@jbrowse/react-linear-genome-view2 3.2.0

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 (76) hide show
  1. package/LICENSE +201 -0
  2. package/README.md +72 -0
  3. package/dist/JBrowseLinearGenomeView/JBrowseLinearGenomeView.d.ts +5 -0
  4. package/dist/JBrowseLinearGenomeView/JBrowseLinearGenomeView.js +19 -0
  5. package/dist/JBrowseLinearGenomeView/JBrowseLinearGenomeView.test.d.ts +1 -0
  6. package/dist/JBrowseLinearGenomeView/JBrowseLinearGenomeView.test.js +77 -0
  7. package/dist/JBrowseLinearGenomeView/index.d.ts +1 -0
  8. package/dist/JBrowseLinearGenomeView/index.js +8 -0
  9. package/dist/corePlugins.d.ts +3 -0
  10. package/dist/corePlugins.js +38 -0
  11. package/dist/createModel/AboutDialog.d.ts +1 -0
  12. package/dist/createModel/AboutDialog.js +5 -0
  13. package/dist/createModel/createConfigModel.d.ts +94 -0
  14. package/dist/createModel/createConfigModel.js +43 -0
  15. package/dist/createModel/createModel.d.ts +3165 -0
  16. package/dist/createModel/createModel.js +118 -0
  17. package/dist/createModel/createSessionModel.d.ts +1170 -0
  18. package/dist/createModel/createSessionModel.js +118 -0
  19. package/dist/createModel/index.d.ts +3 -0
  20. package/dist/createModel/index.js +12 -0
  21. package/dist/createViewState.d.ts +8683 -0
  22. package/dist/createViewState.js +79 -0
  23. package/dist/index.d.ts +5 -0
  24. package/dist/index.js +14 -0
  25. package/dist/loadPlugins.d.ts +13 -0
  26. package/dist/loadPlugins.js +12 -0
  27. package/dist/react-linear-genome-view.umd.production.min.js +185 -0
  28. package/dist/react-linear-genome-view.umd.production.min.js.LICENSE.txt +198 -0
  29. package/dist/react-linear-genome-view.umd.production.min.js.map +1 -0
  30. package/dist/rpcWorker.d.ts +2 -0
  31. package/dist/rpcWorker.js +49 -0
  32. package/dist/types.d.ts +5 -0
  33. package/dist/types.js +2 -0
  34. package/dist/version.d.ts +1 -0
  35. package/dist/version.js +4 -0
  36. package/dist/webpack.d.ts +8 -0
  37. package/dist/webpack.js +53 -0
  38. package/dist/workerPolyfill.d.ts +0 -0
  39. package/dist/workerPolyfill.js +32 -0
  40. package/docs/example.md +91 -0
  41. package/docs/img/exampleView.png +0 -0
  42. package/esm/JBrowseLinearGenomeView/JBrowseLinearGenomeView.d.ts +5 -0
  43. package/esm/JBrowseLinearGenomeView/JBrowseLinearGenomeView.js +17 -0
  44. package/esm/JBrowseLinearGenomeView/index.d.ts +1 -0
  45. package/esm/JBrowseLinearGenomeView/index.js +1 -0
  46. package/esm/corePlugins.d.ts +3 -0
  47. package/esm/corePlugins.js +33 -0
  48. package/esm/createModel/AboutDialog.d.ts +1 -0
  49. package/esm/createModel/AboutDialog.js +1 -0
  50. package/esm/createModel/createConfigModel.d.ts +94 -0
  51. package/esm/createModel/createConfigModel.js +37 -0
  52. package/esm/createModel/createModel.d.ts +3165 -0
  53. package/esm/createModel/createModel.js +79 -0
  54. package/esm/createModel/createSessionModel.d.ts +1170 -0
  55. package/esm/createModel/createSessionModel.js +79 -0
  56. package/esm/createModel/index.d.ts +3 -0
  57. package/esm/createModel/index.js +3 -0
  58. package/esm/createViewState.d.ts +8683 -0
  59. package/esm/createViewState.js +73 -0
  60. package/esm/index.d.ts +5 -0
  61. package/esm/index.js +4 -0
  62. package/esm/loadPlugins.d.ts +13 -0
  63. package/esm/loadPlugins.js +6 -0
  64. package/esm/makeWorkerInstance.d.ts +1 -0
  65. package/esm/makeWorkerInstance.js +3 -0
  66. package/esm/rpcWorker.d.ts +2 -0
  67. package/esm/rpcWorker.js +10 -0
  68. package/esm/types.d.ts +5 -0
  69. package/esm/types.js +1 -0
  70. package/esm/version.d.ts +1 -0
  71. package/esm/version.js +1 -0
  72. package/esm/webpack.d.ts +8 -0
  73. package/esm/webpack.js +7 -0
  74. package/esm/workerPolyfill.d.ts +0 -0
  75. package/esm/workerPolyfill.js +32 -0
  76. package/package.json +84 -0
@@ -0,0 +1,3165 @@
1
+ import PluginManager from '@jbrowse/core/PluginManager';
2
+ import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
3
+ import RpcManager from '@jbrowse/core/rpc/RpcManager';
4
+ import type { PluginConstructor } from '@jbrowse/core/Plugin';
5
+ import type { UriLocation } from '@jbrowse/core/util';
6
+ import type { Instance, SnapshotIn } from 'mobx-state-tree';
7
+ export default function createModel(runtimePlugins: PluginConstructor[], makeWorkerInstance?: () => Worker): {
8
+ model: import("mobx-state-tree").IModelType<{
9
+ config: import("mobx-state-tree").IModelType<{
10
+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
11
+ rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
12
+ defaultDriver: {
13
+ type: string;
14
+ description: string;
15
+ defaultValue: string;
16
+ };
17
+ drivers: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IMapType<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> | undefined, import("mobx-state-tree").ModelSnapshotType<Record<string, any>>, ({} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> & import("mobx-state-tree/dist/internal").NonEmptyObject) | undefined>>, [undefined]>;
18
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
19
+ highResolutionScaling: {
20
+ type: string;
21
+ defaultValue: number;
22
+ };
23
+ hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
24
+ sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
25
+ trackNames: {
26
+ type: string;
27
+ defaultValue: boolean;
28
+ };
29
+ categories: {
30
+ type: string;
31
+ defaultValue: boolean;
32
+ };
33
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
34
+ defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
35
+ categoryNames: {
36
+ type: string;
37
+ defaultValue: never[];
38
+ };
39
+ topLevelCategories: {
40
+ type: string;
41
+ defaultValue: boolean;
42
+ };
43
+ subCategories: {
44
+ type: string;
45
+ defaultValue: boolean;
46
+ };
47
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
48
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
49
+ formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
50
+ feature: {
51
+ type: string;
52
+ description: string;
53
+ defaultValue: {};
54
+ contextVariable: string[];
55
+ };
56
+ subfeatures: {
57
+ type: string;
58
+ description: string;
59
+ defaultValue: {};
60
+ contextVariable: string[];
61
+ };
62
+ depth: {
63
+ type: string;
64
+ defaultValue: number;
65
+ description: string;
66
+ };
67
+ maxDepth: {
68
+ type: string;
69
+ defaultValue: number;
70
+ description: string;
71
+ };
72
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
73
+ formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
74
+ config: {
75
+ type: string;
76
+ description: string;
77
+ defaultValue: {};
78
+ contextVariable: string[];
79
+ };
80
+ hideUris: {
81
+ type: string;
82
+ defaultValue: boolean;
83
+ };
84
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
85
+ theme: {
86
+ type: string;
87
+ defaultValue: {};
88
+ };
89
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
90
+ assembly: import("mobx-state-tree").IAnyType;
91
+ tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
92
+ internetAccounts: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
93
+ connections: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
94
+ aggregateTextSearchAdapters: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
95
+ plugins: import("mobx-state-tree").IType<any, any, any>;
96
+ }, {
97
+ readonly assemblies: any[];
98
+ readonly assemblyName: string;
99
+ readonly rpcManager: any;
100
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
101
+ session: import("mobx-state-tree").IModelType<{
102
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
103
+ name: import("mobx-state-tree").ISimpleType<string>;
104
+ margin: import("mobx-state-tree").IType<number | undefined, number, number>;
105
+ } & {
106
+ drawerPosition: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
107
+ drawerWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
108
+ widgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyType>;
109
+ activeWidgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>>;
110
+ minimized: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
111
+ } & {
112
+ connectionInstances: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
113
+ name: import("mobx-state-tree").ISimpleType<string>;
114
+ tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
115
+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
116
+ name: {
117
+ type: string;
118
+ defaultValue: string;
119
+ description: string;
120
+ };
121
+ assemblyNames: {
122
+ type: string;
123
+ defaultValue: never[];
124
+ description: string;
125
+ };
126
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
127
+ }, {
128
+ connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
129
+ } & {
130
+ afterAttach(): void;
131
+ addTrackConf(trackConf: ({
132
+ [x: string]: any;
133
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
134
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
135
+ [x: string]: any;
136
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
137
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
138
+ [x: string]: any;
139
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
140
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
141
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
142
+ addTrackConfs(trackConfs: (({
143
+ [x: string]: any;
144
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
145
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
146
+ [x: string]: any;
147
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
148
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
149
+ [x: string]: any;
150
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
151
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
152
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
153
+ setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
154
+ clear(): void;
155
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
156
+ } & {
157
+ sessionTracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
158
+ } & {
159
+ view: import("@jbrowse/plugin-linear-genome-view").LinearGenomeViewStateModel;
160
+ sessionTracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
161
+ }, {
162
+ selection: unknown;
163
+ hovered: unknown;
164
+ } & {
165
+ readonly root: import("mobx-state-tree").TypeOrStateTreeNodeToStateTreeNode<ROOT_MODEL_TYPE>;
166
+ } & {
167
+ readonly jbrowse: any;
168
+ readonly rpcManager: RpcManager;
169
+ readonly configuration: {
170
+ [x: string]: any;
171
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
172
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
173
+ [x: string]: any;
174
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
175
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
176
+ [x: string]: any;
177
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
178
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
179
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
180
+ readonly adminMode: boolean;
181
+ readonly textSearchManager: TextSearchManager;
182
+ } & {
183
+ readonly assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
184
+ } & {
185
+ setSelection(thing: unknown): void;
186
+ clearSelection(): void;
187
+ setHovered(thing: unknown): void;
188
+ } & {
189
+ readonly visibleWidget: any;
190
+ } & {
191
+ setDrawerPosition(arg: string): void;
192
+ updateDrawerWidth(drawerWidth: number): number;
193
+ resizeDrawer(distance: number): number;
194
+ addWidget(typeName: string, id: string, initialState?: {}, conf?: unknown): any;
195
+ showWidget(widget: any): void;
196
+ hasWidget(widget: any): boolean;
197
+ hideWidget(widget: any): void;
198
+ minimizeWidgetDrawer(): void;
199
+ showWidgetDrawer(): void;
200
+ hideAllWidgets(): void;
201
+ editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
202
+ afterAttach(): void;
203
+ } & {
204
+ readonly connections: import("@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig").BaseConnectionConfigModel[];
205
+ } & {
206
+ makeConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: {}): ({
207
+ name: string;
208
+ 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>>;
209
+ configuration: {
210
+ [x: string]: any;
211
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
212
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
213
+ [x: string]: any;
214
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
215
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
216
+ [x: string]: any;
217
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
218
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
219
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
220
+ name: {
221
+ type: string;
222
+ defaultValue: string;
223
+ description: string;
224
+ };
225
+ assemblyNames: {
226
+ type: string;
227
+ defaultValue: never[];
228
+ description: string;
229
+ };
230
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>;
231
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
232
+ connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
233
+ } & {
234
+ afterAttach(): void;
235
+ addTrackConf(trackConf: ({
236
+ [x: string]: any;
237
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
238
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
239
+ [x: string]: any;
240
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
241
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
242
+ [x: string]: any;
243
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
244
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
245
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
246
+ addTrackConfs(trackConfs: (({
247
+ [x: string]: any;
248
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
249
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
250
+ [x: string]: any;
251
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
252
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
253
+ [x: string]: any;
254
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
255
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
256
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
257
+ setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
258
+ clear(): void;
259
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
260
+ name: import("mobx-state-tree").ISimpleType<string>;
261
+ tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
262
+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
263
+ name: {
264
+ type: string;
265
+ defaultValue: string;
266
+ description: string;
267
+ };
268
+ assemblyNames: {
269
+ type: string;
270
+ defaultValue: never[];
271
+ description: string;
272
+ };
273
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
274
+ }, {
275
+ connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
276
+ } & {
277
+ afterAttach(): void;
278
+ addTrackConf(trackConf: ({
279
+ [x: string]: any;
280
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
281
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
282
+ [x: string]: any;
283
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
284
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
285
+ [x: string]: any;
286
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
287
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
288
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
289
+ addTrackConfs(trackConfs: (({
290
+ [x: string]: any;
291
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
292
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
293
+ [x: string]: any;
294
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
295
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
296
+ [x: string]: any;
297
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
298
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
299
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
300
+ setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
301
+ clear(): void;
302
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
303
+ prepareToBreakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): (Record<string, number> | (() => void))[] | undefined;
304
+ breakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
305
+ deleteConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
306
