliases(aliases: {
1597
- [x: string]: string;
1598
- }): void;
1599
- setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1600
- setLoadingP(p?: Promise<void>): void;
1601
- load(): Promise<void>;
1602
- loadPre(): Promise<void>;
1603
- } & {
1604
- getAdapterMapEntry(adapterConf: {
1605
- [x: string]: unknown;
1606
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1607
- getRefNameMapForAdapter(adapterConf: {
1608
- [x: string]: unknown;
1609
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1610
- [x: string]: string;
1611
- }>;
1612
- getReverseRefNameMapForAdapter(adapterConf: {
1613
- [x: string]: unknown;
1614
- }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1615
- [x: string]: string;
1616
- }>;
1617
- afterCreate(): void;
1618
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1619
- getRefNameMapForAdapter(adapterConf: {
1620
- [x: string]: unknown;
1621
- }, assemblyName: string | undefined, opts: {
1622
- stopToken?: string;
1623
- sessionId: string;
1624
- }): Promise<{
1625
- [x: string]: string;
1626
- } | undefined>;
1627
- getReverseRefNameMapForAdapter(adapterConf: {
1628
- [x: string]: unknown;
1629
- }, assemblyName: string | undefined, opts: {
1630
- stopToken?: string;
1631
- sessionId: string;
1632
- }): Promise<{
1633
- [x: string]: string;
1634
- } | undefined>;
1635
- isValidRefName(refName: string, assemblyName: string): boolean;
1636
- } & {
1637
- afterAttach(): void;
1638
- removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1639
- addAssembly(configuration: any): void;
1640
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
1641
- }, {
1642
- rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1643
- adminMode: boolean;
1644
- error: unknown;
1645
- textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1646
- pluginManager: PluginManager;
1647
- } & {
1648
- setError(error: unknown): void;
1649
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1650
- setDefaultSession(): void;
1651
- setSessionPath(path: string): void;
1652
- renameCurrentSession(newName: string): void;
1653
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1654
- } & {
1655
- readonly jbrowse: any;
1656
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1657
- readonly configuration: {
1658
- [x: string]: any;
1659
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1660
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1661
- [x: string]: any;
1662
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1663
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1664
- [x: string]: any;
1665
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1666
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1667
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1668
- readonly adminMode: boolean;
1669
- readonly textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1670
- } & {
1671
- readonly assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
1672
- } & {
1673
- setSelection(thing: unknown): void;
1674
- clearSelection(): void;
1675
- setHovered(thing: unknown): void;
1676
- } & {
1677
- readonly visibleWidget: any;
1678
- } & {
1679
- setDrawerPosition(arg: string): void;
1680
- updateDrawerWidth(drawerWidth: number): number;
1681
- resizeDrawer(distance: number): number;
1682
- addWidget(typeName: string, id: string, initialState?: {}, conf?: unknown): any;
1683
- showWidget(widget: any): void;
1684
- hasWidget(widget: any): boolean;
1685
- hideWidget(widget: any): void;
1686
- minimizeWidgetDrawer(): void;
1687
- showWidgetDrawer(): void;
1688
- hideAllWidgets(): void;
1689
- editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1690
- afterAttach(): void;
1691
- } & {
1692
- readonly connections: import("@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig").BaseConnectionConfigModel[];
1693
- } & {
1694
- makeConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: {}): ({
1695
- name: string;
1696
- 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>>;
1697
- configuration: {
1698
- [x: string]: any;
1699
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1700
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1701
- [x: string]: any;
1702
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1703
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1704
- [x: string]: any;
1705
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1706
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1707
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1708
- name: {
1709
- type: string;
1710
- defaultValue: string;
1711
- description: string;
1712
- };
1713
- assemblyNames: {
1714
- type: string;
1715
- defaultValue: never[];
1716
- description: string;
1717
- };
1718
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>;
1719
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1720
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1721
- } & {
1722
- afterAttach(): void;
1723
- addTrackConf(trackConf: ({
1724
- [x: string]: any;
1725
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1726
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1727
- [x: string]: any;
1728
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1729
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1730
- [x: string]: any;
1731
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1732
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1733
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
1734
- addTrackConfs(trackConfs: (({
1735
- [x: string]: any;
1736
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1737
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1738
- [x: string]: any;
1739
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1740
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1741
- [x: string]: any;
1742
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1743
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1744
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
1745
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
1746
- clear(): void;
1747
