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

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (55) hide show
  1. package/esm/JBrowseCircularGenomeView/JBrowseCircularGenomeView.d.ts +1 -1
  2. package/esm/JBrowseCircularGenomeView/JBrowseCircularGenomeView.js +1 -1
  3. package/esm/JBrowseCircularGenomeView/index.d.ts +1 -1
  4. package/esm/JBrowseCircularGenomeView/index.js +1 -1
  5. package/esm/corePlugins.d.ts +2 -2
  6. package/esm/createModel/createConfigModel.d.ts +25 -29
  7. package/esm/createModel/createConfigModel.js +1 -1
  8. package/esm/createModel/createModel.d.ts +524 -629
  9. package/esm/createModel/createModel.js +5 -5
  10. package/esm/createModel/createSessionModel.d.ts +250 -305
  11. package/esm/createModel/createSessionModel.js +5 -4
  12. package/esm/createModel/index.d.ts +3 -3
  13. package/esm/createModel/index.js +3 -3
  14. package/esm/createViewState.d.ts +1323 -1625
  15. package/esm/createViewState.js +3 -4
  16. package/esm/index.d.ts +4 -4
  17. package/esm/index.js +4 -4
  18. package/esm/loadPlugins.js +1 -1
  19. package/esm/types.d.ts +1 -1
  20. package/esm/version.d.ts +1 -1
  21. package/esm/version.js +1 -1
  22. package/esm/webpack.d.ts +4 -4
  23. package/esm/webpack.js +4 -4
  24. package/package.json +38 -40
  25. package/dist/JBrowseCircularGenomeView/JBrowseCircularGenomeView.d.ts +0 -5
  26. package/dist/JBrowseCircularGenomeView/JBrowseCircularGenomeView.js +0 -23
  27. package/dist/JBrowseCircularGenomeView/index.d.ts +0 -1
  28. package/dist/JBrowseCircularGenomeView/index.js +0 -8
  29. package/dist/corePlugins.d.ts +0 -3
  30. package/dist/corePlugins.js +0 -22
  31. package/dist/createModel/AboutDialog.d.ts +0 -1
  32. package/dist/createModel/AboutDialog.js +0 -5
  33. package/dist/createModel/createConfigModel.d.ts +0 -104
  34. package/dist/createModel/createConfigModel.js +0 -43
  35. package/dist/createModel/createModel.d.ts +0 -4530
  36. package/dist/createModel/createModel.js +0 -117
  37. package/dist/createModel/createSessionModel.d.ts +0 -1845
  38. package/dist/createModel/createSessionModel.js +0 -115
  39. package/dist/createModel/index.d.ts +0 -3
  40. package/dist/createModel/index.js +0 -12
  41. package/dist/createViewState.d.ts +0 -11620
  42. package/dist/createViewState.js +0 -64
  43. package/dist/index.d.ts +0 -4
  44. package/dist/index.js +0 -14
  45. package/dist/loadPlugins.d.ts +0 -13
  46. package/dist/loadPlugins.js +0 -12
  47. package/dist/react-circular-genome-view.umd.production.min.js +0 -229
  48. package/dist/react-circular-genome-view.umd.production.min.js.LICENSE.txt +0 -135
  49. package/dist/react-circular-genome-view.umd.production.min.js.map +0 -1
  50. package/dist/types.d.ts +0 -5
  51. package/dist/types.js +0 -2
  52. package/dist/version.d.ts +0 -1
  53. package/dist/version.js +0 -4
  54. package/dist/webpack.d.ts +0 -7
  55. package/dist/webpack.js +0 -53
package/esm/createModel/createSessionModel.d.ts CHANGED
@@ -1,62 +1,20 @@
1
1
  import type PluginManager from '@jbrowse/core/PluginManager';
2
- import type { Instance } from 'mobx-state-tree';
3
- export default function sessionModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
4
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
5
- name: import("mobx-state-tree").ISimpleType<string>;
6
- margin: import("mobx-state-tree").IType<number | undefined, number, number>;
2
+ import type { MenuItem } from '@jbrowse/core/ui';
3
+ import type { Instance } from '@jbrowse/mobx-state-tree';
4
+ export default function sessionModelFactory(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
5
+ id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
6
+ name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
7
+ margin: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
7
8
  } & {
8
- drawerPosition: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
9
- drawerWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
10
- widgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyType>;
11
- activeWidgets: import("mobx-state-tree").IMapType<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>>;
12
- minimized: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
9
+ drawerPosition: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
10
+ drawerWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
11
+ widgets: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IAnyType>;
12
+ 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>>>;
13
+ minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
13
14
  } & {
14
- connectionInstances: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
15
- name: import("mobx-state-tree").ISimpleType<string>;
16
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
17
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
18
- name: {
19
- type: string;
20
- defaultValue: string;
21
- description: string;
22
- };
23
- assemblyNames: {
24
- type: string;
25
- defaultValue: never[];
26
- description: string;
27
- };
28
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
29
- }, {
30
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
31
- } & {
32
- afterAttach(): void;
33
- addTrackConf(trackConf: Record<string, unknown> | ({
34
- [x: string]: any;
35
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
36
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
37
- [x: string]: any;
38
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
39
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
40
- [x: string]: any;
41
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
42
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
43
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
44
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
45
- [x: string]: any;
46
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
47
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
48
- [x: string]: any;
49
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
50
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
51
- [x: string]: any;
52
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
53
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
54
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
55
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
56
- clear(): void;
57
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
15
+ connectionInstances: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
58
16
  } & {
59
- view: import("mobx-state-tree").IAnyModelType;
17
+ view: import("@jbrowse/mobx-state-tree").IAnyModelType;
60
18
  }, {
61
19
  selection: unknown;
62
20
  hovered: unknown;
@@ -66,8 +24,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
66
24
  session: any;
67
25
  sessionPath: string;
68
26
  assemblyManager: {
69
- assemblies: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
70
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
27
+ assemblies: import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").IModelType<{
28
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
71
29
  }, {
72
30
  error: unknown;
73
31
  loadingP: Promise<void> | undefined;
@@ -75,6 +33,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
75
33
  refNameAliases: {
76
34
  [x: string]: string;
77
35
  } | undefined;
36
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
78
37
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
79
38
  } & {
80
39
  getConf(arg: string): any;
@@ -98,22 +57,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
98
57
  readonly refNames: string[] | undefined;
99
58
  } & {
100
59
  getCanonicalRefName(refName: string): string | undefined;
60
+ getCanonicalRefName2(refName: string): string;
101
61
  getRefNameColor(refName: string): string | undefined;
102
62
  isValidRefName(refName: string): boolean;
63