+ addConnectionConf(connectionConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
307
+ clearConnections(): void;
308
+ } & {
309
+ queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, unknown][];
310
+ } & {
311
+ readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType | undefined;
312
+ readonly DialogProps: unknown;
313
+ } & {
314
+ removeActiveDialog(): void;
315
+ queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, unknown]): void;
316
+ } & {
317
+ getReferring(object: import("mobx-state-tree").IAnyStateTreeNode): import("@jbrowse/product-core").ReferringNode[];
318
+ } & {
319
+ removeReferring(referring: import("@jbrowse/product-core").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
320
+ } & {
321
+ readonly tracks: import("@jbrowse/core/configuration").AnyConfigurationModel[];
322
+ } & {
323
+ addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfiguration): any;
324
+ deleteTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
325
+ } & {
326
+ readonly tracks: import("@jbrowse/core/configuration").AnyConfigurationModel[];
327
+ } & {
328
+ addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfiguration): any;
329
+ deleteTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
330
+ } & {
331
+ snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
332
+ } & {
333
+ readonly snackbarMessageSet: Map<string, import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
334
+ } & {
335
+ notify(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction): void;
336
+ notifyError(errorMessage: string, error?: unknown, extra?: unknown): void;
337
+ pushSnackbarMessage(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction): void;
338
+ popSnackbarMessage(): import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage | undefined;
339
+ removeSnackbarMessage(message: string): void;
340
+ } & {
341
+ readonly version: any;
342
+ readonly disableAddTracks: any;
343
+ readonly assemblies: any[];
344
+ readonly assemblyNames: any[];
345
+ readonly connections: any;
346
+ readonly assemblyManager: any;
347
+ readonly views: ({
348
+ id: string;
349
+ displayName: string | undefined;
350
+ minimized: boolean;
351
+ type: string;
352
+ offsetPx: number;
353
+ bpPerPx: number;
354
+ displayedRegions: import("@jbrowse/core/util").Region[] & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>>;
355
+ 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>>;
356
+ hideHeader: boolean;
357
+ hideHeaderOverview: boolean;
358
+ hideNoTracksActive: boolean;
359
+ trackSelectorType: string;
360
+ showCenterLine: boolean;
361
+ showCytobandsSetting: boolean;
362
+ trackLabels: string;
363
+ showGridlines: boolean;
364
+ 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]>>;
365
+ colorByCDS: boolean;
366
+ showTrackOutlines: boolean;
367
+ 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;
368
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
369
+ width: number;
370
+ } & {
371
+ menuItems(): import("@jbrowse/core/ui").MenuItem[];
372
+ } & {
373
+ setDisplayName(name: string): void;
374
+ setWidth(newWidth: number): void;
375
+ setMinimized(flag: boolean): void;
376
+ } & {
377
+ volatileWidth: number | undefined;
378
+ minimumBlockWidth: number;
379
+ draggingTrackId: undefined | string;
380
+ volatileError: unknown;
381
+ afterDisplayedRegionsSetCallbacks: (() => void)[];
382
+ scaleFactor: number;
383
+ trackRefs: Record<string, HTMLDivElement>;
384
+ coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
385
+ coarseTotalBp: number;
386
+ leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
387
+ rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
388
+ } & {
389
+ readonly pinnedTracks: any[];
390
+ readonly unpinnedTracks: any[];
391
+ readonly trackLabelsSetting: any;
392
+ readonly width: number;
393
+ readonly interRegionPaddingWidth: number;
394
+ readonly assemblyNames: string[];
395
+ readonly stickyViewHeaders: boolean;
396
+ readonly rubberbandTop: number;
397
+ readonly pinnedTracksTop: number;
398
+ } & {
399
+ scaleBarDisplayPrefix(): string | undefined;
400
+ MiniControlsComponent(): React.FC<any>;
401
+ HeaderComponent(): React.FC<any>;
402
+ readonly assembliesNotFound: string | undefined;
403
+ readonly assemblyErrors: string;
404
+ readonly assembliesInitialized: boolean;
405
+ readonly initialized: boolean;
406
+ readonly hasDisplayedRegions: boolean;
407
+ readonly scaleBarHeight: number;
408
+ readonly headerHeight: number;
409
+ readonly trackHeights: number;
410
+ readonly trackHeightsWithResizeHandles: number;
411
+ readonly height: number;
412
+ readonly totalBp: number;
413
+ readonly maxBpPerPx: number;
414
+ readonly minBpPerPx: number;
415
+ readonly error: unknown;
416
+ readonly maxOffset: number;
417
+ readonly minOffset: number;
418
+ readonly displayedRegionsTotalPx: number;
419
+ renderProps(): any;
420
+ searchScope(assemblyName: string): {
421
+ assemblyName: string;
422
+ includeAggregateIndexes: boolean;
423
+ 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>>;
424
+ };
425
+ getTrack(id: string): any;
426
+ rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
427
+ rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
428
+ readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
429
+ } & {
430
+ setShowTrackOutlines(arg: boolean): void;
431
+ setColorByCDS(flag: boolean): void;
432
+ setShowCytobands(flag: boolean): void;
433
+ setWidth(newWidth: number): void;
434
+ setError(error: unknown): void;
435
+ setHideHeader(b: boolean): void;
436
+ setHideHeaderOverview(b: boolean): void;
437
+ setHideNoTracksActive(b: boolean): void;
438
+ setShowGridlines(b: boolean): void;
439
+ addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
440
+ setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
441
+ removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
442
+ scrollTo(offsetPx: number): number;
443
+ zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
444
+ setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
445
+ setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
446
+ setNewView(bpPerPx: number, offsetPx: number): void;
447
+ horizontallyFlip(): void;
448
+ showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
449
+ hideTrack(trackId: string): number;
450
+ } & {
451
+ moveTrackDown(id: string): void;
452
+ moveTrackUp(id: string): void;
453
+ moveTrackToTop(id: string): void;
454
+ moveTrackToBottom(id: string): void;
455
+ moveTrack(movingId: string, targetId: string): void;
456
+ toggleTrack(trackId: string): boolean;
457
+ setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
458
+ setShowCenterLine(b: boolean): void;
459
+ setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
460
+ activateTrackSelector(): import("@jbrowse/core/util").Widget;
461
+ getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
462
+ start: number;
463
+ end: number;
464
+ type: string;
465
+ regionNumber?: number;
466
+ reversed?: boolean;
467
+ refName: string;
468
+ assemblyName: string;
469
+ key: string;
470
+ offsetPx: number;
471
+ widthPx: number;
472
+ variant?: string;
473
+ isLeftEndOfDisplayedRegion?: boolean;
474
+ }[];
475
+ afterDisplayedRegionsSet(cb: () => void): void;
476
+ horizontalScroll(distance: number): number;
477
+ center(): void;
478
+ showAllRegions(): void;
479
+ showAllRegionsInAssembly(assemblyName?: string): void;
480
+ setDraggingTrackId(idx?: string): void;
481
+ setScaleFactor(factor: number): void;
482
+ clearView(): void;
483
+ setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
484
+ exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
485
+ } & {
486
+ slide: (viewWidths: number) => void;
487
+ } & {
488
+ zoom: (targetBpPerPx: number) => void;
489
+ } & {
490
+ readonly canShowCytobands: boolean;
491
+ readonly showCytobands: boolean;
492
+ readonly anyCytobandsExist: boolean;
493
+ readonly cytobandOffset: number;
494
+ } & {
495
+ menuItems(): import("@jbrowse/core/ui").MenuItem[];
496
+ } & {
497
+ readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
498
+ readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
499
+ readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
500
+ readonly visibleLocStrings: string;
501
+ readonly coarseVisibleLocStrings: string;
502
+ } & {
503
+ setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
504
+ } & {
505
+ moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
506
+ navToLocString(input: string, optAssemblyName?: string): Promise<void>;
507
+ navToSearchString({ input, assembly, }: {
508
+ input: string;
509
+ assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
510
+ }): Promise<void>;
511
+ navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
512
+ navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
513
+ navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
514
+ } & {
515
+ rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
516
+ bpToPx({ refName, coord, regionNumber, }: {
517
+ refName: string;
518
+ coord: number;
519
+ regionNumber?: number;
520
+ }): {
521
+ index: number;
522
+ offsetPx: number;
523
+ } | undefined;
524
+ centerAt(coord: number, refName: string, regionNumber?: number): void;
525
+ pxToBp(px: number): {
526
+ coord: number;
527
+ index: number;
528
+ refName: string;
529
+ oob: boolean;
530
+ assemblyName: string;
531
+ offset: number;
532
+ start: number;
533
+ end: number;
534
+ reversed?: boolean;
535
+ };
536
+ readonly centerLineInfo: {
537
+ coord: number;
538
+ index: number;
539
+ refName: string;
540
+ oob: boolean;
541
+ assemblyName: string;
542
+ offset: number;
543
+ start: number;
544
+ end: number;
545
+ reversed?: boolean;
546
+ } | undefined;
547
+ } & {
548
+ afterCreate(): void;
549
+ afterAttach(): void;
550
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
551
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
552
+ displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
553
+ minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
554
+ } & {
555
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
556
+ type: import("mobx-state-tree").IType<string | undefined, string, string>;
557
+ offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
558
+ bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
559
+ displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
560
+ tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
561
+ hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
562
+ hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
563
+ hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
564
+ trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
565
+ showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
566
+ showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
567
+ trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
568
+ showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
569
+ 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]>;
570
+ colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
571
+ showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
572
+ 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>;
573
+ }, {
574
+ width: number;
575
+ } & {
576
+ menuItems(): import("@jbrowse/core/ui").MenuItem[];
577
+ } & {
578
+ setDisplayName(name: string): void;
579
+ setWidth(newWidth: number): void;
580
+ setMinimized(flag: boolean): void;
581
+ } & {
582
+ volatileWidth: number | undefined;
583
+ minimumBlockWidth: number;
584
+ draggingTrackId: undefined | string;
585
+ volatileError: unknown;
586
+ afterDisplayedRegionsSetCallbacks: (() => void)[];
587
+ scaleFactor: number;
588
+ trackRefs: Record<string, HTMLDivElement>;
589
+ coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
590
+ coarseTotalBp: number;
591
+ leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
592
+ rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
593
+ } & {
594
+ readonly pinnedTracks: any[];
595
+ readonly unpinnedTracks: any[];
596
+ readonly trackLabelsSetting: any;
597
+ readonly width: number;
598
+ readonly interRegionPaddingWidth: number;
599
+ readonly assemblyNames: string[];
600
+ readonly stickyViewHeaders: boolean;
601
+ readonly rubberbandTop: number;
602
+ readonly pinnedTracksTop: number;
603
+ } & {
604
+ scaleBarDisplayPrefix(): string | undefined;
605
+ MiniControlsComponent(): React.FC<any>;
606
+ HeaderComponent(): React.FC<any>;
607
+ readonly assembliesNotFound: string | undefined;
608
+ readonly assemblyErrors: string;
609
+ readonly assembliesInitialized: boolean;
610
+ readonly initialized: boolean;
611
+ readonly hasDisplayedRegions: boolean;
612
+ readonly scaleBarHeight: number;
613
+ readonly headerHeight: number;
614
+ readonly trackHeights: number;
615
+ readonly trackHeightsWithResizeHandles: number;
616
+ readonly height: number;
617
+ readonly totalBp: number;
618
+ readonly maxBpPerPx: number;
619
+ readonly minBpPerPx: number;
620
+ readonly error: unknown;
621
+ readonly maxOffset: number;
622
+ readonly minOffset: number;
623
+ readonly displayedRegionsTotalPx: number;
624
+ renderProps(): any;
625
+ searchScope(assemblyName: string): {
626
+ assemblyName: string;
627
+ includeAggregateIndexes: boolean;
628
+ 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>>;
629
+ };
630
+ getTrack(id: string): any;
631
+ rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
632
+ rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
633
+ readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
634
+ } & {
635
+ setShowTrackOutlines(arg: boolean): void;
636
+ setColorByCDS(flag: boolean): void;
637
+ setShowCytobands(flag: boolean): void;
638
+ setWidth(newWidth: number): void;
639
+ setError(error: unknown): void;
640
+ setHideHeader(b: boolean): void;
641
+ setHideHeaderOverview(b: boolean): void;
642
+ setHideNoTracksActive(b: boolean): void;
643
+ setShowGridlines(b: boolean): void;
644
+ addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
645
+ setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
646
+ removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
647
+ scrollTo(offsetPx: number): number;
648
+ zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
649
+ setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
650
+ setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
651
+ setNewView(bpPerPx: number, offsetPx: number): void;
652
+ horizontallyFlip(): void;
653
+ showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
654
+ hideTrack(trackId: string): number;
655
+ } & {
656
+ moveTrackDown(id: string): void;
657
+ moveTrackUp(id: string): void;
658
+ moveTrackToTop(id: string): void;
659
+ moveTrackToBottom(id: string): void;
660
+ moveTrack(movingId: string, targetId: string): void;
661
+ toggleTrack(trackId: string): boolean;
662
+ setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
663
+ setShowCenterLine(b: boolean): void;
664
+ setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
665
+ activateTrackSelector(): import("@jbrowse/core/util").Widget;
666
+ getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
667
+ start: number;
668
+ end: number;
669
+ type: string;
670
+ regionNumber?: number;
671
+ reversed?: boolean;
672
+ refName: string;
673
+ assemblyName: string;
674
+ key: string;
675
+ offsetPx: number;
676
+ widthPx: number;
677
+ variant?: string;
678
+ isLeftEndOfDisplayedRegion?: boolean;
679
+ }[];
680
+ afterDisplayedRegionsSet(cb: () => void): void;
681
+ horizontalScroll(distance: number): number;
682
+ center(): void;
683
+ showAllRegions(): void;
684
+ showAllRegionsInAssembly(assemblyName?: string): void;
685
+ setDraggingTrackId(idx?: string): void;
686
+ setScaleFactor(factor: number): void;
687
+ clearView(): void;
688
+ setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
689
+ exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
690
+ } & {
691
+ slide: (viewWidths: number) => void;
692
+ } & {
693
+ zoom: (targetBpPerPx: number) => void;
694
+ } & {
695
+ readonly canShowCytobands: boolean;
696
+ readonly showCytobands: boolean;
697
+ readonly anyCytobandsExist: boolean;
698
+ readonly cytobandOffset: number;
699
+ } & {
700
+ menuItems(): import("@jbrowse/core/ui").MenuItem[];
701