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1748
- name: import("mobx-state-tree").ISimpleType<string>;
1749
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
1750
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1751
- name: {
1752
- type: string;
1753
- defaultValue: string;
1754
- description: string;
1755
- };
1756
- assemblyNames: {
1757
- type: string;
1758
- defaultValue: never[];
1759
- description: string;
1760
- };
1761
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
1762
- }, {
1763
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1764
- } & {
1765
- afterAttach(): void;
1766
- addTrackConf(trackConf: ({
1767
- [x: string]: any;
1768
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1769
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1770
- [x: string]: any;
1771
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1772
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1773
- [x: string]: any;
1774
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1775
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1776
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
1777
- addTrackConfs(trackConfs: (({
1778
- [x: string]: any;
1779
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1780
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1781
- [x: string]: any;
1782
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1783
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1784
- [x: string]: any;
1785
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1786
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1787
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
1788
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
1789
- clear(): void;
1790
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1791
- prepareToBreakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): (Record<string, number> | (() => void))[] | undefined;
1792
- breakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1793
- deleteConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1794
- addConnectionConf(connectionConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1795
- clearConnections(): void;
1796
- } & {
1797
- queueOfDialogs: [import("@jbrowse/core/util/types").DialogComponentType, unknown][];
1798
- } & {
1799
- readonly DialogComponent: import("@jbrowse/core/util/types").DialogComponentType | undefined;
1800
- readonly DialogProps: unknown;
1801
- } & {
1802
- removeActiveDialog(): void;
1803
- queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util/types").DialogComponentType, unknown]): void;
1804
- } & {
1805
- getReferring(object: import("mobx-state-tree").IAnyStateTreeNode): import("@jbrowse/product-core").ReferringNode[];
1806
- } & {
1807
- removeReferring(referring: import("@jbrowse/product-core").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
1808
- } & {
1809
- readonly tracks: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1810
- } & {
1811
- addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfiguration): any;
1812
- deleteTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1813
- } & {
1814
- readonly tracks: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1815
- } & {
1816
- addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfiguration): any;
1817
- deleteTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1818
- } & {
1819
- snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1820
- } & {
1821
- readonly snackbarMessageSet: Map<string, import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1822
- } & {
1823
- notify(message: string, level?: import("@jbrowse/core/util/types").NotificationLevel, action?: import("@jbrowse/core/util/types").SnackAction): void;
1824
- notifyError(errorMessage: string, error?: unknown, extra?: unknown): void;
1825
- pushSnackbarMessage(message: string, level?: import("@jbrowse/core/util/types").NotificationLevel, action?: import("@jbrowse/core/util/types").SnackAction): void;
1826
- popSnackbarMessage(): import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage | undefined;
1827
- removeSnackbarMessage(message: string): void;
1828
- } & {
1829
- readonly version: any;
1830
- readonly disableAddTracks: any;
1831
- readonly assemblies: any[];
1832
- readonly assemblyNames: any[];
1833
- readonly connections: any;
1834
- readonly assemblyManager: any;
1835
- readonly views: ({
1836
- id: string;
1837
- displayName: string | undefined;
1838
- minimized: boolean;
1839
- type: string;
1840
- offsetPx: number;
1841
- bpPerPx: number;
1842
- 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]>>;
1843
- 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>>;
1844
- hideHeader: boolean;
1845
- hideHeaderOverview: boolean;
1846
- hideNoTracksActive: boolean;
1847
- trackSelectorType: string;
1848
- showCenterLine: boolean;
1849
- showCytobandsSetting: boolean;
1850
- trackLabels: string;
1851
- showGridlines: boolean;
1852
- 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]>>;
1853
- colorByCDS: boolean;
1854
- showTrackOutlines: boolean;
1855
- 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;
1856
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1857
- width: number;
1858
- } & {
1859
- menuItems(): import("@jbrowse/core/ui").MenuItem[];
1860
- } & {
1861
- setDisplayName(name: string): void;
1862
- setWidth(newWidth: number): void;
1863
- setMinimized(flag: boolean): void;
1864
- } & {
1865
- volatileWidth: number | undefined;
1866
- minimumBlockWidth: number;
1867
- draggingTrackId: undefined | string;
1868
- volatileError: unknown;
1869
- afterDisplayedRegionsSetCallbacks: (() => void)[];
1870
- scaleFactor: number;
1871
- trackRefs: Record<string, HTMLDivElement>;
1872
- coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
1873
- coarseTotalBp: number;
1874
- leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
1875
- rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
1876
- } & {
1877
- readonly pinnedTracks: any[];
1878
- readonly unpinnedTracks: any[];
1879
- readonly trackLabelsSetting: any;