+ getSeqAdapterRefName(canonicalRefName: string): string;
103
64
  } & {
104
65
  setLoaded({ regions, refNameAliases, cytobands, }: {
105
- regions: import("@jbrowse/core/util/types").Region[];
66
+ regions: import("@jbrowse/core/util").Region[];
106
67
  refNameAliases: {
107
68
  [x: string]: string;
108
69
  };
109
70
  cytobands: import("@jbrowse/core/util").Feature[];
110
71
  }): void;
111
72
  setError(e: unknown): void;
112
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
73
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
113
74
  setRefNameAliases(aliases: {
114
75
  [x: string]: string;
115
76
  }): void;
116
77
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
78
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
117
79
  setLoadingP(p?: Promise<void>): void;
118
80
  load(): Promise<void>;
119
81
  loadPre(): Promise<void>;
@@ -132,8 +94,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
132
94
  [x: string]: string;
133
95
  }>;
134
96
  afterCreate(): void;
135
- }, 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<{
136
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
97
+ }, 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<{
98
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
137
99
  }, {
138
100
  error: unknown;
139
101
  loadingP: Promise<void> | undefined;
@@ -141,6 +103,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
141
103
  refNameAliases: {
142
104
  [x: string]: string;
143
105
  } | undefined;
106
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
144
107
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
145
108
  } & {
146
109
  getConf(arg: string): any;
@@ -164,22 +127,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
164
127
  readonly refNames: string[] | undefined;
165
128
  } & {
166
129
  getCanonicalRefName(refName: string): string | undefined;
130
+ getCanonicalRefName2(refName: string): string;
167
131
  getRefNameColor(refName: string): string | undefined;
168
132
  isValidRefName(refName: string): boolean;
133
+ getSeqAdapterRefName(canonicalRefName: string): string;
169
134
  } & {
170
135
  setLoaded({ regions, refNameAliases, cytobands, }: {
171
- regions: import("@jbrowse/core/util/types").Region[];
136
+ regions: import("@jbrowse/core/util").Region[];
172
137
  refNameAliases: {
173
138
  [x: string]: string;
174
139
  };
175
140
  cytobands: import("@jbrowse/core/util").Feature[];
176
141
  }): void;
177
142
  setError(e: unknown): void;
178
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
143
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
179
144
  setRefNameAliases(aliases: {
180
145
  [x: string]: string;
181
146
  }): void;
182
147
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
148
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
183
149
  setLoadingP(p?: Promise<void>): void;
184
150
  load(): Promise<void>;
185
151
  loadPre(): Promise<void>;
@@ -198,17 +164,18 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
198
164
  [x: string]: string;
199
165
  }>;
200
166
  afterCreate(): void;
201
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
202
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
167
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
168
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
203
169
  readonly assemblyNameMap: Record<string, {
204
170
  configuration: any;
205
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
171
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
206
172
  error: unknown;
207
173
  loadingP: Promise<void> | undefined;
208
174
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
209
175
  refNameAliases: {
210
176
  [x: string]: string;
211
177
  } | undefined;
178
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
212
179
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
213
180
  } & {
214
181
  getConf(arg: string): any;
@@ -232,22 +199,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
232
199
  readonly refNames: string[] | undefined;
233
200
  } & {
234
201
  getCanonicalRefName(refName: string): string | undefined;
202
+ getCanonicalRefName2(refName: string): string;
235
203
  getRefNameColor(refName: string): string | undefined;
236
204
  isValidRefName(refName: string): boolean;
205
+ getSeqAdapterRefName(canonicalRefName: string): string;
237
206
  } & {
238
207
  setLoaded({ regions, refNameAliases, cytobands, }: {
239
- regions: import("@jbrowse/core/util/types").Region[];
208
+ regions: import("@jbrowse/core/util").Region[];
240
209
  refNameAliases: {
241
210
  [x: string]: string;
242
211
  };
243
212
  cytobands: import("@jbrowse/core/util").Feature[];
244
213
  }): void;
245
214
  setError(e: unknown): void;
246
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
215
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
247
216
  setRefNameAliases(aliases: {
248
217
  [x: string]: string;
249
218
  }): void;
250
219
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
220
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
251
221
  setLoadingP(p?: Promise<void>): void;
252
222
  load(): Promise<void>;
253
223
  loadPre(): Promise<void>;
@@ -266,8 +236,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
266
236
  [x: string]: string;
267
237
  }>;
268
238
  afterCreate(): void;
269
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
270
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
239
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
240
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
271
241
  }, {
272
242
  error: unknown;
273
243
  loadingP: Promise<void> | undefined;
@@ -275,6 +245,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
275
245
  refNameAliases: {
276
246
  [x: string]: string;
277
247
  } | undefined;
248
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
278
249
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
279
250
  } & {
280
251
  getConf(arg: string): any;
@@ -298,22 +269,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
298
269
  readonly refNames: string[] | undefined;
299
270
  } & {
300
271
  getCanonicalRefName(refName: string): string | undefined;
272
+ getCanonicalRefName2(refName: string): string;
301
273
  getRefNameColor(refName: string): string | undefined;
302
274
  isValidRefName(refName: string): boolean;
275
+ getSeqAdapterRefName(canonicalRefName: string): string;
303
276
  } & {
304
277
  setLoaded({ regions, refNameAliases, cytobands, }: {
305
- regions: import("@jbrowse/core/util/types").Region[];
278
+ regions: import("@jbrowse/core/util").Region[];
306
279
  refNameAliases: {
307
280
  [x: string]: string;
308
281
  };
309
282
  cytobands: import("@jbrowse/core/util").Feature[];
310
283
  }): void;
311
284
  setError(e: unknown): void;
312
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
285
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
313
286
  setRefNameAliases(aliases: {
314
287
  [x: string]: string;
315
288
  }): void;
316
289
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
290
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
317
291
  setLoadingP(p?: Promise<void>): void;
318
292
  load(): Promise<void>;
319
293
  loadPre(): Promise<void>;
@@ -332,18 +306,20 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
332
306
  [x: string]: string;
333
307
  }>;
334
308
  afterCreate(): void;
335
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
309
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
336
310
  } & {
337
311
  getCanonicalAssemblyName(asmName: string): string | undefined;
312
+ getCanonicalAssemblyName2(asmName: string): string;
338
313
  get(asmName: string): ({
339
314
  configuration: any;
340
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
315
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
341
316
  error: unknown;
342
317