+ } & {
702
+ readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
703
+ readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
704
+ readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
705
+ readonly visibleLocStrings: string;
706
+ readonly coarseVisibleLocStrings: string;
707
+ } & {
708
+ setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
709
+ } & {
710
+ moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
711
+ navToLocString(input: string, optAssemblyName?: string): Promise<void>;
712
+ navToSearchString({ input, assembly, }: {
713
+ input: string;
714
+ assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
715
+ }): Promise<void>;
716
+ navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
717
+ navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
718
+ navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
719
+ } & {
720
+ rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
721
+ bpToPx({ refName, coord, regionNumber, }: {
722
+ refName: string;
723
+ coord: number;
724
+ regionNumber?: number;
725
+ }): {
726
+ index: number;
727
+ offsetPx: number;
728
+ } | undefined;
729
+ centerAt(coord: number, refName: string, regionNumber?: number): void;
730
+ pxToBp(px: number): {
731
+ coord: number;
732
+ index: number;
733
+ refName: string;
734
+ oob: boolean;
735
+ assemblyName: string;
736
+ offset: number;
737
+ start: number;
738
+ end: number;
739
+ reversed?: boolean;
740
+ };
741
+ readonly centerLineInfo: {
742
+ coord: number;
743
+ index: number;
744
+ refName: string;
745
+ oob: boolean;
746
+ assemblyName: string;
747
+ offset: number;
748
+ start: number;
749
+ end: number;
750
+ reversed?: boolean;
751
+ } | undefined;
752
+ } & {
753
+ afterCreate(): void;
754
+ afterAttach(): void;
755
+ }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
756
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
757
+ displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
758
+ minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
759
+ } & {
760
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
761
+ type: import("mobx-state-tree").IType<string | undefined, string, string>;
762
+ offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
763
+ bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
764
+ displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
765
+ tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
766
+ hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
767
+ hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
768
+ hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
769
+ trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
770
+ showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
771
+ showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
772
+ trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
773
+ showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
774
+ 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]>;
775
+ colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
776
+ showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
777
+ 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>;
778
+ }>>, {
779
+ type: string;
780
+ id: string;
781
+ displayName: string | undefined;
782
+ tracks: any[];
783
+ minimized: boolean;
784
+ displayedRegions: import("@jbrowse/core/util").Region[];
785
+ offsetPx: number;
786
+ bpPerPx: number;
787
+ hideHeader: boolean;
788
+ hideHeaderOverview: boolean;
789
+ hideNoTracksActive: boolean;
790
+ trackSelectorType: string;
791
+ showCenterLine: boolean;
792
+ showCytobandsSetting: boolean;
793
+ trackLabels: string;
794
+ showGridlines: boolean;
795
+ highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[];
796
+ colorByCDS: boolean;
797
+ showTrackOutlines: boolean;
798
+ }>>)[];
799
+ renderProps(): {
800
+ theme: any;
801
+ highResolutionScaling: any;
802
+ };
803
+ } & {
804
+ addView(typeName: string, initialState?: {}): {
805
+ id: string;
806
+ displayName: string | undefined;
807
+ minimized: boolean;
808
+ type: string;
809
+ offsetPx: number;
810
+ bpPerPx: number;
811
+ displayedRegions: import("@jbrowse/core/util").Region[] & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>>;
812
+ 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>>;
813
+ hideHeader: boolean;
814
+ hideHeaderOverview: boolean;
815
+ hideNoTracksActive: boolean;
816
+ trackSelectorType: string;
817
+ showCenterLine: boolean;
818
+ showCytobandsSetting: boolean;
819
+ trackLabels: string;
820
+ showGridlines: boolean;
821
+ 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]>>;
822
+ colorByCDS: boolean;
823
+ showTrackOutlines: boolean;
824
+ 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;
825
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
826
+ width: number;
827
+ } & {
828
+ menuItems(): import("@jbrowse/core/ui").MenuItem[];
829
+ } & {
830
+ setDisplayName(name: string): void;
831
+ setWidth(newWidth: number): void;
832
+ setMinimized(flag: boolean): void;
833
+ } & {
834
+ volatileWidth: number | undefined;
835
+ minimumBlockWidth: number;
836
+ draggingTrackId: undefined | string;
837
+ volatileError: unknown;
838
+ afterDisplayedRegionsSetCallbacks: (() => void)[];
839
+ scaleFactor: number;
840
+ trackRefs: Record<string, HTMLDivElement>;
841
+ coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
842
+ coarseTotalBp: number;
843
+ leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
844
+ rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
845
+ } & {
846
+ readonly pinnedTracks: any[];
847
+ readonly unpinnedTracks: any[];
848
+ readonly trackLabelsSetting: any;
849
+ readonly width: number;
850
+ readonly interRegionPaddingWidth: number;
851
+ readonly assemblyNames: string[];
852
+ readonly stickyViewHeaders: boolean;
853
+ readonly rubberbandTop: number;
854
+ readonly pinnedTracksTop: number;
855
+ } & {
856
+ scaleBarDisplayPrefix(): string | undefined;
857
+ MiniControlsComponent(): React.FC<any>;
858
+ HeaderComponent(): React.FC<any>;
859
+ readonly assembliesNotFound: string | undefined;
860
+ readonly assemblyErrors: string;
861
+ readonly assembliesInitialized: boolean;
862
+ readonly initialized: boolean;
863
+ readonly hasDisplayedRegions: boolean;
864
+ readonly scaleBarHeight: number;
865
+ readonly headerHeight: number;
866
+ readonly trackHeights: number;
867
+ readonly trackHeightsWithResizeHandles: number;
868
+ readonly height: number;
869
+ readonly totalBp: number;
870
+ readonly maxBpPerPx: number;
871
+ readonly minBpPerPx: number;
872
+ readonly error: unknown;
873
+ readonly maxOffset: number;
874
+ readonly minOffset: number;
875
+ readonly displayedRegionsTotalPx: number;
876
+ renderProps(): any;
877
+ searchScope(assemblyName: string): {
878
+ assemblyName: string;
879
+ includeAggregateIndexes: boolean;
880
+ 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>>;
881
+ };
882
+ getTrack(id: string): any;
883
+ rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
884
+ rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
885
+ readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
886
+ } & {
887
+ setShowTrackOutlines(arg: boolean): void;
888
+ setColorByCDS(flag: boolean): void;
889
+ setShowCytobands(flag: boolean): void;
890
+ setWidth(newWidth: number): void;
891
+ setError(error: unknown): void;
892
+ setHideHeader(b: boolean): void;
893
+ setHideHeaderOverview(b: boolean): void;
894
+ setHideNoTracksActive(b: boolean): void;
895
+ setShowGridlines(b: boolean): void;
896
+ addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
897
+ setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
898
+ removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
899
+ scrollTo(offsetPx: number): number;
900
+ zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
901
+ setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
902
+ setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
903
+ setNewView(bpPerPx: number, offsetPx: number): void;
904
+ horizontallyFlip(): void;
905
+ showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
906
+ hideTrack(trackId: string): number;
907
+ } & {
908
+ moveTrackDown(id: string): void;
909
+ moveTrackUp(id: string): void;
910
+ moveTrackToTop(id: string): void;
911
+ moveTrackToBottom(id: string): void;
912
+ moveTrack(movingId: string, targetId: string): void;
913
+ toggleTrack(trackId: string): boolean;
914
+ setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
915
+ setShowCenterLine(b: boolean): void;
916
+ setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
917
+ activateTrackSelector(): import("@jbrowse/core/util").Widget;
918
+ getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
919
+ start: number;
920
+ end: number;
921
+ type: string;
922
+ regionNumber?: number;
923
+ reversed?: boolean;
924
+ refName: string;
925
+ assemblyName: string;
926
+ key: string;
927
+ offsetPx: number;
928
+ widthPx: number;
929
+ variant?: string;
930
+ isLeftEndOfDisplayedRegion?: boolean;
931
+ }[];
932
+ afterDisplayedRegionsSet(cb: () => void): void;
933
+ horizontalScroll(distance: number): number;
934
+ center(): void;
935
+ showAllRegions(): void;
936
+ showAllRegionsInAssembly(assemblyName?: string): void;
937
+ setDraggingTrackId(idx?: string): void;
938
+ setScaleFactor(factor: number): void;
939
+ clearView(): void;
940
+ setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
941
+ exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
942
+ } & {
943
+ slide: (viewWidths: number) => void;
944
+ } & {
945
+ zoom: (targetBpPerPx: number) => void;
946
+ } & {
947
+ readonly canShowCytobands: boolean;
948
+ readonly showCytobands: boolean;
949
+ readonly anyCytobandsExist: boolean;
950
+ readonly cytobandOffset: number;
951
+ } & {
952
+ menuItems(): import("@jbrowse/core/ui").MenuItem[];
953
+ } & {
954
+ readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
955
+ readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
956
+ readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
957
+ readonly visibleLocStrings: string;
958
+ readonly coarseVisibleLocStrings: string;
959
+ } & {
960
+ setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
961
+ } & {
962
+ moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
963
+ navToLocString(input: string, optAssemblyName?: string): Promise<void>;
964
+ navToSearchString({ input, assembly, }: {
965
+ input: string;
966
+ assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
967
+ }): Promise<void>;
968
+ navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
969
+ navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
970
+ navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
971
+ } & {
972
+ rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
973
+ bpToPx({ refName, coord, regionNumber, }: {
974
+ refName: string;
975
+ coord: number;
976
+ regionNumber?: number;
977
+ }): {
978
+ index: number;
979
+ offsetPx: number;
980
+ } | undefined;
981
+ centerAt(coord: number, refName: string, regionNumber?: number): void;
982
+ pxToBp(px: number): {
983
+ coord: number;
984
+ index: number;
985
+ refName: string;
986
+ oob: boolean;
987
+ assemblyName: string;
988
+ offset: number;
989
+ start: number;
990
+ end: number;
991
+ reversed?: boolean;
992
+ };
993
+ readonly centerLineInfo: {
994
+ coord: number;
995
+ index: number;
996
+ refName: string;
997
+ oob: boolean;
998
+ assemblyName: string;
999
+ offset: number;
1000
+ start: number;
1001
+ end: number;
1002
+ reversed?: boolean;
1003
+ } | undefined;
1004
+ } & {
1005
+ afterCreate(): void;
1006
+ afterAttach(): void;
1007
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1008
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1009
+ displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
1010
+ minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1011
+ } & {
1012
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1013
+ type: import("mobx-state-tree").IType<string | undefined, string, string>;
1014
+ offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
1015
+ bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
1016
+ displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
1017
+ tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
1018
+ hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1019
+ hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1020
+ hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1021
+ trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1022
+ showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1023
+ showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1024
+ trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1025
+ showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1026
+ 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]>;
1027
+ colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1028
+ showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1029
+ 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>;
1030
+ }, {
1031
+ width: number;
1032
+ } & {
1033
+ menuItems(): import("@jbrowse/core/ui").MenuItem[];
1034
+ } & {
1035
+ setDisplayName(name: string): void;
1036
+ setWidth(newWidth: number): void;
1037
+ setMinimized(flag: boolean): void;
1038
+ } & {
1039
+ volatileWidth: number | undefined;
1040
+ minimumBlockWidth: number;
1041
+ draggingTrackId: undefined | string;
1042
+ volatileError: unknown;
1043
+ afterDisplayedRegionsSetCallbacks: (() => void)[];
1044
+ scaleFactor: number;
1045
+ trackRefs: Record<string, HTMLDivElement>;
1046
+ coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
1047
+ coarseTotalBp: number;
1048
+ leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
1049
+ rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
1050
+ } & {
1051
+ readonly pinnedTracks: any[];
1052
+ readonly unpinnedTracks: any[];
1053
+ readonly trackLabelsSetting: any;
1054
+ readonly width: number;
1055
+ readonly interRegionPaddingWidth: number;
1056
+ readonly assemblyNames: string[];
1057
+ readonly stickyViewHeaders: boolean;
1058
+ readonly rubberbandTop: number;
1059
+ readonly pinnedTracksTop: number;
1060
+ } & {
1061
+ scaleBarDisplayPrefix(): string | undefined;
1062
+ MiniControlsComponent(): React.FC<any>;
1063
+ HeaderComponent(): React.FC<any>;
1064
+ readonly assembliesNotFound: string | undefined;
1065
+ readonly assemblyErrors: string;
1066
+ readonly assembliesInitialized: boolean;
1067
+ readonly initialized: boolean;
1068
+ readonly hasDisplayedRegions: boolean;
1069
+ readonly scaleBarHeight: number;
1070
+ readonly headerHeight: number;
1071
+ readonly trackHeights: number;
1072
+ readonly trackHeightsWithResizeHandles: number;
1073
+ readonly height: number;
1074
+ readonly totalBp: number;
1075
+ readonly maxBpPerPx: number;
1076
+ readonly minBpPerPx: number;
1077
+ readonly error: unknown;
1078
+ readonly maxOffset: number;
1079
+ readonly minOffset: number;
1080
+ readonly displayedRegionsTotalPx: number;
1081
+ renderProps(): any;
1082
+ searchScope(assemblyName: string): {
1083
+ assemblyName: string;
1084
+ includeAggregateIndexes: boolean;
1085
+ 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>>;
1086
+ };
1087
+ getTrack(id: string): any;
1088
+ rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
1089
+ rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
1090
+ readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
1091
+ } & {
1092
+ setShowTrackOutlines(arg: boolean): void;
1093
+ setColorByCDS(flag: boolean): void;
1094
+ setShowCytobands(flag: boolean): void;
1095
+ setWidth(newWidth: number): void;
1096
+ setError(error: unknown): void;
1097
+ setHideHeader(b: boolean): void;
1098
+ setHideHeaderOverview(b: boolean): void;
1099
+ setHideNoTracksActive(b: boolean): void;
1100
+ setShowGridlines(b: boolean): void;
1101
+ addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
1102
+ setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
1103
+ removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
1104
+ scrollTo(offsetPx: number): number;
1105
+ zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
1106
+ setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