1880
- readonly width: number;
1881
- readonly interRegionPaddingWidth: number;
1882
- readonly assemblyNames: string[];
1883
- readonly assemblyDisplayNames: string[];
1884
- readonly isTopLevelView: boolean;
1885
- readonly stickyViewHeaders: boolean;
1886
- readonly rubberbandTop: number;
1887
- readonly pinnedTracksTop: number;
1888
- } & {
1889
- scaleBarDisplayPrefix(): string | undefined;
1890
- MiniControlsComponent(): React.FC<any>;
1891
- HeaderComponent(): React.FC<any>;
1892
- readonly assembliesNotFound: string | undefined;
1893
- readonly assemblyErrors: string;
1894
- readonly assembliesInitialized: boolean;
1895
- readonly initialized: boolean;
1896
- readonly hasDisplayedRegions: boolean;
1897
- readonly scaleBarHeight: number;
1898
- readonly headerHeight: number;
1899
- readonly trackHeights: number;
1900
- readonly trackHeightsWithResizeHandles: number;
1901
- readonly height: number;
1902
- readonly totalBp: number;
1903
- readonly maxBpPerPx: number;
1904
- readonly minBpPerPx: number;
1905
- readonly error: unknown;
1906
- readonly maxOffset: number;
1907
- readonly minOffset: number;
1908
- readonly displayedRegionsTotalPx: number;
1909
- renderProps(): any;
1910
- searchScope(assemblyName: string): {
1911
- assemblyName: string;
1912
- includeAggregateIndexes: boolean;
1913
- 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>>;
1914
- };
1915
- getTrack(id: string): any;
1916
- rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
1917
- rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
1918
- readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
1919
- } & {
1920
- setShowTrackOutlines(arg: boolean): void;
1921
- setColorByCDS(flag: boolean): void;
1922
- setShowCytobands(flag: boolean): void;
1923
- setWidth(newWidth: number): void;
1924
- setError(error: unknown): void;
1925
- setHideHeader(b: boolean): void;
1926
- setHideHeaderOverview(b: boolean): void;
1927
- setHideNoTracksActive(b: boolean): void;
1928
- setShowGridlines(b: boolean): void;
1929
- addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
1930
- setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
1931
- removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
1932
- scrollTo(offsetPx: number): number;
1933
- zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
1934
- setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
1935
- setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
1936
- setNewView(bpPerPx: number, offsetPx: number): void;
1937
- horizontallyFlip(): void;
1938
- showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
1939
- hideTrack(trackId: string): number;
1940
- } & {
1941
- moveTrackDown(id: string): void;
1942
- moveTrackUp(id: string): void;
1943
- moveTrackToTop(id: string): void;
1944
- moveTrackToBottom(id: string): void;
1945
- moveTrack(movingId: string, targetId: string): void;
1946
- toggleTrack(trackId: string): boolean;
1947
- setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
1948
- setShowCenterLine(b: boolean): void;
1949
- setDisplayedRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1950
- activateTrackSelector(): import("@jbrowse/core/util/types").Widget;
1951
- getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
1952
- start: number;
1953
- end: number;
1954
- type: string;
1955
- regionNumber?: number;
1956
- reversed?: boolean;
1957
- refName: string;
1958
- assemblyName: string;
1959
- key: string;
1960
- offsetPx: number;
1961
- widthPx: number;
1962
- variant?: string;
1963
- isLeftEndOfDisplayedRegion?: boolean;
1964
- }[];
1965
- afterDisplayedRegionsSet(cb: () => void): void;
1966
- horizontalScroll(distance: number): number;
1967
- center(): void;
1968
- showAllRegions(): void;
1969
- showAllRegionsInAssembly(assemblyName?: string): void;
1970
- setDraggingTrackId(idx?: string): void;
1971
- setScaleFactor(factor: number): void;
1972
- clearView(): void;
1973
- setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
1974
- exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
1975
- } & {
1976
- slide: (viewWidths: number) => void;
1977
- } & {
1978
- zoom: (targetBpPerPx: number) => void;
1979
- } & {
1980
- readonly canShowCytobands: boolean;
1981
- readonly showCytobands: boolean;
1982
- readonly anyCytobandsExist: boolean;
1983
- readonly cytobandOffset: number;
1984
- } & {
1985
- menuItems(): import("@jbrowse/core/ui").MenuItem[];
1986
- } & {
1987
- readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
1988
- readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
1989
- readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
1990
- readonly visibleLocStrings: string;
1991
- readonly coarseVisibleLocStrings: string;
1992
- } & {
1993
- setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
1994
- } & {
1995
- moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
1996
- navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
1997
- navToSearchString({ input, assembly, }: {
1998
- input: string;
1999
- assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
2000
- }): Promise<void>;
2001
- navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
2002
- navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
2003
- navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
2004
- navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
2005
- } & {
2006
- rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
2007
- bpToPx({ refName, coord, regionNumber, }: {
2008
- refName: string;
2009
- coord: number;
2010
- regionNumber?: number;
2011
- }): {
2012
- index: number;
2013
- offsetPx: number;
2014
- } | undefined;
2015
- centerAt(coord: number, refName: string, regionNumber?: number): void;
2016
- pxToBp(px: number): {
2017
- coord: number;
2018
- index: number;
2019
- refName: string;
2020
- oob: boolean;
2021
- assemblyName: string;
2022
- offset: number;
2023
- start: number;
2024
- end: number;
2025
- reversed?: boolean;
2026
- };
2027
- readonly centerLineInfo: {
2028
- coord: number;
2029
- index: number;
2030