  loadingP: Promise<void> | undefined;
343
318
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
344
319
  refNameAliases: {
345
320
  [x: string]: string;
346
321
  } | undefined;
322
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
347
323
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
348
324
  } & {
349
325
  getConf(arg: string): any;
@@ -367,22 +343,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
367
343
  readonly refNames: string[] | undefined;
368
344
  } & {
369
345
  getCanonicalRefName(refName: string): string | undefined;
346
+ getCanonicalRefName2(refName: string): string;
370
347
  getRefNameColor(refName: string): string | undefined;
371
348
  isValidRefName(refName: string): boolean;
349
+ getSeqAdapterRefName(canonicalRefName: string): string;
372
350
  } & {
373
351
  setLoaded({ regions, refNameAliases, cytobands, }: {
374
- regions: import("@jbrowse/core/util/types").Region[];
352
+ regions: import("@jbrowse/core/util").Region[];
375
353
  refNameAliases: {
376
354
  [x: string]: string;
377
355
  };
378
356
  cytobands: import("@jbrowse/core/util").Feature[];
379
357
  }): void;
380
358
  setError(e: unknown): void;
381
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
359
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
382
360
  setRefNameAliases(aliases: {
383
361
  [x: string]: string;
384
362
  }): void;
385
363
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
364
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
386
365
  setLoadingP(p?: Promise<void>): void;
387
366
  load(): Promise<void>;
388
367
  loadPre(): Promise<void>;
@@ -401,8 +380,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
401
380
  [x: string]: string;
402
381
  }>;
403
382
  afterCreate(): void;
404
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
405
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
383
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
384
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
406
385
  }, {
407
386
  error: unknown;
408
387
  loadingP: Promise<void> | undefined;
@@ -410,6 +389,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
410
389
  refNameAliases: {
411
390
  [x: string]: string;
412
391
  } | undefined;
392
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
413
393
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
414
394
  } & {
415
395
  getConf(arg: string): any;
@@ -433,22 +413,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
433
413
  readonly refNames: string[] | undefined;
434
414
  } & {
435
415
  getCanonicalRefName(refName: string): string | undefined;
416
+ getCanonicalRefName2(refName: string): string;
436
417
  getRefNameColor(refName: string): string | undefined;
437
418
  isValidRefName(refName: string): boolean;
419
+ getSeqAdapterRefName(canonicalRefName: string): string;
438
420
  } & {
439
421
  setLoaded({ regions, refNameAliases, cytobands, }: {
440
- regions: import("@jbrowse/core/util/types").Region[];
422
+ regions: import("@jbrowse/core/util").Region[];
441
423
  refNameAliases: {
442
424
  [x: string]: string;
443
425
  };
444
426
  cytobands: import("@jbrowse/core/util").Feature[];
445
427
  }): void;
446
428
  setError(e: unknown): void;
447
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
429
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
448
430
  setRefNameAliases(aliases: {
449
431
  [x: string]: string;
450
432
  }): void;
451
433
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
434
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
452
435
  setLoadingP(p?: Promise<void>): void;
453
436
  load(): Promise<void>;
454
437
  loadPre(): Promise<void>;
@@ -467,20 +450,21 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
467
450
  [x: string]: string;
468
451
  }>;
469
452
  afterCreate(): void;
470
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
453
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
471
454
  readonly assemblyNamesList: any[];
472
455
  readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
473
456
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
474
457
  } & {
475
458
  waitForAssembly(assemblyName: string): Promise<({
476
459
  configuration: any;
477
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
460
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
478
461
  error: unknown;
479
462
  loadingP: Promise<void> | undefined;
480
463
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
481
464
  refNameAliases: {
482
465
  [x: string]: string;
483
466
  } | undefined;
467
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
484
468
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
485
469
  } & {
486
470
  getConf(arg: string): any;
@@ -504,22 +488,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
504
488
  readonly refNames: string[] | undefined;
505
489
  } & {
506
490
  getCanonicalRefName(refName: string): string | undefined;
491
+ getCanonicalRefName2(refName: string): string;
507
492
  getRefNameColor(refName: string): string | undefined;
508
493
  isValidRefName(refName: string): boolean;
494
+ getSeqAdapterRefName(canonicalRefName: string): string;
509
495
  } & {
510
496
  setLoaded({ regions, refNameAliases, cytobands, }: {
511
- regions: import("@jbrowse/core/util/types").Region[];
497
+ regions: import("@jbrowse/core/util").Region[];
512
498
  refNameAliases: {
513
499
  [x: string]: string;
514
500
  };
515
501
  cytobands: import("@jbrowse/core/util").Feature[];
516
502
  }): void;
517
503
  setError(e: unknown): void;
518
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
504
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
519
505
  setRefNameAliases(aliases: {
520
506
  [x: string]: string;
521
507
  }): void;
522
508
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
509
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
523
510
  setLoadingP(p?: Promise<void>): void;
524
511
  load(): Promise<void>;
525
512
  loadPre(): Promise<void>;
@@ -538,8 +525,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
538
525
  [x: string]: string;
539
526
  }>;
540
527
  afterCreate(): void;
541
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
542
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
528
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
529
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
543
530
  }, {
544
531
  error: unknown;
545
532
  loadingP: Promise<void> | undefined;
@@ -547,6 +534,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
547
534
  refNameAliases: {
548
535
  [x: string]: string;
549
536
  } | undefined;
537
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
550
538
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
551
539
  } & {
552
540
  getConf(arg: string): any;
@@ -570,22 +558,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
570
558
  readonly refNames: string[] | undefined;
571
559
  } & {
572
560
  getCanonicalRefName(refName: string): string | undefined;
561
+ getCanonicalRefName2(refName: string): string;
573
562
  getRefNameColor(refName: string): string | undefined;
574
563
  isValidRefName(refName: string): boolean;
564
+ getSeqAdapterRefName(canonicalRefName: string): string;
575
565
  } & {
576
566
  setLoaded({ regions, refNameAliases, cytobands, }: {
577
- regions: import("@jbrowse/core/util/types").Region[];
567
+ regions: import("@jbrowse/core/util").Region[];
578
568
  refNameAliases: {
579
569
  [x: string]: string;
580
570
  };
581
571
  cytobands: import("@jbrowse/core/util").Feature[];
582
572
  }): void;
583
573
  setError(e: unknown): void;
584
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
574
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
585
575
  setRefNameAliases(aliases: {
586
576
  [x: string]: string;
587
577
  }): void;
588
578