1107
+ setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
1108
+ setNewView(bpPerPx: number, offsetPx: number): void;
1109
+ horizontallyFlip(): void;
1110
+ showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
1111
+ hideTrack(trackId: string): number;
1112
+ } & {
1113
+ moveTrackDown(id: string): void;
1114
+ moveTrackUp(id: string): void;
1115
+ moveTrackToTop(id: string): void;
1116
+ moveTrackToBottom(id: string): void;
1117
+ moveTrack(movingId: string, targetId: string): void;
1118
+ toggleTrack(trackId: string): boolean;
1119
+ setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
1120
+ setShowCenterLine(b: boolean): void;
1121
+ setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
1122
+ activateTrackSelector(): import("@jbrowse/core/util").Widget;
1123
+ getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
1124
+ start: number;
1125
+ end: number;
1126
+ type: string;
1127
+ regionNumber?: number;
1128
+ reversed?: boolean;
1129
+ refName: string;
1130
+ assemblyName: string;
1131
+ key: string;
1132
+ offsetPx: number;
1133
+ widthPx: number;
1134
+ variant?: string;
1135
+ isLeftEndOfDisplayedRegion?: boolean;
1136
+ }[];
1137
+ afterDisplayedRegionsSet(cb: () => void): void;
1138
+ horizontalScroll(distance: number): number;
1139
+ center(): void;
1140
+ showAllRegions(): void;
1141
+ showAllRegionsInAssembly(assemblyName?: string): void;
1142
+ setDraggingTrackId(idx?: string): void;
1143
+ setScaleFactor(factor: number): void;
1144
+ clearView(): void;
1145
+ setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
1146
+ exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
1147
+ } & {
1148
+ slide: (viewWidths: number) => void;
1149
+ } & {
1150
+ zoom: (targetBpPerPx: number) => void;
1151
+ } & {
1152
+ readonly canShowCytobands: boolean;
1153
+ readonly showCytobands: boolean;
1154
+ readonly anyCytobandsExist: boolean;
1155
+ readonly cytobandOffset: number;
1156
+ } & {
1157
+ menuItems(): import("@jbrowse/core/ui").MenuItem[];
1158
+ } & {
1159
+ readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
1160
+ readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
1161
+ readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
1162
+ readonly visibleLocStrings: string;
1163
+ readonly coarseVisibleLocStrings: string;
1164
+ } & {
1165
+ setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
1166
+ } & {
1167
+ moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
1168
+ navToLocString(input: string, optAssemblyName?: string): Promise<void>;
1169
+ navToSearchString({ input, assembly, }: {
1170
+ input: string;
1171
+ assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
1172
+ }): Promise<void>;
1173
+ navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
1174
+ navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
1175
+ navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
1176
+ } & {
1177
+ rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
1178
+ bpToPx({ refName, coord, regionNumber, }: {
1179
+ refName: string;
1180
+ coord: number;
1181
+ regionNumber?: number;
1182
+ }): {
1183
+ index: number;
1184
+ offsetPx: number;
1185
+ } | undefined;
1186
+ centerAt(coord: number, refName: string, regionNumber?: number): void;
1187
+ pxToBp(px: number): {
1188
+ coord: number;
1189
+ index: number;
1190
+ refName: string;
1191
+ oob: boolean;
1192
+ assemblyName: string;
1193
+ offset: number;
1194
+ start: number;
1195
+ end: number;
1196
+ reversed?: boolean;
1197
+ };
1198
+ readonly centerLineInfo: {
1199
+ coord: number;
1200
+ index: number;
1201
+ refName: string;
1202
+ oob: boolean;
1203
+ assemblyName: string;
1204
+ offset: number;
1205
+ start: number;
1206
+ end: number;
1207
+ reversed?: boolean;
1208
+ } | undefined;
1209
+ } & {
1210
+ afterCreate(): void;
1211
+ afterAttach(): void;
1212
+ }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
1213
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1214
+ displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
1215
+ minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1216
+ } & {
1217
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1218
+ type: import("mobx-state-tree").IType<string | undefined, string, string>;
1219
+ offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
1220
+ bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
1221
+ displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
1222
+ tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
1223
+ hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1224
+ hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1225
+ hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1226
+ trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1227
+ showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1228
+ showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1229
+ trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1230
+ showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1231
+ 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]>;
1232
+ colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1233
+ showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1234
+ 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>;
1235
+ }>>, {
1236
+ type: string;
1237
+ id: string;
1238
+ displayName: string | undefined;
1239
+ tracks: any[];
1240
+ minimized: boolean;
1241
+ displayedRegions: import("@jbrowse/core/util").Region[];
1242
+ offsetPx: number;
1243
+ bpPerPx: number;
1244
+ hideHeader: boolean;
1245
+ hideHeaderOverview: boolean;
1246
+ hideNoTracksActive: boolean;
1247
+ trackSelectorType: string;
1248
+ showCenterLine: boolean;
1249
+ showCytobandsSetting: boolean;
1250
+ trackLabels: string;
1251
+ showGridlines: boolean;
1252
+ highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[];
1253
+ colorByCDS: boolean;
1254
+ showTrackOutlines: boolean;
1255
+ }>>;
1256
+ removeView(): void;
1257
+ } & {
1258
+ getTrackActionMenuItems(config: any): {
1259
+ label: string;
1260
+ onClick: () => void;
1261
+ icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
1262
+ muiName: string;
1263
+ };
1264
+ }[];
1265
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
1266
+ assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1267
+ assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1268
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1269
+ }, {
1270
+ error: unknown;
1271
+ loadingP: Promise<void> | undefined;
1272
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1273
+ refNameAliases: {
1274
+ [x: string]: string;
1275
+ } | undefined;
1276
+ lowerCaseRefNameAliases: {
1277
+ [x: string]: string;
1278
+ } | undefined;
1279
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1280
+ } & {
1281
+ getConf(arg: string): any;
1282
+ } & {
1283
+ readonly initialized: boolean;
1284
+ readonly name: string;
1285
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1286
+ readonly aliases: string[];
1287
+ readonly displayName: string | undefined;
1288
+ hasName(name: string): boolean;
1289
+ readonly allAliases: string[];
1290
+ readonly allRefNames: string[] | undefined;
1291
+ readonly lowerCaseRefNames: string[] | undefined;
1292
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1293
+ readonly rpcManager: RpcManager;
1294
+ readonly refNameColors: string[];
1295
+ } & {
1296
+ readonly refNames: string[] | undefined;
1297
+ } & {
1298
+ getCanonicalRefName(refName: string): string | undefined;
1299
+ getRefNameColor(refName: string): string | undefined;
1300
+ isValidRefName(refName: string): boolean;
1301
+ } & {
1302
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1303
+ regions: import("@jbrowse/core/util").Region[];
1304
+ refNameAliases: {
1305
+ [x: string]: string;
1306
+ };
1307
+ lowerCaseRefNameAliases: {
1308
+ [x: string]: string;
1309
+ };
1310
+ cytobands: import("@jbrowse/core/util").Feature[];
1311
+ }): void;
1312
+ setError(e: unknown): void;
1313
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1314
+ setRefNameAliases(aliases: {
1315
+ [x: string]: string;
1316
+ }, lowerCaseAliases: {
1317
+ [x: string]: string;
1318
+ }): void;
1319
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1320
+ setLoadingP(p?: Promise<void>): void;
1321
+ load(): Promise<void>;
1322
+ loadPre(): Promise<void>;
1323
+ } & {
1324
+ getAdapterMapEntry(adapterConf: {
1325
+ [x: string]: unknown;
1326
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1327
+ getRefNameMapForAdapter(adapterConf: {
1328
+ [x: string]: unknown;
1329
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1330
+ [x: string]: string;
1331
+ }>;
1332
+ getReverseRefNameMapForAdapter(adapterConf: {
1333
+ [x: string]: unknown;
1334
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1335
+ [x: string]: string;
1336
+ }>;
1337
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1338
+ }, {
1339
+ readonly assemblyNameMap: Record<string, {
1340
+ configuration: any;
1341
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1342
+ error: unknown;
1343
+ loadingP: Promise<void> | undefined;
1344
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1345
+ refNameAliases: {
1346
+ [x: string]: string;
1347
+ } | undefined;
1348
+ lowerCaseRefNameAliases: {
1349
+ [x: string]: string;
1350
+ } | undefined;
1351
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1352
+ } & {
1353
+ getConf(arg: string): any;
1354
+ } & {
1355
+ readonly initialized: boolean;
1356
+ readonly name: string;
1357
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1358
+ readonly aliases: string[];
1359
+ readonly displayName: string | undefined;
1360
+ hasName(name: string): boolean;
1361
+ readonly allAliases: string[];
1362
+ readonly allRefNames: string[] | undefined;
1363
+ readonly lowerCaseRefNames: string[] | undefined;
1364
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1365
+ readonly rpcManager: RpcManager;
1366
+ readonly refNameColors: string[];
1367
+ } & {
1368
+ readonly refNames: string[] | undefined;
1369
+ } & {
1370
+ getCanonicalRefName(refName: string): string | undefined;
1371
+ getRefNameColor(refName: string): string | undefined;
1372
+ isValidRefName(refName: string): boolean;
1373
+ } & {
1374
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1375
+ regions: import("@jbrowse/core/util").Region[];
1376
+ refNameAliases: {
1377
+ [x: string]: string;
1378
+ };
1379
+ lowerCaseRefNameAliases: {
1380
+ [x: string]: string;
1381
+ };
1382
+ cytobands: import("@jbrowse/core/util").Feature[];
1383
+ }): void;
1384
+ setError(e: unknown): void;
1385
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1386
+ setRefNameAliases(aliases: {
1387
+ [x: string]: string;
1388
+ }, lowerCaseAliases: {
1389
+ [x: string]: string;
1390
+ }): void;
1391
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1392
+ setLoadingP(p?: Promise<void>): void;
1393
+ load(): Promise<void>;
1394
+ loadPre(): Promise<void>;
1395
+ } & {
1396
+ getAdapterMapEntry(adapterConf: {
1397
+ [x: string]: unknown;
1398
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1399
+ getRefNameMapForAdapter(adapterConf: {
1400
+ [x: string]: unknown;
1401
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1402
+ [x: string]: string;
1403
+ }>;
1404
+ getReverseRefNameMapForAdapter(adapterConf: {
1405
+ [x: string]: unknown;
1406
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1407
+ [x: string]: string;
1408
+ }>;
1409
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1410
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1411
+ }, {
1412
+ error: unknown;
1413
+ loadingP: Promise<void> | undefined;
1414
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1415
+ refNameAliases: {
1416
+ [x: string]: string;
1417
+ } | undefined;
1418
+ lowerCaseRefNameAliases: {
1419
+ [x: string]: string;
1420
+ } | undefined;
1421
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1422
+ } & {
1423
+ getConf(arg: string): any;
1424
+ } & {
1425
+ readonly initialized: boolean;
1426
+ readonly name: string;
1427
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1428
+ readonly aliases: string[];
1429
+ readonly displayName: string | undefined;
1430
+ hasName(name: string): boolean;
1431
+ readonly allAliases: string[];
1432
+ readonly allRefNames: string[] | undefined;
1433
+ readonly lowerCaseRefNames: string[] | undefined;
1434
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1435
+ readonly rpcManager: RpcManager;
1436
+ readonly refNameColors: string[];
1437
+ } & {
1438
+ readonly refNames: string[] | undefined;
1439
+ } & {
1440
+ getCanonicalRefName(refName: string): string | undefined;
1441
+ getRefNameColor(refName: string): string | undefined;
1442
+ isValidRefName(refName: string): boolean;
1443
+ } & {
1444
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1445
+ regions: import("@jbrowse/core/util").Region[];
1446
+ refNameAliases: {
1447
+ [x: string]: string;
1448
+ };
1449
+ lowerCaseRefNameAliases: {
1450
+ [x: string]: string;
1451
+ };
1452
+ cytobands: import("@jbrowse/core/util").Feature[];
1453
+ }): void;
1454
+ setError(e: unknown): void;
1455
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1456
+ setRefNameAliases(aliases: {
1457
+ [x: string]: string;
1458
+ }, lowerCaseAliases: {
1459
+ [x: string]: string;
1460
+ }): void;
1461
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1462
+ setLoadingP(p?: Promise<void>): void;
1463
+ load(): Promise<void>;
1464
+ loadPre(): Promise<void>;
1465
+ } & {
1466
+ getAdapterMapEntry(adapterConf: {
1467
+ [x: string]: unknown;
1468
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1469
+ getRefNameMapForAdapter(adapterConf: {
1470
+ [x: string]: unknown;
1471
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1472
+ [x: string]: string;
1473
+ }>;
1474
+ getReverseRefNameMapForAdapter(adapterConf: {
1475
+ [x: string]: unknown;
1476
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1477
+ [x: string]: string;
1478
+ }>;
1479
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
1480
+ } & {
1481
+ get(asmName: string): ({
1482
+ configuration: any;
1483
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1484
+ error: unknown;
1485
+ loadingP: Promise<void> | undefined;
1486
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1487
+ refNameAliases: {
1488
+ [x: string]: string;
1489
+ } | undefined;
1490
+ lowerCaseRefNameAliases: {
1491
+ [x: string]: string;
1492
+ } | undefined;
1493
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1494
+ } & {
1495
+ getConf(arg: string): any;
1496
+ } & {
1497
+ readonly initialized: boolean;
1498
+ readonly name: string;
1499
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1500
+ readonly aliases: string[];
1501
+ readonly displayName: string | undefined;
1502
+ hasName(name: string): boolean;
1503
+ readonly allAliases: string[];
1504
+ readonly allRefNames: string[] | undefined;
1505
+ readonly lowerCaseRefNames: string[] | undefined;
1506
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1507
+ readonly rpcManager: RpcManager;
1508
+ readonly refNameColors: string[];
1509
+ } & {
1510
+ readonly refNames: string[] | undefined;
1511
+ } & {
1512
+ getCanonicalRefName(refName: string): string | undefined;
1513
+ getRefNameColor(refName: string): string | undefined;
1514
+ isValidRefName(refName: string): boolean;
1515
+ } & {
1516
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1517
+ regions: import("@jbrowse/core/util").Region[];
1518
+ refNameAliases: {
1519
+ [x: string]: string;
1520
+ };
1521
+ lowerCaseRefNameAliases: {
1522
+ [x: string]: string;
1523
+ };
1524
+ cytobands: import("@jbrowse/core/util").Feature[];
1525
+ }): void;
1526
+ setError(e: unknown): void;
1527
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1528
+ setRefNameAliases(aliases: {
1529
+ [x: string]: string;
1530
+ }, lowerCaseAliases: {
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
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1552
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1553
+ }, {
1554
+ error: unknown;
1555
+ loadingP: Promise<void> | undefined;
1556
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1557
+ refNameAliases: {
1558
