@jbrowse/react-linear-genome-view2 3.7.0 → 4.0.0

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