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
579
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
589
580
  setLoadingP(p?: Promise<void>): void;
590
581
  load(): Promise<void>;
591
582
  loadPre(): Promise<void>;
@@ -604,21 +595,15 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
604
595
  [x: string]: string;
605
596
  }>;
606
597
  afterCreate(): void;
607
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
598
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
608
599
  getRefNameMapForAdapter(adapterConf: {
609
600
  [x: string]: unknown;
610
- }, assemblyName: string | undefined, opts: {
611
- stopToken?: string;
612
- sessionId: string;
613
- }): Promise<{
601
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
614
602
  [x: string]: string;
615
603
  } | undefined>;
616
604
  getReverseRefNameMapForAdapter(adapterConf: {
617
605
  [x: string]: unknown;
618
- }, assemblyName: string | undefined, opts: {
619
- stopToken?: string;
620
- sessionId: string;
621
- }): Promise<{
606
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
622
607
  [x: string]: string;
623
608
  } | undefined>;
624
609
  isValidRefName(refName: string, assemblyName: string): boolean;
@@ -626,9 +611,9 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
626
611
  afterAttach(): void;
627
612
  removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
628
613
  addAssembly(configuration: any): void;
629
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
630
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
631
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
614
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
615
+ assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
616
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
632
617
  }, {
633
618
  error: unknown;
634
619
  loadingP: Promise<void> | undefined;
@@ -636,6 +621,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
636
621
  refNameAliases: {
637
622
  [x: string]: string;
638
623
  } | undefined;
624
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
639
625
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
640
626
  } & {
641
627
  getConf(arg: string): any;
@@ -659,22 +645,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
659
645
  readonly refNames: string[] | undefined;
660
646
  } & {
661
647
  getCanonicalRefName(refName: string): string | undefined;
648
+ getCanonicalRefName2(refName: string): string;
662
649
  getRefNameColor(refName: string): string | undefined;
663
650
  isValidRefName(refName: string): boolean;
651
+ getSeqAdapterRefName(canonicalRefName: string): string;
664
652
  } & {
665
653
  setLoaded({ regions, refNameAliases, cytobands, }: {
666
- regions: import("@jbrowse/core/util/types").Region[];
654
+ regions: import("@jbrowse/core/util").Region[];
667
655
  refNameAliases: {
668
656
  [x: string]: string;
669
657
  };
670
658
  cytobands: import("@jbrowse/core/util").Feature[];
671
659
  }): void;
672
660
  setError(e: unknown): void;
673
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
661
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
674
662
  setRefNameAliases(aliases: {
675
663
  [x: string]: string;
676
664
  }): void;
677
665
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
666
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
678
667
  setLoadingP(p?: Promise<void>): void;
679
668
  load(): Promise<void>;
680
669
  loadPre(): Promise<void>;
@@ -693,17 +682,18 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
693
682
  [x: string]: string;
694
683
  }>;
695
684
  afterCreate(): void;
696
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
685
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
697
686
  }, {
698
687
  readonly assemblyNameMap: Record<string, {
699
688
  configuration: any;
700
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
689
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
701
690
  error: unknown;
702
691
  loadingP: Promise<void> | undefined;
703
692
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
704
693
  refNameAliases: {
705
694
  [x: string]: string;
706
695
  } | undefined;
696
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
707
697
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
708
698
  } & {
709
699
  getConf(arg: string): any;
@@ -727,22 +717,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
727
717
  readonly refNames: string[] | undefined;
728
718
  } & {
729
719
  getCanonicalRefName(refName: string): string | undefined;
720
+ getCanonicalRefName2(refName: string): string;
730
721
  getRefNameColor(refName: string): string | undefined;
731
722
  isValidRefName(refName: string): boolean;
723
+ getSeqAdapterRefName(canonicalRefName: string): string;
732
724
  } & {
733
725
  setLoaded({ regions, refNameAliases, cytobands, }: {
734
- regions: import("@jbrowse/core/util/types").Region[];
726
+ regions: import("@jbrowse/core/util").Region[];
735
727
  refNameAliases: {
736
728
  [x: string]: string;
737
729
  };
738
730
  cytobands: import("@jbrowse/core/util").Feature[];
739
731
  }): void;
740
732
  setError(e: unknown): void;
741
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
733
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
742
734
  setRefNameAliases(aliases: {
743
735
  [x: string]: string;
744
736
  }): void;
745
737
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
738
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
746
739
  setLoadingP(p?: Promise<void>): void;
747
740
  load(): Promise<void>;
748
741
  loadPre(): Promise<void>;
@@ -761,8 +754,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
761
754
  [x: string]: string;
762
755
  }>;
763
756
  afterCreate(): void;
764
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
765
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
757
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
758
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
766
759
  }, {
767
760
  error: unknown;
768
761
  loadingP: Promise<void> | undefined;
@@ -770,6 +763,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
770
763
  refNameAliases: {
771
764
  [x: string]: string;
772
765
  } | undefined;
766
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
773
767
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
774
768
  } & {
775
769
  getConf(arg: string): any;
@@ -793,22 +787,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
793
787
  readonly refNames: string[] | undefined;
794
788
  } & {
795
789
  getCanonicalRefName(refName: string): string | undefined;
790
+ getCanonicalRefName2(refName: string): string;
796
791
  getRefNameColor(refName: string): string | undefined;
797
792
  isValidRefName(refName: string): boolean;
793
+ getSeqAdapterRefName(canonicalRefName: string): string;
798
794
  } & {
799
795
  setLoaded({ regions, refNameAliases, cytobands, }: {
800
- regions: import("@jbrowse/core/util/types").Region[];
796
+ regions: import("@jbrowse/core/util").Region[];
801
797
  refNameAliases: {
802
798
  [x: string]: string;
803
799
  };
804
800
  cytobands: import("@jbrowse/core/util").Feature[];
805
801
  }): void;
806
802
  setError(e: unknown): void;
807
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
803
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
808
804
  setRefNameAliases(aliases: {
809
805
  [x: string]: string;
810
806
  }): void;
811
807
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
808
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
812
809
  setLoadingP(p?: Promise<void>): void;
813
810
  load(): Promise<void>;
814
811
  loadPre(): Promise<void>;
@@ -827,18 +824,20 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
827
824
  [x: string]: string;
828
825
  }>;
829
826
  afterCreate(): void;
830
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