+ [x: string]: string;
1559
+ } | undefined;
1560
+ lowerCaseRefNameAliases: {
1561
+ [x: string]: string;
1562
+ } | undefined;
1563
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1564
+ } & {
1565
+ getConf(arg: string): any;
1566
+ } & {
1567
+ readonly initialized: boolean;
1568
+ readonly name: string;
1569
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1570
+ readonly aliases: string[];
1571
+ readonly displayName: string | undefined;
1572
+ hasName(name: string): boolean;
1573
+ readonly allAliases: string[];
1574
+ readonly allRefNames: string[] | undefined;
1575
+ readonly lowerCaseRefNames: string[] | undefined;
1576
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1577
+ readonly rpcManager: RpcManager;
1578
+ readonly refNameColors: string[];
1579
+ } & {
1580
+ readonly refNames: string[] | undefined;
1581
+ } & {
1582
+ getCanonicalRefName(refName: string): string | undefined;
1583
+ getRefNameColor(refName: string): string | undefined;
1584
+ isValidRefName(refName: string): boolean;
1585
+ } & {
1586
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1587
+ regions: import("@jbrowse/core/util").Region[];
1588
+ refNameAliases: {
1589
+ [x: string]: string;
1590
+ };
1591
+ lowerCaseRefNameAliases: {
1592
+ [x: string]: string;
1593
+ };
1594
+ cytobands: import("@jbrowse/core/util").Feature[];
1595
+ }): void;
1596
+ setError(e: unknown): void;
1597
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1598
+ setRefNameAliases(aliases: {
1599
+ [x: string]: string;
1600
+ }, lowerCaseAliases: {
1601
+ [x: string]: string;
1602
+ }): void;
1603
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1604
+ setLoadingP(p?: Promise<void>): void;
1605
+ load(): Promise<void>;
1606
+ loadPre(): Promise<void>;
1607
+ } & {
1608
+ getAdapterMapEntry(adapterConf: {
1609
+ [x: string]: unknown;
1610
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1611
+ getRefNameMapForAdapter(adapterConf: {
1612
+ [x: string]: unknown;
1613
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1614
+ [x: string]: string;
1615
+ }>;
1616
+ getReverseRefNameMapForAdapter(adapterConf: {
1617
+ [x: string]: unknown;
1618
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1619
+ [x: string]: string;
1620
+ }>;
1621
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1622
+ readonly assemblyNamesList: any[];
1623
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1624
+ readonly rpcManager: RpcManager;
1625
+ } & {
1626
+ waitForAssembly(assemblyName: string): Promise<({
1627
+ configuration: any;
1628
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1629
+ error: unknown;
1630
+ loadingP: Promise<void> | undefined;
1631
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1632
+ refNameAliases: {
1633
+ [x: string]: string;
1634
+ } | undefined;
1635
+ lowerCaseRefNameAliases: {
1636
+ [x: string]: string;
1637
+ } | undefined;
1638
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1639
+ } & {
1640
+ getConf(arg: string): any;
1641
+ } & {
1642
+ readonly initialized: boolean;
1643
+ readonly name: string;
1644
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1645
+ readonly aliases: string[];
1646
+ readonly displayName: string | undefined;
1647
+ hasName(name: string): boolean;
1648
+ readonly allAliases: string[];
1649
+ readonly allRefNames: string[] | undefined;
1650
+ readonly lowerCaseRefNames: string[] | undefined;
1651
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1652
+ readonly rpcManager: RpcManager;
1653
+ readonly refNameColors: string[];
1654
+ } & {
1655
+ readonly refNames: string[] | undefined;
1656
+ } & {
1657
+ getCanonicalRefName(refName: string): string | undefined;
1658
+ getRefNameColor(refName: string): string | undefined;
1659
+ isValidRefName(refName: string): boolean;
1660
+ } & {
1661
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1662
+ regions: import("@jbrowse/core/util").Region[];
1663
+ refNameAliases: {
1664
+ [x: string]: string;
1665
+ };
1666
+ lowerCaseRefNameAliases: {
1667
+ [x: string]: string;
1668
+ };
1669
+ cytobands: import("@jbrowse/core/util").Feature[];
1670
+ }): void;
1671
+ setError(e: unknown): void;
1672
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1673
+ setRefNameAliases(aliases: {
1674
+ [x: string]: string;
1675
+ }, lowerCaseAliases: {
1676
+ [x: string]: string;
1677
+ }): void;
1678
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1679
+ setLoadingP(p?: Promise<void>): void;
1680
+ load(): Promise<void>;
1681
+ loadPre(): Promise<void>;
1682
+ } & {
1683
+ getAdapterMapEntry(adapterConf: {
1684
+ [x: string]: unknown;
1685
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1686
+ getRefNameMapForAdapter(adapterConf: {
1687
+ [x: string]: unknown;
1688
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1689
+ [x: string]: string;
1690
+ }>;
1691
+ getReverseRefNameMapForAdapter(adapterConf: {
1692
+ [x: string]: unknown;
1693
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1694
+ [x: string]: string;
1695
+ }>;
1696
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1697
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1698
+ }, {
1699
+ error: unknown;
1700
+ loadingP: Promise<void> | undefined;
1701
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1702
+ refNameAliases: {
1703
+ [x: string]: string;
1704
+ } | undefined;
1705
+ lowerCaseRefNameAliases: {
1706
+ [x: string]: string;
1707
+ } | undefined;
1708
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1709
+ } & {
1710
+ getConf(arg: string): any;
1711
+ } & {
1712
+ readonly initialized: boolean;
1713
+ readonly name: string;
1714
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1715
+ readonly aliases: string[];
1716
+ readonly displayName: string | undefined;
1717
+ hasName(name: string): boolean;
1718
+ readonly allAliases: string[];
1719
+ readonly allRefNames: string[] | undefined;
1720
+ readonly lowerCaseRefNames: string[] | undefined;
1721
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1722
+ readonly rpcManager: RpcManager;
1723
+ readonly refNameColors: string[];
1724
+ } & {
1725
+ readonly refNames: string[] | undefined;
1726
+ } & {
1727
+ getCanonicalRefName(refName: string): string | undefined;
1728
+ getRefNameColor(refName: string): string | undefined;
1729
+ isValidRefName(refName: string): boolean;
1730
+ } & {
1731
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1732
+ regions: import("@jbrowse/core/util").Region[];
1733
+ refNameAliases: {
1734
+ [x: string]: string;
1735
+ };
1736
+ lowerCaseRefNameAliases: {
1737
+ [x: string]: string;
1738
+ };
1739
+ cytobands: import("@jbrowse/core/util").Feature[];
1740
+ }): void;
1741
+ setError(e: unknown): void;
1742
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1743
+ setRefNameAliases(aliases: {
1744
+ [x: string]: string;
1745
+ }, lowerCaseAliases: {
1746
+ [x: string]: string;
1747
+ }): void;
1748
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1749
+ setLoadingP(p?: Promise<void>): void;
1750
+ load(): Promise<void>;
1751
+ loadPre(): Promise<void>;
1752
+ } & {
1753
+ getAdapterMapEntry(adapterConf: {
1754
+ [x: string]: unknown;
1755
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1756
+ getRefNameMapForAdapter(adapterConf: {
1757
+ [x: string]: unknown;
1758
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1759
+ [x: string]: string;
1760
+ }>;
1761
+ getReverseRefNameMapForAdapter(adapterConf: {
1762
+ [x: string]: unknown;
1763
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1764
+ [x: string]: string;
1765
+ }>;
1766
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1767
+ getRefNameMapForAdapter(adapterConf: {
1768
+ [x: string]: unknown;
1769
+ }, assemblyName: string | undefined, opts: {
1770
+ stopToken?: string;
1771
+ sessionId: string;
1772
+ }): Promise<{
1773
+ [x: string]: string;
1774
+ } | undefined>;
1775
+ getReverseRefNameMapForAdapter(adapterConf: {
1776
+ [x: string]: unknown;
1777
+ }, assemblyName: string | undefined, opts: {
1778
+ stopToken?: string;
1779
+ sessionId: string;
1780
+ }): Promise<{
1781
+ [x: string]: string;
1782
+ } | undefined>;
1783
+ isValidRefName(refName: string, assemblyName: string): boolean;
1784
+ } & {
1785
+ afterAttach(): void;
1786
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1787
+ addAssembly(configuration: any): void;
1788
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
1789
+ disableAddTracks: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1790
+ internetAccounts: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
1791
+ }, {
1792
+ error: unknown;
1793
+ rpcManager: RpcManager;
1794
+ textSearchManager: TextSearchManager;
1795
+ adminMode: boolean;
1796
+ version: string;
1797
+ } & {
1798
+ setSession(sessionSnapshot: SnapshotIn<import("mobx-state-tree").IModelType<{
1799
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1800
+ name: import("mobx-state-tree").ISimpleType<string>;
1801
+ margin: import("mobx-state-tree").IType<number | undefined, number, number>;
1802
+ } & {
1803
+ drawerPosition: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1804
+ drawerWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
1805
+ widgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyType>;
1806
+ activeWidgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>>;
1807
+ minimized: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1808
+ } & {
1809
+ connectionInstances: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1810
+ name: import("mobx-state-tree").ISimpleType<string>;
1811
+ tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
1812
+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1813
+ name: {
1814
+ type: string;
1815
+ defaultValue: string;
1816
+ description: string;
1817
+ };
1818
+ assemblyNames: {
1819
+ type: string;
1820
+ defaultValue: never[];
1821
+ description: string;
1822
+ };
1823
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
1824
+ }, {
1825
+ connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1826
+ } & {
1827
+ afterAttach(): void;
1828
+ addTrackConf(trackConf: ({
1829
+ [x: string]: any;
1830
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1831
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1832
+ [x: string]: any;
1833
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1834
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1835
+ [x: string]: any;
1836
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1837
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1838
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
1839
+ addTrackConfs(trackConfs: (({
1840
+ [x: string]: any;
1841
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1842
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1843
+ [x: string]: any;
1844
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1845
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1846
+ [x: string]: any;
1847
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1848
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1849
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
1850
+ setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
1851
+ clear(): void;
1852
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1853
+ } & {
1854
+ sessionTracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
1855
+ } & {
1856
+ view: import("@jbrowse/plugin-linear-genome-view").LinearGenomeViewStateModel;
1857
+ sessionTracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
1858
+ }, {
1859
+ selection: unknown;
1860
+ hovered: unknown;
1861
+ } & {
1862
+ readonly root: import("mobx-state-tree").TypeOrStateTreeNodeToStateTreeNode<ROOT_MODEL_TYPE>;
1863
+ } & {
1864
+ readonly jbrowse: any;
1865
+ readonly rpcManager: RpcManager;
1866
+ readonly configuration: {
1867
+ [x: string]: any;
1868
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1869
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1870
+ [x: string]: any;
1871
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1872
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1873
+ [x: string]: any;
1874
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1875
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1876
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1877
+ readonly adminMode: boolean;
1878
+ readonly textSearchManager: TextSearchManager;
1879
+ } & {
1880
+ readonly assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
1881
+ } & {
1882
+ setSelection(thing: unknown): void;
1883
+ clearSelection(): void;
1884
+ setHovered(thing: unknown): void;
1885
+ } & {
1886
+ readonly visibleWidget: any;
1887
+ } & {
1888
+ setDrawerPosition(arg: string): void;
1889
+ updateDrawerWidth(drawerWidth: number): number;
1890
+ resizeDrawer(distance: number): number;
1891
+ addWidget(typeName: string, id: string, initialState?: {}, conf?: unknown): any;
1892
+ showWidget(widget: any): void;
1893
+ hasWidget(widget: any): boolean;
1894
+ hideWidget(widget: any): void;
1895
+ minimizeWidgetDrawer(): void;
1896
+ showWidgetDrawer(): void;
1897
+ hideAllWidgets(): void;
1898
+ editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1899
+ afterAttach(): void;
1900
+ } & {
1901
+ readonly connections: import("@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig").BaseConnectionConfigModel[];
1902
+ } & {
1903
+ makeConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: {}): ({
1904
+ name: string;
1905
+ 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>>;
1906
+ configuration: {
1907
+ [x: string]: any;
1908
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1909
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1910
+ [x: string]: any;
1911
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1912
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1913
+ [x: string]: any;
1914
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1915
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1916
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1917
+ name: {
1918
+ type: string;
1919
+ defaultValue: string;
1920
+ description: string;
1921
+ };
1922
+ assemblyNames: {
1923
+ type: string;
1924
+ defaultValue: never[];
1925
+ description: string;
1926
+ };
1927
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>;
1928
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1929
+ connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1930
+ } & {
1931
+ afterAttach(): void;
1932
+ addTrackConf(trackConf: ({
1933
+ [x: string]: any;
1934
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1935
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1936
+ [x: string]: any;
1937
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1938
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1939
+ [x: string]: any;
1940
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1941
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1942
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
1943
+ addTrackConfs(trackConfs: (({
1944
+ [x: string]: any;
1945
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1946
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1947
+ [x: string]: any;
1948
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1949
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1950
+ [x: string]: any;
1951
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1952
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1953
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
1954
+ setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
1955
+ clear(): void;
1956
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1957
+ name: import("mobx-state-tree").ISimpleType<string>;
1958
+ tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
1959
+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1960
+ name: {
1961
+ type: string;
1962
+ defaultValue: string;
1963
+ description: string;
1964
+ };
1965
+ assemblyNames: {
1966
+ type: string;
1967
+ defaultValue: never[];
1968
+ description: string;
1969
+ };
1970
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
1971
+ }, {
1972
+ connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1973
+ } & {
1974
+ afterAttach(): void;
1975
+ addTrackConf(trackConf: ({
1976