- refName: string;
2031
- oob: boolean;
2032
- assemblyName: string;
2033
- offset: number;
2034
- start: number;
2035
- end: number;
2036
- reversed?: boolean;
2037
- } | undefined;
2038
- } & {
2039
- afterCreate(): void;
2040
- afterAttach(): void;
2041
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2042
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2043
- displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
2044
- minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2045
- } & {
2046
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2047
- type: import("mobx-state-tree").IType<string | undefined, string, string>;
2048
- offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2049
- bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2050
- 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]>;
2051
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
2052
- hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2053
- hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2054
- hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2055
- trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2056
- showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2057
- showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2058
- trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2059
- showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2060
- 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]>;
2061
- colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2062
- showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2063
- 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>;
2064
- }, {
2065
- width: number;
2066
- } & {
2067
- menuItems(): import("@jbrowse/core/ui").MenuItem[];
2068
- } & {
2069
- setDisplayName(name: string): void;
2070
- setWidth(newWidth: number): void;
2071
- setMinimized(flag: boolean): void;
2072
- } & {
2073
- volatileWidth: number | undefined;
2074
- minimumBlockWidth: number;
2075
- draggingTrackId: undefined | string;
2076
- volatileError: unknown;
2077
- afterDisplayedRegionsSetCallbacks: (() => void)[];
2078
- scaleFactor: number;
2079
- trackRefs: Record<string, HTMLDivElement>;
2080
- coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2081
- coarseTotalBp: number;
2082
- leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
2083
- rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
2084
- } & {
2085
- readonly pinnedTracks: any[];
2086
- readonly unpinnedTracks: any[];
2087
- readonly trackLabelsSetting: any;
2088
- readonly width: number;
2089
- readonly interRegionPaddingWidth: number;
2090
- readonly assemblyNames: string[];
2091
- readonly assemblyDisplayNames: string[];
2092
- readonly isTopLevelView: boolean;
2093
- readonly stickyViewHeaders: boolean;
2094
- readonly rubberbandTop: number;
2095
- readonly pinnedTracksTop: number;
2096
- } & {
2097
- scaleBarDisplayPrefix(): string | undefined;
2098
- MiniControlsComponent(): React.FC<any>;
2099
- HeaderComponent(): React.FC<any>;
2100
- readonly assembliesNotFound: string | undefined;
2101
- readonly assemblyErrors: string;
2102
- readonly assembliesInitialized: boolean;
2103
- readonly initialized: boolean;
2104
- readonly hasDisplayedRegions: boolean;
2105
- readonly scaleBarHeight: number;
2106
- readonly headerHeight: number;
2107
- readonly trackHeights: number;
2108
- readonly trackHeightsWithResizeHandles: number;
2109
- readonly height: number;
2110
- readonly totalBp: number;
2111
- readonly maxBpPerPx: number;
2112
- readonly minBpPerPx: number;
2113
- readonly error: unknown;
2114
- readonly maxOffset: number;
2115
- readonly minOffset: number;
2116
- readonly displayedRegionsTotalPx: number;
2117
- renderProps(): any;
2118
- searchScope(assemblyName: string): {
2119
- assemblyName: string;
2120
- includeAggregateIndexes: boolean;
2121
- 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>>;
2122
- };
2123
- getTrack(id: string): any;
2124
- rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
2125
- rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
2126
- readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
2127
- } & {
2128
- setShowTrackOutlines(arg: boolean): void;
2129
- setColorByCDS(flag: boolean): void;
2130
- setShowCytobands(flag: boolean): void;
2131
- setWidth(newWidth: number): void;
2132
- setError(error: unknown): void;
2133
- setHideHeader(b: boolean): void;
2134
- setHideHeaderOverview(b: boolean): void;
2135
- setHideNoTracksActive(b: boolean): void;
2136
- setShowGridlines(b: boolean): void;
2137
- addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
2138
- setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
2139
- removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
2140
- scrollTo(offsetPx: number): number;
2141
- zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
2142
- setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2143
- setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
2144
- setNewView(bpPerPx: number, offsetPx: number): void;
2145
- horizontallyFlip(): void;
2146
- showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
2147
- hideTrack(trackId: string): number;
2148
- } & {
2149
- moveTrackDown(id: string): void;
2150
- moveTrackUp(id: string): void;
2151
- moveTrackToTop(id: string): void;
2152
- moveTrackToBottom(id: string): void;
2153
- moveTrack(movingId: string, targetId: string): void;
2154
- toggleTrack(trackId: string): boolean;
2155
- setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
2156
- setShowCenterLine(b: boolean): void;
2157
- setDisplayedRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
2158
- activateTrackSelector(): import("@jbrowse/core/util/types").Widget;
2159
- getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
2160
- start: number;
2161
- end: number;
2162
- type: string;
2163
- regionNumber?: number;
2164
- reversed?: boolean;
2165
- refName: string;
2166
- assemblyName: string;
2167
- key: string;
2168
- offsetPx: number;
2169
- widthPx: number;
2170
- variant?: string;