827
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
831
828
  } & {
832
829
  getCanonicalAssemblyName(asmName: string): string | undefined;
830
+ getCanonicalAssemblyName2(asmName: string): string;
833
831
  get(asmName: string): ({
834
832
  configuration: any;
835
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
833
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
836
834
  error: unknown;
837
835
  loadingP: Promise<void> | undefined;
838
836
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
839
837
  refNameAliases: {
840
838
  [x: string]: string;
841
839
  } | undefined;
840
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
842
841
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
843
842
  } & {
844
843
  getConf(arg: string): any;
@@ -862,22 +861,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
862
861
  readonly refNames: string[] | undefined;
863
862
  } & {
864
863
  getCanonicalRefName(refName: string): string | undefined;
864
+ getCanonicalRefName2(refName: string): string;
865
865
  getRefNameColor(refName: string): string | undefined;
866
866
  isValidRefName(refName: string): boolean;
867
+ getSeqAdapterRefName(canonicalRefName: string): string;
867
868
  } & {
868
869
  setLoaded({ regions, refNameAliases, cytobands, }: {
869
- regions: import("@jbrowse/core/util/types").Region[];
870
+ regions: import("@jbrowse/core/util").Region[];
870
871
  refNameAliases: {
871
872
  [x: string]: string;
872
873
  };
873
874
  cytobands: import("@jbrowse/core/util").Feature[];
874
875
  }): void;
875
876
  setError(e: unknown): void;
876
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
877
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
877
878
  setRefNameAliases(aliases: {
878
879
  [x: string]: string;
879
880
  }): void;
880
881
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
882
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
881
883
  setLoadingP(p?: Promise<void>): void;
882
884
  load(): Promise<void>;
883
885
  loadPre(): Promise<void>;
@@ -896,8 +898,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
896
898
  [x: string]: string;
897
899
  }>;
898
900
  afterCreate(): void;
899
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
900
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
901
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
902
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
901
903
  }, {
902
904
  error: unknown;
903
905
  loadingP: Promise<void> | undefined;
@@ -905,6 +907,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
905
907
  refNameAliases: {
906
908
  [x: string]: string;
907
909
  } | undefined;
910
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
908
911
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
909
912
  } & {
910
913
  getConf(arg: string): any;
@@ -928,22 +931,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
928
931
  readonly refNames: string[] | undefined;
929
932
  } & {
930
933
  getCanonicalRefName(refName: string): string | undefined;
934
+ getCanonicalRefName2(refName: string): string;
931
935
  getRefNameColor(refName: string): string | undefined;
932
936
  isValidRefName(refName: string): boolean;
937
+ getSeqAdapterRefName(canonicalRefName: string): string;
933
938
  } & {
934
939
  setLoaded({ regions, refNameAliases, cytobands, }: {
935
- regions: import("@jbrowse/core/util/types").Region[];
940
+ regions: import("@jbrowse/core/util").Region[];
936
941
  refNameAliases: {
937
942
  [x: string]: string;
938
943
  };
939
944
  cytobands: import("@jbrowse/core/util").Feature[];
940
945
  }): void;
941
946
  setError(e: unknown): void;
942
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
947
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
943
948
  setRefNameAliases(aliases: {
944
949
  [x: string]: string;
945
950
  }): void;
946
951
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
952
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
947
953
  setLoadingP(p?: Promise<void>): void;
948
954
  load(): Promise<void>;
949
955
  loadPre(): Promise<void>;
@@ -962,20 +968,21 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
962
968
  [x: string]: string;
963
969
  }>;
964
970
  afterCreate(): void;
965
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
971
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
966
972
  readonly assemblyNamesList: any[];
967
973
  readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
968
974
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
969
975
  } & {
970
976
  waitForAssembly(assemblyName: string): Promise<({
971
977
  configuration: any;
972
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
978
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
973
979
  error: unknown;
974
980
  loadingP: Promise<void> | undefined;
975
981
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
976
982
  refNameAliases: {
977
983
  [x: string]: string;
978
984
  } | undefined;
985
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
979
986
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
980
987
  } & {
981
988
  getConf(arg: string): any;
@@ -999,22 +1006,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
999
1006
  readonly refNames: string[] | undefined;
1000
1007
  } & {
1001
1008
  getCanonicalRefName(refName: string): string | undefined;
1009
+ getCanonicalRefName2(refName: string): string;
1002
1010
  getRefNameColor(refName: string): string | undefined;
1003
1011
  isValidRefName(refName: string): boolean;
1012
+ getSeqAdapterRefName(canonicalRefName: string): string;
1004
1013
  } & {
1005
1014
  setLoaded({ regions, refNameAliases, cytobands, }: {
1006
- regions: import("@jbrowse/core/util/types").Region[];
1015
+ regions: import("@jbrowse/core/util").Region[];
1007
1016
  refNameAliases: {
1008
1017
  [x: string]: string;
1009
1018
  };
1010
1019
  cytobands: import("@jbrowse/core/util").Feature[];
1011
1020
  }): void;
1012
1021
  setError(e: unknown): void;
1013
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1022
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1014
1023
  setRefNameAliases(aliases: {
1015
1024
  [x: string]: string;
1016
1025
  }): void;
1017
1026
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1027
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1018
1028
  setLoadingP(p?: Promise<void>): void;
1019
1029
  load(): Promise<void>;
1020
1030
  loadPre(): Promise<void>;
@@ -1033,8 +1043,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1033
1043
  [x: string]: string;
1034
1044
  }>;
1035
1045
  afterCreate(): void;
1036
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1037
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1046
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1047
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1038
1048
  }, {
1039
1049
  error: unknown;
1040
1050
  loadingP: Promise<void> | undefined;
@@ -1042,6 +1052,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1042
1052
  refNameAliases: {
1043
1053
  [x: string]: string;
1044
1054
  } | undefined;
1055
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1045
1056
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1046
1057
  } & {
1047
1058
  getConf(arg: string): any;
@@ -1065,22 +1076,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1065
1076
  readonly refNames: string[] | undefined;
1066
1077
  } & {
1067
1078
  getCanonicalRefName(refName: string): string | undefined;
1079
+ getCanonicalRefName2(refName: string): string;
1068
1080
  getRefNameColor(refName: string): string | undefined;
1069
1081
  isValidRefName(refName: string): boolean;
1082
+ getSeqAdapterRefName(canonicalRefName: string): string;
1070
1083
  } & {
1071
1084
  setLoaded({ regions, refNameAliases, cytobands, }: {
1072