+ [x: string]: any;
1977
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1978
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1979
+ [x: string]: any;
1980
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1981
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1982
+ [x: string]: any;
1983
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1984
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1985
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
1986
+ addTrackConfs(trackConfs: (({
1987
+ [x: string]: any;
1988
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1989
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1990
+ [x: string]: any;
1991
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1992
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1993
+ [x: string]: any;
1994
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1995
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1996
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
1997
+ setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
1998
+ clear(): void;
1999
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
2000
+ prepareToBreakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): (Record<string, number> | (() => void))[] | undefined;
2001
+ breakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
2002
+ deleteConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
2003
+ addConnectionConf(connectionConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
2004
+ clearConnections(): void;
2005
+ } & {
2006
+ queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, unknown][];
2007
+ } & {
2008
+ readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType | undefined;
2009
+ readonly DialogProps: unknown;
2010
+ } & {
2011
+ removeActiveDialog(): void;
2012
+ queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, unknown]): void;
2013
+ } & {
2014
+ getReferring(object: import("mobx-state-tree").IAnyStateTreeNode): import("@jbrowse/product-core").ReferringNode[];
2015
+ } & {
2016
+ removeReferring(referring: import("@jbrowse/product-core").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
2017
+ } & {
2018
+ readonly tracks: import("@jbrowse/core/configuration").AnyConfigurationModel[];
2019
+ } & {
2020
+ addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfiguration): any;
2021
+ deleteTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
2022
+ } & {
2023
+ readonly tracks: import("@jbrowse/core/configuration").AnyConfigurationModel[];
2024
+ } & {
2025
+ addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfiguration): any;
2026
+ deleteTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
2027
+ } & {
2028
+ snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
2029
+ } & {
2030
+ readonly snackbarMessageSet: Map<string, import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
2031
+ } & {
2032
+ notify(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction): void;
2033
+ notifyError(errorMessage: string, error?: unknown, extra?: unknown): void;
2034
+ pushSnackbarMessage(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction): void;
2035
+ popSnackbarMessage(): import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage | undefined;
2036
+ removeSnackbarMessage(message: string): void;
2037
+ } & {
2038
+ readonly version: any;
2039
+ readonly disableAddTracks: any;
2040
+ readonly assemblies: any[];
2041
+ readonly assemblyNames: any[];
2042
+ readonly connections: any;
2043
+ readonly assemblyManager: any;
2044
+ readonly views: ({
2045
+ id: string;
2046
+ displayName: string | undefined;
2047
+ minimized: boolean;
2048
+ type: string;
2049
+ offsetPx: number;
2050
+ bpPerPx: number;
2051
+ displayedRegions: import("@jbrowse/core/util").Region[] & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>>;
2052
+ 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>>;
2053
+ hideHeader: boolean;
2054
+ hideHeaderOverview: boolean;
2055
+ hideNoTracksActive: boolean;
2056
+ trackSelectorType: string;
2057
+ showCenterLine: boolean;
2058
+ showCytobandsSetting: boolean;
2059
+ trackLabels: string;
2060
+ showGridlines: boolean;
2061
+ 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]>>;
2062
+ colorByCDS: boolean;
2063
+ showTrackOutlines: boolean;
2064
+ 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;
2065
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2066
+ width: number;
2067
+ } & {
2068
+ menuItems(): import("@jbrowse/core/ui").MenuItem[];
2069
+ } & {
2070
+ setDisplayName(name: string): void;
2071
+ setWidth(newWidth: number): void;
2072
+ setMinimized(flag: boolean): void;
2073
+ } & {
2074
+ volatileWidth: number | undefined;
2075
+ minimumBlockWidth: number;
2076
+ draggingTrackId: undefined | string;
2077
+ volatileError: unknown;
2078
+ afterDisplayedRegionsSetCallbacks: (() => void)[];
2079
+ scaleFactor: number;
2080
+ trackRefs: Record<string, HTMLDivElement>;
2081
+ coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2082
+ coarseTotalBp: number;
2083
+ leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
2084
+ rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
2085
+ } & {
2086
+ readonly pinnedTracks: any[];
2087
+ readonly unpinnedTracks: any[];
2088
+ readonly trackLabelsSetting: any;
2089
+ readonly width: number;
2090
+ readonly interRegionPaddingWidth: number;
2091
+ readonly assemblyNames: string[];
2092
+ readonly stickyViewHeaders: boolean;
2093
+ readonly rubberbandTop: number;
2094
+ readonly pinnedTracksTop: number;
2095
+ } & {
2096
+ scaleBarDisplayPrefix(): string | undefined;
2097
+ MiniControlsComponent(): React.FC<any>;
2098
+ HeaderComponent(): React.FC<any>;
2099
+ readonly assembliesNotFound: string | undefined;
2100
+ readonly assemblyErrors: string;
2101
+ readonly assembliesInitialized: boolean;
2102
+ readonly initialized: boolean;
2103
+ readonly hasDisplayedRegions: boolean;
2104
+ readonly scaleBarHeight: number;
2105
+ readonly headerHeight: number;
2106
+ readonly trackHeights: number;
2107
+ readonly trackHeightsWithResizeHandles: number;
2108
+ readonly height: number;
2109
+ readonly totalBp: number;
2110
+ readonly maxBpPerPx: number;
2111
+ readonly minBpPerPx: number;
2112
+ readonly error: unknown;
2113
+ readonly maxOffset: number;
2114
+ readonly minOffset: number;
2115
+ readonly displayedRegionsTotalPx: number;
2116
+ renderProps(): any;
2117
+ searchScope(assemblyName: string): {
2118
+ assemblyName: string;
2119
+ includeAggregateIndexes: boolean;
2120
+ 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>>;
2121
+ };
2122
+ getTrack(id: string): any;
2123
+ rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
2124
+ rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
2125
+ readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
2126
+ } & {
2127
+ setShowTrackOutlines(arg: boolean): void;
2128
+ setColorByCDS(flag: boolean): void;
2129
+ setShowCytobands(flag: boolean): void;
2130
+ setWidth(newWidth: number): void;
2131
+ setError(error: unknown): void;
2132
+ setHideHeader(b: boolean): void;
2133
+ setHideHeaderOverview(b: boolean): void;
2134
+ setHideNoTracksActive(b: boolean): void;
2135
+ setShowGridlines(b: boolean): void;
2136
+ addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
2137
+ setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
2138
+ removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
2139
+ scrollTo(offsetPx: number): number;
2140
+ zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
2141
+ setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2142
+ setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
2143
+ setNewView(bpPerPx: number, offsetPx: number): void;
2144
+ horizontallyFlip(): void;
2145
+ showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
2146
+ hideTrack(trackId: string): number;
2147
+ } & {
2148
+ moveTrackDown(id: string): void;
2149
+ moveTrackUp(id: string): void;
2150
+ moveTrackToTop(id: string): void;
2151
+ moveTrackToBottom(id: string): void;
2152
+ moveTrack(movingId: string, targetId: string): void;
2153
+ toggleTrack(trackId: string): boolean;
2154
+ setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
2155
+ setShowCenterLine(b: boolean): void;
2156
+ setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
2157
+ activateTrackSelector(): import("@jbrowse/core/util").Widget;
2158
+ getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
2159
+ start: number;
2160
+ end: number;
2161
+ type: string;
2162
+ regionNumber?: number;
2163
+ reversed?: boolean;
2164
+ refName: string;
2165
+ assemblyName: string;
2166
+ key: string;
2167
+ offsetPx: number;
2168
+ widthPx: number;
2169
+ variant?: string;
2170
+ isLeftEndOfDisplayedRegion?: boolean;
2171
+ }[];
2172
+ afterDisplayedRegionsSet(cb: () => void): void;
2173
+ horizontalScroll(distance: number): number;
2174
+ center(): void;
2175
+ showAllRegions(): void;
2176
+ showAllRegionsInAssembly(assemblyName?: string): void;
2177
+ setDraggingTrackId(idx?: string): void;
2178
+ setScaleFactor(factor: number): void;
2179
+ clearView(): void;
2180
+ setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
2181
+ exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
2182
+ } & {
2183
+ slide: (viewWidths: number) => void;
2184
+ } & {
2185
+ zoom: (targetBpPerPx: number) => void;
2186
+ } & {
2187
+ readonly canShowCytobands: boolean;
2188
+ readonly showCytobands: boolean;
2189
+ readonly anyCytobandsExist: boolean;
2190
+ readonly cytobandOffset: number;
2191
+ } & {
2192
+ menuItems(): import("@jbrowse/core/ui").MenuItem[];
2193
+ } & {
2194
+ readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2195
+ readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2196
+ readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2197
+ readonly visibleLocStrings: string;
2198
+ readonly coarseVisibleLocStrings: string;
2199
+ } & {
2200
+ setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
2201
+ } & {
2202
+ moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2203
+ navToLocString(input: string, optAssemblyName?: string): Promise<void>;
2204
+ navToSearchString({ input, assembly, }: {
2205
+ input: string;
2206
+ assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
2207
+ }): Promise<void>;
2208
+ navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
2209
+ navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
2210
+ navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
2211
+ } & {
2212
+ rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
2213
+ bpToPx({ refName, coord, regionNumber, }: {
2214
+ refName: string;
2215
+ coord: number;
2216
+ regionNumber?: number;
2217
+ }): {
2218
+ index: number;
2219
+ offsetPx: number;
2220
+ } | undefined;
2221
+ centerAt(coord: number, refName: string, regionNumber?: number): void;
2222
+ pxToBp(px: number): {
2223
+ coord: number;
2224
+ index: number;
2225
+ refName: string;
2226
+ oob: boolean;
2227
+ assemblyName: string;
2228
+ offset: number;
2229
+ start: number;
2230
+ end: number;
2231
+ reversed?: boolean;
2232
+ };
2233
+ readonly centerLineInfo: {
2234
+ coord: number;
2235
+ index: number;
2236
+ refName: string;
2237
+ oob: boolean;
2238
+ assemblyName: string;
2239
+ offset: number;
2240
+ start: number;
2241
+ end: number;
2242
+ reversed?: boolean;
2243
+ } | undefined;
2244
+ } & {
2245
+ afterCreate(): void;
2246
+ afterAttach(): void;
2247
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2248
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2249
+ displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
2250
+ minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2251
+ } & {
2252
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2253
+ type: import("mobx-state-tree").IType<string | undefined, string, string>;
2254
+ offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2255
+ bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2256
+ displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
2257
+ tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
2258
+ hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2259
+ hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2260
+ hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2261
+ trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2262
+ showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2263
+ showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2264
+ trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2265
+ showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2266
+ 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]>;
2267
+ colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2268
+ showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2269
+ 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>;
2270
+ }, {
2271
+ width: number;
2272
+ } & {
2273
+ menuItems(): import("@jbrowse/core/ui").MenuItem[];
2274
+ } & {
2275
+ setDisplayName(name: string): void;
2276
+ setWidth(newWidth: number): void;
2277
+ setMinimized(flag: boolean): void;
2278
+ } & {
2279
+ volatileWidth: number | undefined;
2280
+ minimumBlockWidth: number;
2281
+ draggingTrackId: undefined | string;
2282
+ volatileError: unknown;
2283
+ afterDisplayedRegionsSetCallbacks: (() => void)[];
2284
+ scaleFactor: number;
2285
+ trackRefs: Record<string, HTMLDivElement>;
2286
+ coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2287
+ coarseTotalBp: number;
2288
+ leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
2289
+ rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
2290
+ } & {
2291
+ readonly pinnedTracks: any[];
2292
+ readonly unpinnedTracks: any[];
2293
+ readonly trackLabelsSetting: any;
2294
+ readonly width: number;
2295
+ readonly interRegionPaddingWidth: number;
2296
+ readonly assemblyNames: string[];
2297
+ readonly stickyViewHeaders: boolean;
2298
+ readonly rubberbandTop: number;
2299
+ readonly pinnedTracksTop: number;
2300
+ } & {
2301
+ scaleBarDisplayPrefix(): string | undefined;
2302
+ MiniControlsComponent(): React.FC<any>;
2303
+ HeaderComponent(): React.FC<any>;
2304
+ readonly assembliesNotFound: string | undefined;
2305
+ readonly assemblyErrors: string;
2306
+ readonly assembliesInitialized: boolean;
2307
+ readonly initialized: boolean;
2308
+ readonly hasDisplayedRegions: boolean;
2309
+ readonly scaleBarHeight: number;
2310
+ readonly headerHeight: number;
2311
+ readonly trackHeights: number;
2312
+ readonly trackHeightsWithResizeHandles: number;
2313
+ readonly height: number;
2314
+ readonly totalBp: number;
2315
+ readonly maxBpPerPx: number;
2316
+ readonly minBpPerPx: number;
2317
+ readonly error: unknown;
2318
+ readonly maxOffset: number;
2319
+ readonly minOffset: number;
2320
+ readonly displayedRegionsTotalPx: number;
2321
+ renderProps(): any;
2322
+ searchScope(assemblyName: string): {
2323
+ assemblyName: string;
2324
+ includeAggregateIndexes: boolean;
2325
+ 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>>;
2326
+ };
2327
+ getTrack(id: string): any;
2328
+ rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
2329
+ rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
2330
+ readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
2331
+ } & {
2332
+ setShowTrackOutlines(arg: boolean): void;
2333
+ setColorByCDS(flag: boolean): void;
2334
+ setShowCytobands(flag: boolean): void;
2335
+ setWidth(newWidth: number): void;
2336
+ setError(error: unknown): void;
2337
+ setHideHeader(b: boolean): void;
2338
+ setHideHeaderOverview(b: boolean): void;
2339
+ setHideNoTracksActive(b: boolean): void;
2340
+ setShowGridlines(b: boolean): void;
2341
+ addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
2342
+ setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
2343
+ removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
2344
+ scrollTo(offsetPx: number): number;
2345
+ zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
2346
+ setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2347
+ setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
2348
+ setNewView(bpPerPx: number, offsetPx: number): void;
2349
+ horizontallyFlip(): void;
2350
+ showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