2171
- isLeftEndOfDisplayedRegion?: boolean;
2172
- }[];
2173
- afterDisplayedRegionsSet(cb: () => void): void;
2174
- horizontalScroll(distance: number): number;
2175
- center(): void;
2176
- showAllRegions(): void;
2177
- showAllRegionsInAssembly(assemblyName?: string): void;
2178
- setDraggingTrackId(idx?: string): void;
2179
- setScaleFactor(factor: number): void;
2180
- clearView(): void;
2181
- setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
2182
- exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
2183
- } & {
2184
- slide: (viewWidths: number) => void;
2185
- } & {
2186
- zoom: (targetBpPerPx: number) => void;
2187
- } & {
2188
- readonly canShowCytobands: boolean;
2189
- readonly showCytobands: boolean;
2190
- readonly anyCytobandsExist: boolean;
2191
- readonly cytobandOffset: number;
2192
- } & {
2193
- menuItems(): import("@jbrowse/core/ui").MenuItem[];
2194
- } & {
2195
- readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2196
- readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2197
- readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2198
- readonly visibleLocStrings: string;
2199
- readonly coarseVisibleLocStrings: string;
2200
- } & {
2201
- setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
2202
- } & {
2203
- moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2204
- navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
2205
- navToSearchString({ input, assembly, }: {
2206
- input: string;
2207
- assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
2208
- }): Promise<void>;
2209
- navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
2210
- navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
2211
- navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
2212
- navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
2213
- } & {
2214
- rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
2215
- bpToPx({ refName, coord, regionNumber, }: {
2216
- refName: string;
2217
- coord: number;
2218
- regionNumber?: number;
2219
- }): {
2220
- index: number;
2221
- offsetPx: number;
2222
- } | undefined;
2223
- centerAt(coord: number, refName: string, regionNumber?: number): void;
2224
- pxToBp(px: number): {
2225
- coord: number;
2226
- index: number;
2227
- refName: string;
2228
- oob: boolean;
2229
- assemblyName: string;
2230
- offset: number;
2231
- start: number;
2232
- end: number;
2233
- reversed?: boolean;
2234
- };
2235
- readonly centerLineInfo: {
2236
- coord: number;
2237
- index: number;
2238
- refName: string;
2239
- oob: boolean;
2240
- assemblyName: string;
2241
- offset: number;
2242
- start: number;
2243
- end: number;
2244
- reversed?: boolean;
2245
- } | undefined;
2246
- } & {
2247
- afterCreate(): void;
2248
- afterAttach(): void;
2249
- }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
2250
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2251
- displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
2252
- minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2253
- } & {
2254
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2255
- type: import("mobx-state-tree").IType<string | undefined, string, string>;
2256
- offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2257
- bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2258
- 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]>;
2259
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
2260
- hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2261
- hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2262
- hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2263
- trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2264
- showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2265
- showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2266
- trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2267
- showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2268
- 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]>;
2269
- colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2270
- showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2271
- 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>;
2272
- }>>, {
2273
- type: string;
2274
- id: string;
2275
- displayName: string | undefined;
2276
- tracks: any[];
2277
- minimized: boolean;
2278
- offsetPx: number;
2279
- bpPerPx: number;
2280
- displayedRegions: import("@jbrowse/core/util/types").Region[];
2281
- hideHeader: boolean;
2282
- hideHeaderOverview: boolean;
2283
- hideNoTracksActive: boolean;
2284
- trackSelectorType: string;
2285
- showCenterLine: boolean;
2286
- showCytobandsSetting: boolean;
2287
- trackLabels: string;
2288
- showGridlines: boolean;
2289
- highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[];
2290
- colorByCDS: boolean;
2291
- showTrackOutlines: boolean;
2292
- }>>)[];
2293
- renderProps(): {
2294
- theme: any;
2295
- highResolutionScaling: any;
2296
- };
2297
- } & {
2298
- addView(typeName: string, initialState?: {}): {
2299
- id: string;
2300
- displayName: string | undefined;
2301
- minimized: boolean;
2302
- type: string;
2303
- offsetPx: number;
2304
- bpPerPx: number;
2305
- 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]>>;
2306
- 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>>;
2307
- hideHeader: boolean;
2308
- hideHeaderOverview: boolean;
2309
- hideNoTracksActive: boolean;
2310
- trackSelectorType: string;
2311
- showCenterLine: boolean;
2312
- showCytobandsSetting: boolean;
2313
- trackLabels: string;
2314
- showGridlines: boolean;
2315
- 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]>>;
2316
- colorByCDS: boolean;
2317
- showTrackOutlines: boolean;
2318
- 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;
2319
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2320
- width: number;
2321
- } & {
2322
- menuItems(): import("@jbrowse/core/ui").MenuItem[];
2323
- } & {
2324
- setDisplayName(name: string): void;
2325
- setWidth(newWidth: number): void;
2326
- setMinimized(flag: boolean): void;
2327
- } & {
2328