- regions: import("@jbrowse/core/util/types").Region[];
1085
+ regions: import("@jbrowse/core/util").Region[];
1073
1086
  refNameAliases: {
1074
1087
  [x: string]: string;
1075
1088
  };
1076
1089
  cytobands: import("@jbrowse/core/util").Feature[];
1077
1090
  }): void;
1078
1091
  setError(e: unknown): void;
1079
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1092
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1080
1093
  setRefNameAliases(aliases: {
1081
1094
  [x: string]: string;
1082
1095
  }): void;
1083
1096
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1097
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1084
1098
  setLoadingP(p?: Promise<void>): void;
1085
1099
  load(): Promise<void>;
1086
1100
  loadPre(): Promise<void>;
@@ -1099,21 +1113,15 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1099
1113
  [x: string]: string;
1100
1114
  }>;
1101
1115
  afterCreate(): void;
1102
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1116
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
1103
1117
  getRefNameMapForAdapter(adapterConf: {
1104
1118
  [x: string]: unknown;
1105
- }, assemblyName: string | undefined, opts: {
1106
- stopToken?: string;
1107
- sessionId: string;
1108
- }): Promise<{
1119
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
1109
1120
  [x: string]: string;
1110
1121
  } | undefined>;
1111
1122
  getReverseRefNameMapForAdapter(adapterConf: {
1112
1123
  [x: string]: unknown;
1113
- }, assemblyName: string | undefined, opts: {
1114
- stopToken?: string;
1115
- sessionId: string;
1116
- }): Promise<{
1124
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
1117
1125
  [x: string]: string;
1118
1126
  } | undefined>;
1119
1127
  isValidRefName(refName: string, assemblyName: string): boolean;
@@ -1121,26 +1129,26 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1121
1129
  afterAttach(): void;
1122
1130
  removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1123
1131
  addAssembly(configuration: any): void;
1124
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
1125
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1132
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>>;
1133
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
1126
1134
  rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1127
1135
  adminMode: boolean;
1128
1136
  error: unknown;
1129
- textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1137
+ textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1130
1138
  pluginManager: PluginManager;
1131
1139
  } & {
1132
1140
  setError(error: unknown): void;
1133
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1141
+ setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
1134
1142
  setDefaultSession(): void;
1135
1143
  setSessionPath(path: string): void;
1136
1144
  renameCurrentSession(newName: string): void;
1137
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1138
- jbrowse: import("mobx-state-tree").IAnyType;
1139
- session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
1140
- sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1141
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1142
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1143
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1145
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1146
+ jbrowse: import("@jbrowse/mobx-state-tree").IAnyType;
1147
+ session: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IAnyType>;
1148
+ sessionPath: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
1149
+ assemblyManager: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
1150
+ assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
1151
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1144
1152
  }, {
1145
1153
  error: unknown;
1146
1154
  loadingP: Promise<void> | undefined;
@@ -1148,6 +1156,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1148
1156
  refNameAliases: {
1149
1157
  [x: string]: string;
1150
1158
  } | undefined;
1159
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1151
1160
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1152
1161
  } & {
1153
1162
  getConf(arg: string): any;
@@ -1171,22 +1180,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1171
1180
  readonly refNames: string[] | undefined;
1172
1181
  } & {
1173
1182
  getCanonicalRefName(refName: string): string | undefined;
1183
+ getCanonicalRefName2(refName: string): string;
1174
1184
  getRefNameColor(refName: string): string | undefined;
1175
1185
  isValidRefName(refName: string): boolean;
1186
+ getSeqAdapterRefName(canonicalRefName: string): string;
1176
1187
  } & {
1177
1188
  setLoaded({ regions, refNameAliases, cytobands, }: {
1178
- regions: import("@jbrowse/core/util/types").Region[];
1189
+ regions: import("@jbrowse/core/util").Region[];
1179
1190
  refNameAliases: {
1180
1191
  [x: string]: string;
1181
1192
  };
1182
1193
  cytobands: import("@jbrowse/core/util").Feature[];
1183
1194
  }): void;
1184
1195
  setError(e: unknown): void;
1185
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1196
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1186
1197
  setRefNameAliases(aliases: {
1187
1198
  [x: string]: string;
1188
1199
  }): void;
1189
1200
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1201
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1190
1202
  setLoadingP(p?: Promise<void>): void;
1191
1203
  load(): Promise<void>;
1192
1204
  loadPre(): Promise<void>;
@@ -1205,17 +1217,18 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1205
1217
  [x: string]: string;
1206
1218
  }>;
1207
1219
  afterCreate(): void;
1208
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1220
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1209
1221
  }, {
1210
1222
  readonly assemblyNameMap: Record<string, {
1211
1223
  configuration: any;
1212
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1224
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
1213
1225
  error: unknown;
1214
1226
  loadingP: Promise<void> | undefined;
1215
1227
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1216
1228
  refNameAliases: {
1217
1229
  [x: string]: string;
1218
1230
  } | undefined;
1231
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1219
1232
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1220
1233
  } & {
1221
1234
  getConf(arg: string): any;
@@ -1239,22 +1252,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1239
1252
  readonly refNames: string[] | undefined;
1240
1253
  } & {
1241
1254
  getCanonicalRefName(refName: string): string | undefined;
1255
+ getCanonicalRefName2(refName: string): string;
1242
1256
  getRefNameColor(refName: string): string | undefined;
1243
1257
  isValidRefName(refName: string): boolean;
1258
+ getSeqAdapterRefName(canonicalRefName: string): string;
1244
1259
  } & {
1245
1260
  setLoaded({ regions, refNameAliases, cytobands, }: {
1246
- regions: import("@jbrowse/core/util/types").Region[];
1261
+ regions: import("@jbrowse/core/util").Region[];
1247
1262
  refNameAliases: {
1248
1263
  [x: string]: string;
1249
1264
  };
1250
1265
  cytobands: import("@jbrowse/core/util").Feature[];
1251
1266
  }): void;
1252
1267
  setError(e: unknown): void;
1253
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1268
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1254
1269
  setRefNameAliases(aliases: {
1255
1270
  [x: string]: string;
1256
1271
  }): void;
1257
1272
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1273
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1258
1274
  setLoadingP(p?: Promise<void>): void;
1259
1275
  load(): Promise<void>;
1260
1276
  loadPre(): Promise<void>;
@@ -1273,8 +1289,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1273
1289
  [x: string]: string;
1274
1290
  }>;
1275
1291