2351
+ hideTrack(trackId: string): number;
2352
+ } & {
2353
+ moveTrackDown(id: string): void;
2354
+ moveTrackUp(id: string): void;
2355
+ moveTrackToTop(id: string): void;
2356
+ moveTrackToBottom(id: string): void;
2357
+ moveTrack(movingId: string, targetId: string): void;
2358
+ toggleTrack(trackId: string): boolean;
2359
+ setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
2360
+ setShowCenterLine(b: boolean): void;
2361
+ setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
2362
+ activateTrackSelector(): import("@jbrowse/core/util").Widget;
2363
+ getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
2364
+ start: number;
2365
+ end: number;
2366
+ type: string;
2367
+ regionNumber?: number;
2368
+ reversed?: boolean;
2369
+ refName: string;
2370
+ assemblyName: string;
2371
+ key: string;
2372
+ offsetPx: number;
2373
+ widthPx: number;
2374
+ variant?: string;
2375
+ isLeftEndOfDisplayedRegion?: boolean;
2376
+ }[];
2377
+ afterDisplayedRegionsSet(cb: () => void): void;
2378
+ horizontalScroll(distance: number): number;
2379
+ center(): void;
2380
+ showAllRegions(): void;
2381
+ showAllRegionsInAssembly(assemblyName?: string): void;
2382
+ setDraggingTrackId(idx?: string): void;
2383
+ setScaleFactor(factor: number): void;
2384
+ clearView(): void;
2385
+ setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
2386
+ exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
2387
+ } & {
2388
+ slide: (viewWidths: number) => void;
2389
+ } & {
2390
+ zoom: (targetBpPerPx: number) => void;
2391
+ } & {
2392
+ readonly canShowCytobands: boolean;
2393
+ readonly showCytobands: boolean;
2394
+ readonly anyCytobandsExist: boolean;
2395
+ readonly cytobandOffset: number;
2396
+ } & {
2397
+ menuItems(): import("@jbrowse/core/ui").MenuItem[];
2398
+ } & {
2399
+ readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2400
+ readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2401
+ readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2402
+ readonly visibleLocStrings: string;
2403
+ readonly coarseVisibleLocStrings: string;
2404
+ } & {
2405
+ setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
2406
+ } & {
2407
+ moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2408
+ navToLocString(input: string, optAssemblyName?: string): Promise<void>;
2409
+ navToSearchString({ input, assembly, }: {
2410
+ input: string;
2411
+ assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
2412
+ }): Promise<void>;
2413
+ navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
2414
+ navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
2415
+ navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
2416
+ } & {
2417
+ rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
2418
+ bpToPx({ refName, coord, regionNumber, }: {
2419
+ refName: string;
2420
+ coord: number;
2421
+ regionNumber?: number;
2422
+ }): {
2423
+ index: number;
2424
+ offsetPx: number;
2425
+ } | undefined;
2426
+ centerAt(coord: number, refName: string, regionNumber?: number): void;
2427
+ pxToBp(px: number): {
2428
+ coord: number;
2429
+ index: number;
2430
+ refName: string;
2431
+ oob: boolean;
2432
+ assemblyName: string;
2433
+ offset: number;
2434
+ start: number;
2435
+ end: number;
2436
+ reversed?: boolean;
2437
+ };
2438
+ readonly centerLineInfo: {
2439
+ coord: number;
2440
+ index: number;
2441
+ refName: string;
2442
+ oob: boolean;
2443
+ assemblyName: string;
2444
+ offset: number;
2445
+ start: number;
2446
+ end: number;
2447
+ reversed?: boolean;
2448
+ } | undefined;
2449
+ } & {
2450
+ afterCreate(): void;
2451
+ afterAttach(): void;
2452
+ }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
2453
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2454
+ displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
2455
+ minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2456
+ } & {
2457
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2458
+ type: import("mobx-state-tree").IType<string | undefined, string, string>;
2459
+ offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2460
+ bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2461
+ displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
2462
+ tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
2463
+ hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2464
+ hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2465
+ hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2466
+ trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2467
+ showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2468
+ showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2469
+ trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2470
+ showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2471
+ 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]>;
2472
+ colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2473
+ showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2474
+ 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>;
2475
+ }>>, {
2476
+ type: string;
2477
+ id: string;
2478
+ displayName: string | undefined;
2479
+ tracks: any[];
2480
+ minimized: boolean;
2481
+ displayedRegions: import("@jbrowse/core/util").Region[];
2482
+ offsetPx: number;
2483
+ bpPerPx: number;
2484
+ hideHeader: boolean;
2485
+ hideHeaderOverview: boolean;
2486
+ hideNoTracksActive: boolean;
2487
+ trackSelectorType: string;
2488
+ showCenterLine: boolean;
2489
+ showCytobandsSetting: boolean;
2490
+ trackLabels: string;
2491
+ showGridlines: boolean;
2492
+ highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[];
2493
+ colorByCDS: boolean;
2494
+ showTrackOutlines: boolean;
2495
+ }>>)[];
2496
+ renderProps(): {
2497
+ theme: any;
2498
+ highResolutionScaling: any;
2499
+ };
2500
+ } & {
2501
+ addView(typeName: string, initialState?: {}): {
2502
+ id: string;
2503
+ displayName: string | undefined;
2504
+ minimized: boolean;
2505
+ type: string;
2506
+ offsetPx: number;
2507
+ bpPerPx: number;
2508
+ displayedRegions: import("@jbrowse/core/util").Region[] & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>>;
2509
+ 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>>;
2510
+ hideHeader: boolean;
2511
+ hideHeaderOverview: boolean;
2512
+ hideNoTracksActive: boolean;
2513
+ trackSelectorType: string;
2514
+ showCenterLine: boolean;
2515
+ showCytobandsSetting: boolean;
2516
+ trackLabels: string;
2517
+ showGridlines: boolean;
2518
+ 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]>>;
2519
+ colorByCDS: boolean;
2520
+ showTrackOutlines: boolean;
2521
+ 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;
2522
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2523
+ width: number;
2524
+ } & {
2525
+ menuItems(): import("@jbrowse/core/ui").MenuItem[];
2526
+ } & {
2527
+ setDisplayName(name: string): void;
2528
+ setWidth(newWidth: number): void;
2529
+ setMinimized(flag: boolean): void;
2530
+ } & {
2531
+ volatileWidth: number | undefined;
2532
+ minimumBlockWidth: number;
2533
+ draggingTrackId: undefined | string;
2534
+ volatileError: unknown;
2535
+ afterDisplayedRegionsSetCallbacks: (() => void)[];
2536
+ scaleFactor: number;
2537
+ trackRefs: Record<string, HTMLDivElement>;
2538
+ coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2539
+ coarseTotalBp: number;
2540
+ leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
2541
+ rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
2542
+ } & {
2543
+ readonly pinnedTracks: any[];
2544
+ readonly unpinnedTracks: any[];
2545
+ readonly trackLabelsSetting: any;
2546
+ readonly width: number;
2547
+ readonly interRegionPaddingWidth: number;
2548
+ readonly assemblyNames: string[];
2549
+ readonly stickyViewHeaders: boolean;
2550
+ readonly rubberbandTop: number;
2551
+ readonly pinnedTracksTop: number;
2552
+ } & {
2553
+ scaleBarDisplayPrefix(): string | undefined;
2554
+ MiniControlsComponent(): React.FC<any>;
2555
+ HeaderComponent(): React.FC<any>;
2556
+ readonly assembliesNotFound: string | undefined;
2557
+ readonly assemblyErrors: string;
2558
+ readonly assembliesInitialized: boolean;
2559
+ readonly initialized: boolean;
2560
+ readonly hasDisplayedRegions: boolean;
2561
+ readonly scaleBarHeight: number;
2562
+ readonly headerHeight: number;
2563
+ readonly trackHeights: number;
2564
+ readonly trackHeightsWithResizeHandles: number;
2565
+ readonly height: number;
2566
+ readonly totalBp: number;
2567
+ readonly maxBpPerPx: number;
2568
+ readonly minBpPerPx: number;
2569
+ readonly error: unknown;
2570
+ readonly maxOffset: number;
2571
+ readonly minOffset: number;
2572
+ readonly displayedRegionsTotalPx: number;
2573
+ renderProps(): any;
2574
+ searchScope(assemblyName: string): {
2575
+ assemblyName: string;
2576
+ includeAggregateIndexes: boolean;
2577
+ 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>>;
2578
+ };
2579
+ getTrack(id: string): any;
2580
+ rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
2581
+ rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
2582
+ readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
2583
+ } & {
2584
+ setShowTrackOutlines(arg: boolean): void;
2585
+ setColorByCDS(flag: boolean): void;
2586
+ setShowCytobands(flag: boolean): void;
2587
+ setWidth(newWidth: number): void;
2588
+ setError(error: unknown): void;
2589
+ setHideHeader(b: boolean): void;
2590
+ setHideHeaderOverview(b: boolean): void;
2591
+ setHideNoTracksActive(b: boolean): void;
2592
+ setShowGridlines(b: boolean): void;
2593
+ addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
2594
+ setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
2595
+ removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
2596
+ scrollTo(offsetPx: number): number;
2597
+ zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
2598
+ setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2599
+ setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
2600
+ setNewView(bpPerPx: number, offsetPx: number): void;
2601
+ horizontallyFlip(): void;
2602
+ showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
2603
+ hideTrack(trackId: string): number;
2604
+ } & {
2605
+ moveTrackDown(id: string): void;
2606
+ moveTrackUp(id: string): void;
2607
+ moveTrackToTop(id: string): void;
2608
+ moveTrackToBottom(id: string): void;
2609
+ moveTrack(movingId: string, targetId: string): void;
2610
+ toggleTrack(trackId: string): boolean;
2611
+ setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
2612
+ setShowCenterLine(b: boolean): void;
2613
+ setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
2614
+ activateTrackSelector(): import("@jbrowse/core/util").Widget;
2615
+ getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
2616
+ start: number;
2617
+ end: number;
2618
+ type: string;
2619
+ regionNumber?: number;
2620
+ reversed?: boolean;
2621
+ refName: string;
2622
+ assemblyName: string;
2623
+ key: string;
2624
+ offsetPx: number;
2625
+ widthPx: number;
2626
+ variant?: string;
2627
+ isLeftEndOfDisplayedRegion?: boolean;
2628
+ }[];
2629
+ afterDisplayedRegionsSet(cb: () => void): void;
2630
+ horizontalScroll(distance: number): number;
2631
+ center(): void;
2632
+ showAllRegions(): void;
2633
+ showAllRegionsInAssembly(assemblyName?: string): void;
2634
+ setDraggingTrackId(idx?: string): void;
2635
+ setScaleFactor(factor: number): void;
2636
+ clearView(): void;
2637
+ setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
2638
+ exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
2639
+ } & {
2640
+ slide: (viewWidths: number) => void;
2641
+ } & {
2642
+ zoom: (targetBpPerPx: number) => void;
2643
+ } & {
2644
+ readonly canShowCytobands: boolean;
2645
+ readonly showCytobands: boolean;
2646
+ readonly anyCytobandsExist: boolean;
2647
+ readonly cytobandOffset: number;
2648
+ } & {
2649
+ menuItems(): import("@jbrowse/core/ui").MenuItem[];
2650
+ } & {
2651
+ readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2652
+ readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2653
+ readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2654
+ readonly visibleLocStrings: string;
2655
+ readonly coarseVisibleLocStrings: string;
2656
+ } & {
2657
+ setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
2658
+ } & {
2659
+ moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2660
+ navToLocString(input: string, optAssemblyName?: string): Promise<void>;
2661
+ navToSearchString({ input, assembly, }: {
2662
+ input: string;
2663
+ assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
2664
+ }): Promise<void>;
2665
+ navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
2666
+ navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
2667
+ navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
2668
+ } & {
2669
+ rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
2670
+ bpToPx({ refName, coord, regionNumber, }: {
2671
+ refName: string;
2672
+ coord: number;
2673
+ regionNumber?: number;
2674
+ }): {
2675
+ index: number;
2676
+ offsetPx: number;
2677
+ } | undefined;
2678
+ centerAt(coord: number, refName: string, regionNumber?: number): void;
2679
+ pxToBp(px: number): {
2680
+ coord: number;
2681
+ index: number;
2682
+ refName: string;
2683
+ oob: boolean;
2684
+ assemblyName: string;
2685
+ offset: number;
2686
+ start: number;
2687
+ end: number;
2688
+ reversed?: boolean;
2689
+ };
2690
+ readonly centerLineInfo: {
2691
+ coord: number;
2692
+ index: number;
2693
+ refName: string;
2694
+ oob: boolean;
2695
+ assemblyName: string;
2696
+ offset: number;
2697
+ start: number;
2698
+ end: number;
2699
+ reversed?: boolean;
2700
+ } | undefined;
2701
+ } & {
2702
+ afterCreate(): void;
2703
+ afterAttach(): void;
2704
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
2705
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2706
+ displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
2707
+ minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2708
+ } & {
2709
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2710
+ type: import("mobx-state-tree").IType<string | undefined, string, string>;
2711
+ offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2712
+ bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2713
+ displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
2714
+ tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
2715
+ hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2716
+ hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2717
+ hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2718
+ trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2719
+ showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2720
+ showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2721
+ trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2722
+ showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2723
+ 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]>;
2724
+ colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2725
+ showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2726
+ 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>;
2727
+ }, {
2728
+ width: number;
2729
+ } & {
2730
+ menuItems(): import("@jbrowse/core/ui").MenuItem[];
2731
+ } & {
2732
+ setDisplayName(name: string): void;
2733
+ setWidth(newWidth: number): void;
2734
+ setMinimized(flag: boolean): void;
2735
+ } & {
2736
+ volatileWidth: number | undefined;
2737
+ minimumBlockWidth: number;
2738
+ draggingTrackId: undefined | string;
2739
+ volatileError: unknown;
2740
+ afterDisplayedRegionsSetCallbacks: (() => void)[];
2741
+ scaleFactor: number;
2742
+ trackRefs: Record<string, HTMLDivElement>;
2743
+ coarseDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2744
+ coarseTotalBp: number;
2745
+ leftOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
2746
+ rightOffset: undefined | import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset;
2747
+ } & {
2748
+ readonly pinnedTracks: any[];
2749
+ readonly unpinnedTracks: any[];
2750
+ readonly trackLabelsSetting: any;
2751
+ readonly width: number;
2752
+ readonly interRegionPaddingWidth: number;
2753
+ readonly assemblyNames: string[];
2754
+ readonly stickyViewHeaders: boolean;
2755