- volatileWidth: number | undefined;
2329
- minimumBlockWidth: number;
2330
- draggingTrackId: undefined | string;
2331
- volatileError: unknown;
2332
- afterDisplayedRegionsSetCallbacks: (() => void)[];
2333
- scaleFactor: number;
2334
- trackRefs: Record<string, HTMLDivElement>;
2335
- coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2336
- coarseTotalBp: number;
2337
- leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
2338
- rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
2339
- } & {
2340
- readonly pinnedTracks: any[];
2341
- readonly unpinnedTracks: any[];
2342
- readonly trackLabelsSetting: any;
2343
- readonly width: number;
2344
- readonly interRegionPaddingWidth: number;
2345
- readonly assemblyNames: string[];
2346
- readonly assemblyDisplayNames: string[];
2347
- readonly isTopLevelView: boolean;
2348
- readonly stickyViewHeaders: boolean;
2349
- readonly rubberbandTop: number;
2350
- readonly pinnedTracksTop: number;
2351
- } & {
2352
- scaleBarDisplayPrefix(): string | undefined;
2353
- MiniControlsComponent(): React.FC<any>;
2354
- HeaderComponent(): React.FC<any>;
2355
- readonly assembliesNotFound: string | undefined;
2356
- readonly assemblyErrors: string;
2357
- readonly assembliesInitialized: boolean;
2358
- readonly initialized: boolean;
2359
- readonly hasDisplayedRegions: boolean;
2360
- readonly scaleBarHeight: number;
2361
- readonly headerHeight: number;
2362
- readonly trackHeights: number;
2363
- readonly trackHeightsWithResizeHandles: number;
2364
- readonly height: number;
2365
- readonly totalBp: number;
2366
- readonly maxBpPerPx: number;
2367
- readonly minBpPerPx: number;
2368
- readonly error: unknown;
2369
- readonly maxOffset: number;
2370
- readonly minOffset: number;
2371
- readonly displayedRegionsTotalPx: number;
2372
- renderProps(): any;
2373
- searchScope(assemblyName: string): {
2374
- assemblyName: string;
2375
- includeAggregateIndexes: boolean;
2376
- 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>>;
2377
- };
2378
- getTrack(id: string): any;
2379
- rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
2380
- rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
2381
- readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
2382
- } & {
2383
- setShowTrackOutlines(arg: boolean): void;
2384
- setColorByCDS(flag: boolean): void;
2385
- setShowCytobands(flag: boolean): void;
2386
- setWidth(newWidth: number): void;
2387
- setError(error: unknown): void;
2388
- setHideHeader(b: boolean): void;
2389
- setHideHeaderOverview(b: boolean): void;
2390
- setHideNoTracksActive(b: boolean): void;
2391
- setShowGridlines(b: boolean): void;
2392
- addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
2393
- setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
2394
- removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
2395
- scrollTo(offsetPx: number): number;
2396
- zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
2397
- setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2398
- setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
2399
- setNewView(bpPerPx: number, offsetPx: number): void;
2400
- horizontallyFlip(): void;
2401
- showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
2402
- hideTrack(trackId: string): number;
2403
- } & {
2404
- moveTrackDown(id: string): void;
2405
- moveTrackUp(id: string): void;
2406
- moveTrackToTop(id: string): void;
2407
- moveTrackToBottom(id: string): void;
2408
- moveTrack(movingId: string, targetId: string): void;
2409
- toggleTrack(trackId: string): boolean;
2410
- setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
2411
- setShowCenterLine(b: boolean): void;
2412
- setDisplayedRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
2413
- activateTrackSelector(): import("@jbrowse/core/util/types").Widget;
2414
- getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
2415
- start: number;
2416
- end: number;
2417
- type: string;
2418
- regionNumber?: number;
2419
- reversed?: boolean;
2420
- refName: string;
2421
- assemblyName: string;
2422
- key: string;
2423
- offsetPx: number;
2424
- widthPx: number;
2425
- variant?: string;
2426
- isLeftEndOfDisplayedRegion?: boolean;
2427
- }[];
2428
- afterDisplayedRegionsSet(cb: () => void): void;
2429
- horizontalScroll(distance: number): number;
2430
- center(): void;
2431
- showAllRegions(): void;
2432
- showAllRegionsInAssembly(assemblyName?: string): void;
2433
- setDraggingTrackId(idx?: string): void;
2434
- setScaleFactor(factor: number): void;
2435
- clearView(): void;
2436
- setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
2437
- exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
2438
- } & {
2439
- slide: (viewWidths: number) => void;
2440
- } & {
2441
- zoom: (targetBpPerPx: number) => void;
2442
- } & {
2443
- readonly canShowCytobands: boolean;
2444
- readonly showCytobands: boolean;
2445
- readonly anyCytobandsExist: boolean;
2446
- readonly cytobandOffset: number;
2447
- } & {
2448
- menuItems(): import("@jbrowse/core/ui").MenuItem[];
2449
- } & {
2450
- readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2451
- readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2452
- readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2453
- readonly visibleLocStrings: string;
2454
- readonly coarseVisibleLocStrings: string;
2455
- } & {
2456
- setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
2457
- } & {
2458
- moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2459
- navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
2460
- navToSearchString({ input, assembly, }: {
2461
- input: string;
2462
- assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
2463
- }): Promise<void>;
2464
- navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
2465
- navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
2466
- navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
2467
- navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
2468
- } & {
2469
- rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
2470