  afterCreate(): void;
1276
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1277
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1292
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1293
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1278
1294
  }, {
1279
1295
  error: unknown;
1280
1296
  loadingP: Promise<void> | undefined;
@@ -1282,6 +1298,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1282
1298
  refNameAliases: {
1283
1299
  [x: string]: string;
1284
1300
  } | undefined;
1301
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1285
1302
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1286
1303
  } & {
1287
1304
  getConf(arg: string): any;
@@ -1305,22 +1322,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1305
1322
  readonly refNames: string[] | undefined;
1306
1323
  } & {
1307
1324
  getCanonicalRefName(refName: string): string | undefined;
1325
+ getCanonicalRefName2(refName: string): string;
1308
1326
  getRefNameColor(refName: string): string | undefined;
1309
1327
  isValidRefName(refName: string): boolean;
1328
+ getSeqAdapterRefName(canonicalRefName: string): string;
1310
1329
  } & {
1311
1330
  setLoaded({ regions, refNameAliases, cytobands, }: {
1312
- regions: import("@jbrowse/core/util/types").Region[];
1331
+ regions: import("@jbrowse/core/util").Region[];
1313
1332
  refNameAliases: {
1314
1333
  [x: string]: string;
1315
1334
  };
1316
1335
  cytobands: import("@jbrowse/core/util").Feature[];
1317
1336
  }): void;
1318
1337
  setError(e: unknown): void;
1319
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1338
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1320
1339
  setRefNameAliases(aliases: {
1321
1340
  [x: string]: string;
1322
1341
  }): void;
1323
1342
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1343
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1324
1344
  setLoadingP(p?: Promise<void>): void;
1325
1345
  load(): Promise<void>;
1326
1346
  loadPre(): Promise<void>;
@@ -1339,18 +1359,20 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1339
1359
  [x: string]: string;
1340
1360
  }>;
1341
1361
  afterCreate(): void;
1342
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
1362
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
1343
1363
  } & {
1344
1364
  getCanonicalAssemblyName(asmName: string): string | undefined;
1365
+ getCanonicalAssemblyName2(asmName: string): string;
1345
1366
  get(asmName: string): ({
1346
1367
  configuration: any;
1347
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1368
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
1348
1369
  error: unknown;
1349
1370
  loadingP: Promise<void> | undefined;
1350
1371
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1351
1372
  refNameAliases: {
1352
1373
  [x: string]: string;
1353
1374
  } | undefined;
1375
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1354
1376
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1355
1377
  } & {
1356
1378
  getConf(arg: string): any;
@@ -1374,22 +1396,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1374
1396
  readonly refNames: string[] | undefined;
1375
1397
  } & {
1376
1398
  getCanonicalRefName(refName: string): string | undefined;
1399
+ getCanonicalRefName2(refName: string): string;
1377
1400
  getRefNameColor(refName: string): string | undefined;
1378
1401
  isValidRefName(refName: string): boolean;
1402
+ getSeqAdapterRefName(canonicalRefName: string): string;
1379
1403
  } & {
1380
1404
  setLoaded({ regions, refNameAliases, cytobands, }: {
1381
- regions: import("@jbrowse/core/util/types").Region[];
1405
+ regions: import("@jbrowse/core/util").Region[];
1382
1406
  refNameAliases: {
1383
1407
  [x: string]: string;
1384
1408
  };
1385
1409
  cytobands: import("@jbrowse/core/util").Feature[];
1386
1410
  }): void;
1387
1411
  setError(e: unknown): void;
1388
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1412
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1389
1413
  setRefNameAliases(aliases: {
1390
1414
  [x: string]: string;
1391
1415
  }): void;
1392
1416
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1417
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1393
1418
  setLoadingP(p?: Promise<void>): void;
1394
1419
  load(): Promise<void>;
1395
1420
  loadPre(): Promise<void>;
@@ -1408,8 +1433,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1408
1433
  [x: string]: string;
1409
1434
  }>;
1410
1435
  afterCreate(): void;
1411
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1412
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1436
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1437
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1413
1438
  }, {
1414
1439
  error: unknown;
1415
1440
  loadingP: Promise<void> | undefined;
@@ -1417,6 +1442,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1417
1442
  refNameAliases: {
1418
1443
  [x: string]: string;
1419
1444
  } | undefined;
1445
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1420
1446
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1421
1447
  } & {
1422
1448
  getConf(arg: string): any;
@@ -1440,22 +1466,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1440
1466
  readonly refNames: string[] | undefined;
1441
1467
  } & {
1442
1468
  getCanonicalRefName(refName: string): string | undefined;
1469
+ getCanonicalRefName2(refName: string): string;
1443
1470
  getRefNameColor(refName: string): string | undefined;
1444
1471
  isValidRefName(refName: string): boolean;
1472
+ getSeqAdapterRefName(canonicalRefName: string): string;
1445
1473
  } & {
1446
1474
  setLoaded({ regions, refNameAliases, cytobands, }: {
1447
- regions: import("@jbrowse/core/util/types").Region[];
1475
+ regions: import("@jbrowse/core/util").Region[];
1448
1476
  refNameAliases: {
1449
1477
  [x: string]: string;
1450
1478
  };
1451
1479
  cytobands: import("@jbrowse/core/util").Feature[];
1452
1480
  }): void;
1453
1481
  setError(e: unknown): void;
1454
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1482
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1455
1483
  setRefNameAliases(aliases: {
1456
1484
  [x: string]: string;
1457
1485
  }): void;
1458
1486
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1487
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1459
1488
  setLoadingP(p?: Promise<void>): void;
1460
1489
  load(): Promise<void>;
1461
1490
  loadPre(): Promise<void>;
@@ -1474,20 +1503,21 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1474
1503
  [x: string]: string;
1475
1504
  }>;
1476
1505
  afterCreate(): void;
1477
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1506
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1478
1507
  readonly assemblyNamesList: any[];
1479
1508
  readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1480
1509
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1481
1510
  } & {
1482
1511
  waitForAssembly(assemblyName: string): Promise<({
1483
1512
  configuration: any;
1484
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1513
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
1485
1514
  error: unknown;
1486
1515
  loadingP: Promise<void> | undefined;
1487
1516
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1488
1517
  refNameAliases: {
1489
1518
  [x: string]: string;
1490
1519
  } | undefined;
1520
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1491
1521
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1492
1522
  } & {
1493
1523
  getConf(arg: string): any;
@@ -1511,22 +1541,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1511
1541
  readonly refNames: string[] | undefined;
1512
1542
  } & {
1513
1543
  getCanonicalRefName(refName: string): string | undefined;
1544
+ getCanonicalRefName2(refName: string): string;
1514
1545
  getRefNameColor(refName: string): string | undefined;