+ readonly rubberbandTop: number;
2756
+ readonly pinnedTracksTop: number;
2757
+ } & {
2758
+ scaleBarDisplayPrefix(): string | undefined;
2759
+ MiniControlsComponent(): React.FC<any>;
2760
+ HeaderComponent(): React.FC<any>;
2761
+ readonly assembliesNotFound: string | undefined;
2762
+ readonly assemblyErrors: string;
2763
+ readonly assembliesInitialized: boolean;
2764
+ readonly initialized: boolean;
2765
+ readonly hasDisplayedRegions: boolean;
2766
+ readonly scaleBarHeight: number;
2767
+ readonly headerHeight: number;
2768
+ readonly trackHeights: number;
2769
+ readonly trackHeightsWithResizeHandles: number;
2770
+ readonly height: number;
2771
+ readonly totalBp: number;
2772
+ readonly maxBpPerPx: number;
2773
+ readonly minBpPerPx: number;
2774
+ readonly error: unknown;
2775
+ readonly maxOffset: number;
2776
+ readonly minOffset: number;
2777
+ readonly displayedRegionsTotalPx: number;
2778
+ renderProps(): any;
2779
+ searchScope(assemblyName: string): {
2780
+ assemblyName: string;
2781
+ includeAggregateIndexes: boolean;
2782
+ 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>>;
2783
+ };
2784
+ getTrack(id: string): any;
2785
+ rankSearchResults(results: import("@jbrowse/core/TextSearch/BaseResults").default[]): import("@jbrowse/core/TextSearch/BaseResults").default[];
2786
+ rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
2787
+ readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
2788
+ } & {
2789
+ setShowTrackOutlines(arg: boolean): void;
2790
+ setColorByCDS(flag: boolean): void;
2791
+ setShowCytobands(flag: boolean): void;
2792
+ setWidth(newWidth: number): void;
2793
+ setError(error: unknown): void;
2794
+ setHideHeader(b: boolean): void;
2795
+ setHideHeaderOverview(b: boolean): void;
2796
+ setHideNoTracksActive(b: boolean): void;
2797
+ setShowGridlines(b: boolean): void;
2798
+ addToHighlights(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
2799
+ setHighlight(highlight?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[]): void;
2800
+ removeHighlight(highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType): void;
2801
+ scrollTo(offsetPx: number): number;
2802
+ zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
2803
+ setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2804
+ setSearchResults(searchResults: import("@jbrowse/core/TextSearch/BaseResults").default[], searchQuery: string, assemblyName?: string): void;
2805
+ setNewView(bpPerPx: number, offsetPx: number): void;
2806
+ horizontallyFlip(): void;
2807
+ showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
2808
+ hideTrack(trackId: string): number;
2809
+ } & {
2810
+ moveTrackDown(id: string): void;
2811
+ moveTrackUp(id: string): void;
2812
+ moveTrackToTop(id: string): void;
2813
+ moveTrackToBottom(id: string): void;
2814
+ moveTrack(movingId: string, targetId: string): void;
2815
+ toggleTrack(trackId: string): boolean;
2816
+ setTrackLabels(setting: "overlapping" | "offset" | "hidden"): void;
2817
+ setShowCenterLine(b: boolean): void;
2818
+ setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
2819
+ activateTrackSelector(): import("@jbrowse/core/util").Widget;
2820
+ getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): {
2821
+ start: number;
2822
+ end: number;
2823
+ type: string;
2824
+ regionNumber?: number;
2825
+ reversed?: boolean;
2826
+ refName: string;
2827
+ assemblyName: string;
2828
+ key: string;
2829
+ offsetPx: number;
2830
+ widthPx: number;
2831
+ variant?: string;
2832
+ isLeftEndOfDisplayedRegion?: boolean;
2833
+ }[];
2834
+ afterDisplayedRegionsSet(cb: () => void): void;
2835
+ horizontalScroll(distance: number): number;
2836
+ center(): void;
2837
+ showAllRegions(): void;
2838
+ showAllRegionsInAssembly(assemblyName?: string): void;
2839
+ setDraggingTrackId(idx?: string): void;
2840
+ setScaleFactor(factor: number): void;
2841
+ clearView(): void;
2842
+ setInit(arg?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").InitState): void;
2843
+ exportSvg(opts?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").ExportSvgOptions): Promise<void>;
2844
+ } & {
2845
+ slide: (viewWidths: number) => void;
2846
+ } & {
2847
+ zoom: (targetBpPerPx: number) => void;
2848
+ } & {
2849
+ readonly canShowCytobands: boolean;
2850
+ readonly showCytobands: boolean;
2851
+ readonly anyCytobandsExist: boolean;
2852
+ readonly cytobandOffset: number;
2853
+ } & {
2854
+ menuItems(): import("@jbrowse/core/ui").MenuItem[];
2855
+ } & {
2856
+ readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2857
+ readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
2858
+ readonly roundedDynamicBlocks: import("@jbrowse/core/util/blockTypes").BaseBlock[];
2859
+ readonly visibleLocStrings: string;
2860
+ readonly coarseVisibleLocStrings: string;
2861
+ } & {
2862
+ setCoarseDynamicBlocks(blocks: import("@jbrowse/core/util/blockTypes").BlockSet): void;
2863
+ } & {
2864
+ moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").BpOffset): void;
2865
+ navToLocString(input: string, optAssemblyName?: string): Promise<void>;
2866
+ navToSearchString({ input, assembly, }: {
2867
+ input: string;
2868
+ assembly: import("@jbrowse/core/assemblyManager/assembly").Assembly;
2869
+ }): Promise<void>;
2870
+ navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string): Promise<void>;
2871
+ navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation): void;
2872
+ navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").NavLocation[]): void;
2873
+ } & {
2874
+ rubberBandMenuItems(): import("@jbrowse/core/ui").MenuItem[];
2875
+ bpToPx({ refName, coord, regionNumber, }: {
2876
+ refName: string;
2877
+ coord: number;
2878
+ regionNumber?: number;
2879
+ }): {
2880
+ index: number;
2881
+ offsetPx: number;
2882
+ } | undefined;
2883
+ centerAt(coord: number, refName: string, regionNumber?: number): void;
2884
+ pxToBp(px: number): {
2885
+ coord: number;
2886
+ index: number;
2887
+ refName: string;
2888
+ oob: boolean;
2889
+ assemblyName: string;
2890
+ offset: number;
2891
+ start: number;
2892
+ end: number;
2893
+ reversed?: boolean;
2894
+ };
2895
+ readonly centerLineInfo: {
2896
+ coord: number;
2897
+ index: number;
2898
+ refName: string;
2899
+ oob: boolean;
2900
+ assemblyName: string;
2901
+ offset: number;
2902
+ start: number;
2903
+ end: number;
2904
+ reversed?: boolean;
2905
+ } | undefined;
2906
+ } & {
2907
+ afterCreate(): void;
2908
+ afterAttach(): void;
2909
+ }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
2910
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2911
+ displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
2912
+ minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2913
+ } & {
2914
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2915
+ type: import("mobx-state-tree").IType<string | undefined, string, string>;
2916
+ offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2917
+ bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
2918
+ displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
2919
+ tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
2920
+ hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2921
+ hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2922
+ hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2923
+ trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2924
+ showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2925
+ showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2926
+ trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
2927
+ showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
2928
+ 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]>;
2929
+ colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2930
+ showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
2931
+ 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>;
2932
+ }>>, {
2933
+ type: string;
2934
+ id: string;
2935
+ displayName: string | undefined;
2936
+ tracks: any[];
2937
+ minimized: boolean;
2938
+ displayedRegions: import("@jbrowse/core/util").Region[];
2939
+ offsetPx: number;
2940
+ bpPerPx: number;
2941
+ hideHeader: boolean;
2942
+ hideHeaderOverview: boolean;
2943
+ hideNoTracksActive: boolean;
2944
+ trackSelectorType: string;
2945
+ showCenterLine: boolean;
2946
+ showCytobandsSetting: boolean;
2947
+ trackLabels: string;
2948
+ showGridlines: boolean;
2949
+ highlight: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView/types").HighlightType[];
2950
+ colorByCDS: boolean;
2951
+ showTrackOutlines: boolean;
2952
+ }>>;
2953
+ removeView(): void;
2954
+ } & {
2955
+ getTrackActionMenuItems(config: any): {
2956
+ label: string;
2957
+ onClick: () => void;
2958
+ icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
2959
+ muiName: string;
2960
+ };
2961
+ }[];
2962
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): void;
2963
+ renameCurrentSession(sessionName: string): void;
2964
+ setError(error: unknown): void;
2965
+ addInternetAccount(acct: SnapshotIn<any>): void;
2966
+ findAppropriateInternetAccount(location: UriLocation): any;
2967
+ } & {
2968
+ readonly jbrowse: {
2969
+ configuration: {
2970
+ [x: string]: any;
2971
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2972
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
2973
+ [x: string]: any;
2974
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
2975
+ setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
2976
+ [x: string]: any;
2977
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
2978
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
2979
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2980
+ rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2981
+ defaultDriver: {
2982
+ type: string;
2983
+ description: string;
2984
+ defaultValue: string;
2985
+ };
2986
+ drivers: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IMapType<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> | undefined, import("mobx-state-tree").ModelSnapshotType<Record<string, any>>, ({} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> & import("mobx-state-tree/dist/internal").NonEmptyObject) | undefined>>, [undefined]>;
2987
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2988
+ highResolutionScaling: {
2989
+ type: string;
2990
+ defaultValue: number;
2991
+ };
2992
+ hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2993
+ sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2994
+ trackNames: {
2995
+ type: string;
2996
+ defaultValue: boolean;
2997
+ };
2998
+ categories: {
2999
+ type: string;
3000
+ defaultValue: boolean;
3001
+ };
3002
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
3003
+ defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
3004
+ categoryNames: {
3005
+ type: string;
3006
+ defaultValue: never[];
3007
+ };
3008
+ topLevelCategories: {
3009
+ type: string;
3010
+ defaultValue: boolean;
3011
+ };
3012
+ subCategories: {
3013
+ type: string;
3014
+ defaultValue: boolean;
3015
+ };
3016
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
3017
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
3018
+ formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
3019
+ feature: {
3020
+ type: string;
3021
+ description: string;
3022
+ defaultValue: {};
3023
+ contextVariable: string[];
3024
+ };
3025
+ subfeatures: {
3026
+ type: string;
3027
+ description: string;
3028
+ defaultValue: {};
3029
+ contextVariable: string[];
3030
+ };
3031
+ depth: {
3032
+ type: string;
3033
+ defaultValue: number;
3034
+ description: string;
3035
+ };
3036
+ maxDepth: {
3037
+ type: string;
3038
+ defaultValue: number;
3039
+ description: string;
3040
+ };
3041
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
3042
+ formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
3043
+ config: {
3044
+ type: string;
3045
+ description: string;
3046
+ defaultValue: {};
3047
+ contextVariable: string[];
3048
+ };
3049
+ hideUris: {
3050
+ type: string;
3051
+ defaultValue: boolean;
3052
+ };
3053
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
3054
+ theme: {
3055
+ type: string;
3056
+ defaultValue: {};
3057
+ };
3058
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>>;
3059
+ assembly: any;
3060
+ 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>>;
3061
+ internetAccounts: 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>>;
3062
+ connections: 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>>;
3063
+ aggregateTextSearchAdapters: 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>>;
3064
+ plugins: any;
3065
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
3066
+ readonly assemblies: any[];
3067
+ readonly assemblyName: string;
3068
+ readonly rpcManager: any;
3069
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
3070
+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
3071
+ rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
3072
+ defaultDriver: {
3073
+ type: string;
3074
+ description: string;
3075
+ defaultValue: string;
3076
+ };
3077
+ drivers: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IMapType<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> | undefined, import("mobx-state-tree").ModelSnapshotType<Record<string, any>>, ({} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> & import("mobx-state-tree/dist/internal").NonEmptyObject) | undefined>>, [undefined]>;
3078
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
3079
+ highResolutionScaling: {
3080
+ type: string;
3081
+ defaultValue: number;
3082
+ };
3083
+ hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
3084
+ sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
3085
+ trackNames: {
3086
+ type: string;
3087
+ defaultValue: boolean;
3088
+ };
3089
+ categories: {
3090
+ type: string;
3091
+ defaultValue: boolean;
3092
+ };
3093
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
3094
+ defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
3095
+ categoryNames: {
3096
+ type: string;
3097
+ defaultValue: never[];
3098
+ };
3099
+ topLevelCategories: {
3100
+ type: string;
3101
+ defaultValue: boolean;
3102
+ };
3103
+ subCategories: {
3104
+ type: string;
3105
+ defaultValue: boolean;
3106
+ };
3107
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
3108
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
3109
+ formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
3110
+ feature: {
3111
+ type: string;
3112
+ description: string;
3113
+ defaultValue: {};
3114
+ contextVariable: string[];
3115
+ };
3116
+ subfeatures: {
3117
+ type: string;
3118
+ description: string;
3119
+ defaultValue: {};
3120
+ contextVariable: string[];
3121
+ };
3122
+ depth: {
3123
+ type: string;
3124
+ defaultValue: number;
3125
+ description: string;
3126
+ };
3127
+ maxDepth: {
3128
+ type: string;
3129
+ defaultValue: number;
3130
+ description: string;
3131
+ };
3132
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
3133
+ formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
3134
+ config: {
3135
+ type: string;
3136
+ description: string;
3137
+ defaultValue: {};
3138
+ contextVariable: string[];
3139
+ };
3140
+ hideUris: {
3141
+ type: string;
3142
+ defaultValue: boolean;
3143
+ };
3144
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
3145
+ theme: {
3146
+ type: string;
3147
+ defaultValue: {};
3148
+ };
3149
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
3150
+ assembly: import("mobx-state-tree").IAnyType;
3151
+ tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
3152
+ internetAccounts: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
3153
+ connections: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
3154
+ aggregateTextSearchAdapters: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
3155
+ plugins: import("mobx-state-tree").IType<any, any, any>;
3156
+ }, {
3157
+ readonly assemblies: any[];
3158
+ readonly assemblyName: string;
3159
+ readonly rpcManager: any;
3160
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
3161
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
3162
+ pluginManager: PluginManager;
3163
+ };
3164
+ export type ViewStateModel = ReturnType<typeof createModel>['model'];
3165
+ export type ViewModel = Instance<ViewStateModel>;