- bpToPx({ refName, coord, regionNumber, }: {
2471
- refName: string;
2472
- coord: number;
2473
- regionNumber?: number;
2474
- }): {
2475
- index: number;
2476
- offsetPx: number;
2477
- } | undefined;
2478
- centerAt(coord: number, refName: string, regionNumber?: number): void;
2479
- pxToBp(px: number): {
2480
- coord: number;
2481
- index: number;
2482
- refName: string;
2483
- oob: boolean;
2484
- assemblyName: string;
2485
- offset: number;
2486
- start: number;
2487
- end: number;
2488
- reversed?: boolean;
2489
- };
2490
- readonly centerLineInfo: {
2491
- coord: number;
2492
- index: number;
2493
- refName: string;
2494
- oob: boolean;
2495
- assemblyName: string;
2496
- offset: number;
2497
- start: number;
2498
- end: number;
2499
- reversed?: boolean;
2500
- } | undefined;
2501
- } & {
2502
- afterCreate(): void;
2503
- afterAttach(): void;
2504
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2505
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2506
- displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
2507
- minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2508
- } & {
2509
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2510
- type: import("mobx-state-tree").IType<string | undefined, string, string>;
2511
- offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2512
- bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2513
- 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]>;
2514
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
2515
- hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2516
- hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2517
- hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2518
- trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2519
- showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2520
- showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2521
- trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2522
- showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2523
- 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]>;
2524
- colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2525
- showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2526
- 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>;
2527
- }, {
2528
- width: number;
2529
- } & {
2530
- menuItems(): import("@jbrowse/core/ui").MenuItem[];
2531
- } & {
2532
- setDisplayName(name: string): void;
2533
- setWidth(newWidth: number): void;
2534
- setMinimized(flag: boolean): void;
2535
- } & {
2536
- volatileWidth: number | undefined;
2537
- minimumBlockWidth: number;
2538
- draggingTrackId: undefined | string;
2539
- volatileError: unknown;
2540
- afterDisplayedRegionsSetCallbacks: (() => void)[];
2541
- scaleFactor: number;
2542
- trackRefs: Record<string, HTMLDivElement>;
2543
- coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2544
- coarseTotalBp: number;
2545
- leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
2546
- rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
2547
- } & {
2548
- readonly pinnedTracks: any[];
2549
- readonly unpinnedTracks: any[];
2550
- readonly trackLabelsSetting: any;
2551
- readonly width: number;
2552
- readonly interRegionPaddingWidth: number;
2553
- readonly assemblyNames: string[];
2554
- readonly assemblyDisplayNames: string[];
2555
- readonly isTopLevelView: boolean;
2556
- readonly stickyViewHeaders: boolean;
2557
- readonly rubberbandTop: number;
2558
- readonly pinnedTracksTop: number;
2559
- } & {
2560
- scaleBarDisplayPrefix(): string | undefined;
2561
- MiniControlsComponent(): React.FC<any>;
2562
- HeaderComponent(): React.FC<any>;
2563
- readonly assembliesNotFound: string | undefined;
2564
- readonly assemblyErrors: string;
2565
- readonly assembliesInitialized: boolean;
2566
- readonly initialized: boolean;
2567
- readonly hasDisplayedRegions: boolean;
2568
- readonly scaleBarHeight: number;
2569
- readonly headerHeight: number;
2570
- readonly trackHeights: number;
2571
- readonly trackHeightsWithResizeHandles: number;
2572
- readonly height: number;
2573
- readonly totalBp: number;
2574
- readonly maxBpPerPx: number;
2575
- readonly minBpPerPx: number;
2576
- readonly error: unknown;
2577
- readonly maxOffset: number;
2578
- readonly minOffset: number;
2579
- readonly displayedRegionsTotalPx: number;
2580
- renderProps(): any;
2581
- searchScope(assemblyName: string): {
2582
- assemblyName: string;
2583
- includeAggregateIndexes: boolean;
2584
- 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>>;
2585
- };
2586
- getTrack(id: string): any;
2587
- rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
2588
- rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
2589
- readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
2590
- } & {
2591
- setShowTrackOutlines(arg: boolean): void;
2592
- setColorByCDS(flag: boolean): void;
2593
- setShowCytobands(flag: boolean): void;
2594
- setWidth(newWidth: number): void;
2595
- setError(error: unknown): void;
2596
- setHideHeader(b: boolean): void;
2597
- setHideHeaderOverview(b: boolean): void;
2598
- setHideNoTracksActive(b: boolean): void;
2599
- setShowGridlines(b: boolean): void;
2600
- addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
2601
- setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
2602
- removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
2603
- scrollTo(offsetPx: number): number;
2604
- zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
2605
- setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2606
- setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
2607
- setNewView(bpPerPx: number, offsetPx: number): void;
2608
- horizontallyFlip(): void;
2609
- showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
2610
- hideTrack(trackId: string): number;
2611
- } & {
2612
- moveTrackDown(id: string): void;
2613
- moveTrackUp(id: string): void;
2614
- moveTrackToTop(id: string): void;
2615
- moveTrackToBottom(id: string): void;
2616
- moveTrack(movingId: string, targetId: string): void;
2617
- toggleTrack(trackId: string): boolean;
2618
- setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
2619
- setShowCenterLine(b: boolean): void;
2620
- setDisplayedRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
2621
- activateTrackSelector(): import("@jbrowse/core/util/types").Widget;
2622
- getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
2623
- start: number;
2624
- end: number;
2625
- type: string;
2626
- regionNumber?: number;
2627
- reversed?: boolean;
2628
- refName: string;
2629
- assemblyName: string;
2630
- key: string;
2631
- offsetPx: number;
2632
- widthPx: number;
2633
- variant?: string;
2634
- isLeftEndOfDisplayedRegion?: boolean;
2635
- }[];
2636
- afterDisplayedRegionsSet(cb: () => void): void;
2637
- horizontalScroll(distance: number): number;
2638
- center(): void;
2639
- showAllRegions(): void;
2640
- showAllRegionsInAssembly(assemblyName?: string): void;
2641
- setDraggingTrackId(idx?: string): void;
2642
- setScaleFactor(factor: number): void;
2643
- clearView(): void;
2644
- setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
2645
- exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
2646
- } & {
2647
- slide: (viewWidths: number) => void;
2648
- } & {
2649
- zoom: (targetBpPerPx: number) => void;
2650
- } & {
2651
- readonly canShowCytobands: boolean;
2652
- readonly showCytobands: boolean;
2653
- readonly anyCytobandsExist: boolean;
2654
- readonly cytobandOffset: number;
2655
- } & {
2656
- menuItems(): import("@jbrowse/core/ui").MenuItem[];
2657
- } & {
2658
- readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2659
- readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2660
- readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2661
- readonly visibleLocStrings: string;
2662
- readonly coarseVisibleLocStrings: string;
2663
- } & {
2664
- setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
2665
- } & {
2666
- moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2667
- navToLocString(input: string, optAssemblyName?: string, grow?: number): Promise<void>;
2668
- navToSearchString({ input, assembly, }: {
2669
- input: string;
2670
- assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
2671
- }): Promise<void>;
2672
- navToLocation(parsedLocString: import("@jbrowse/core/util").ParsedLocString, assemblyName?: string, grow?: number): Promise<void>;
2673
- navToLocations(regions: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string, grow?: number): Promise<void>;
2674
- navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
2675
- navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
2676
- } & {
2677
- rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
2678
- bpToPx({ refName, coord, regionNumber, }: {
2679
- refName: string;
2680
- coord: number;
2681
- regionNumber?: number;
2682
- }): {
2683
- index: number;
2684
- offsetPx: number;
2685
- } | undefined;
2686
- centerAt(coord: number, refName: string, regionNumber?: number): void;
2687
- pxToBp(px: number): {
2688
- coord: number;
2689
- index: number;
2690
- refName: string;
2691
- oob: boolean;
2692
- assemblyName: string;
2693
- offset: number;
2694
- start: number;
2695
- end: number;
2696
- reversed?: boolean;
2697
- };
2698
- readonly centerLineInfo: {
2699
- coord: number;
2700
- index: number;
2701
- refName: string;
2702
- oob: boolean;
2703
- assemblyName: string;
2704
- offset: number;
2705
- start: number;
2706
- end: number;
2707
- reversed?: boolean;
2708
- } | undefined;
2709
- } & {
2710
- afterCreate(): void;
2711
- afterAttach(): void;
2712
- }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
2713
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2714
- displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
2715
- minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2716
- } & {
2717
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2718
- type: import("mobx-state-tree").IType<string | undefined, string, string>;
2719
- offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2720
- bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2721
- 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]>;
2722
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
2723
- hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2724
- hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2725
- hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2726
- trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2727
- showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2728
- showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2729
- trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2730
- showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2731
- 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]>;
2732
- colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2733
- showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2734
- 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>;
2735
- }>>, {
2736
- type: string;
2737
- id: string;
2738
- displayName: string | undefined;
2739
- tracks: any[];
2740
- minimized: boolean;
2741
- offsetPx: number;
2742
- bpPerPx: number;
2743
- displayedRegions: import("@jbrowse/core/util/types").Region[];
2744
- hideHeader: boolean;
2745
- hideHeaderOverview: boolean;
2746
- hideNoTracksActive: boolean;
2747
- trackSelectorType: string;
2748
- showCenterLine: boolean;
2749
- showCytobandsSetting: boolean;
2750
- trackLabels: string;
2751
- showGridlines: boolean;
2752
- highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[];
2753
- colorByCDS: boolean;
2754
- showTrackOutlines: boolean;
2755
- }>>;
2756
- removeView(): void;
2757
- } & {
2758
- getTrackActionMenuItems(config: any): {
2759
- label: string;
2760
- onClick: () => void;
2761
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
2762
- muiName: string;
2763
- };
2764
- }[];
2765
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
2766
- export type SessionStateModel = ReturnType<typeof sessionModelFactory>;
2767
- export type SessionModel = Instance<SessionStateModel>;