1515
1546
  isValidRefName(refName: string): boolean;
1547
+ getSeqAdapterRefName(canonicalRefName: string): string;
1516
1548
  } & {
1517
1549
  setLoaded({ regions, refNameAliases, cytobands, }: {
1518
- regions: import("@jbrowse/core/util/types").Region[];
1550
+ regions: import("@jbrowse/core/util").Region[];
1519
1551
  refNameAliases: {
1520
1552
  [x: string]: string;
1521
1553
  };
1522
1554
  cytobands: import("@jbrowse/core/util").Feature[];
1523
1555
  }): void;
1524
1556
  setError(e: unknown): void;
1525
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1557
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1526
1558
  setRefNameAliases(aliases: {
1527
1559
  [x: string]: string;
1528
1560
  }): void;
1529
1561
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1562
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1530
1563
  setLoadingP(p?: Promise<void>): void;
1531
1564
  load(): Promise<void>;
1532
1565
  loadPre(): Promise<void>;
@@ -1545,8 +1578,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1545
1578
  [x: string]: string;
1546
1579
  }>;
1547
1580
  afterCreate(): void;
1548
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1549
- configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1581
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1582
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1550
1583
  }, {
1551
1584
  error: unknown;
1552
1585
  loadingP: Promise<void> | undefined;
@@ -1554,6 +1587,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1554
1587
  refNameAliases: {
1555
1588
  [x: string]: string;
1556
1589
  } | undefined;
1590
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1557
1591
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1558
1592
  } & {
1559
1593
  getConf(arg: string): any;
@@ -1577,22 +1611,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1577
1611
  readonly refNames: string[] | undefined;
1578
1612
  } & {
1579
1613
  getCanonicalRefName(refName: string): string | undefined;
1614
+ getCanonicalRefName2(refName: string): string;
1580
1615
  getRefNameColor(refName: string): string | undefined;
1581
1616
  isValidRefName(refName: string): boolean;
1617
+ getSeqAdapterRefName(canonicalRefName: string): string;
1582
1618
  } & {
1583
1619
  setLoaded({ regions, refNameAliases, cytobands, }: {
1584
- regions: import("@jbrowse/core/util/types").Region[];
1620
+ regions: import("@jbrowse/core/util").Region[];
1585
1621
  refNameAliases: {
1586
1622
  [x: string]: string;
1587
1623
  };
1588
1624
  cytobands: import("@jbrowse/core/util").Feature[];
1589
1625
  }): void;
1590
1626
  setError(e: unknown): void;
1591
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1627
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1592
1628
  setRefNameAliases(aliases: {
1593
1629
  [x: string]: string;
1594
1630
  }): void;
1595
1631
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1632
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1596
1633
  setLoadingP(p?: Promise<void>): void;
1597
1634
  load(): Promise<void>;
1598
1635
  loadPre(): Promise<void>;
@@ -1611,21 +1648,15 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1611
1648
  [x: string]: string;
1612
1649
  }>;
1613
1650
  afterCreate(): void;
1614
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1651
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
1615
1652
  getRefNameMapForAdapter(adapterConf: {
1616
1653
  [x: string]: unknown;
1617
- }, assemblyName: string | undefined, opts: {
1618
- stopToken?: string;
1619
- sessionId: string;
1620
- }): Promise<{
1654
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
1621
1655
  [x: string]: string;
1622
1656
  } | undefined>;
1623
1657
  getReverseRefNameMapForAdapter(adapterConf: {
1624
1658
  [x: string]: unknown;
1625
- }, assemblyName: string | undefined, opts: {
1626
- stopToken?: string;
1627
- sessionId: string;
1628
- }): Promise<{
1659
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
1629
1660
  [x: string]: string;
1630
1661
  } | undefined>;
1631
1662
  isValidRefName(refName: string, assemblyName: string): boolean;
@@ -1633,36 +1664,32 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1633
1664
  afterAttach(): void;
1634
1665
  removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1635
1666
  addAssembly(configuration: any): void;
1636
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
1667
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
1637
1668
  }, {
1638
1669
  rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1639
1670
  adminMode: boolean;
1640
1671
  error: unknown;
1641
- textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1672
+ textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1642
1673
  pluginManager: PluginManager;
1643
1674
  } & {
1644
1675
  setError(error: unknown): void;
1645
- setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1676
+ setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
1646
1677
  setDefaultSession(): void;
1647
1678
  setSessionPath(path: string): void;
1648
1679
  renameCurrentSession(newName: string): void;
1649
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1680
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1650
1681
  } & {
1651
1682
  readonly jbrowse: any;
1652
1683
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1653
1684
  readonly configuration: {
1654
1685
  [x: string]: any;
1655
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1686
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
1656
1687
  setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1657
1688
  [x: string]: any;
1658
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1659
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1660
- [x: string]: any;
1661
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1662
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1663
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1689
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1690
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1664
1691
  readonly adminMode: boolean;
1665
- readonly textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1692
+ readonly textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1666
1693
  } & {
1667
1694
  readonly assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
1668
1695
  } & {
@@ -1682,127 +1709,39 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1682
1709
  minimizeWidgetDrawer(): void;
1683
1710
  showWidgetDrawer(): void;
1684
1711
  hideAllWidgets(): void;
1685
- editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1712
+ editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel | {
1713
+ trackId: string;
1714
+ }): void;
1686
1715
  afterAttach(): void;
1687
1716
  } & {
1688
1717
  readonly connections: import("@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig").BaseConnectionConfigModel[];
1689
1718
  } & {
1690
- makeConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: {}): ({
1691
- name: string;
1692
- 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>>;
1693
- configuration: {
1694
- [x: string]: any;
1695
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1696
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1697
- [x: string]: any;
1698
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1699
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1700
- [x: string]: any;
1701
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1702
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1703
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1704
- name: {
1705
- type: string;
1706
- defaultValue: string;
1707
- description: string;
1708
- };
1709
- assemblyNames: {
1710
- type: string;
1711
- defaultValue: never[];
1712
- description: string;
1713
- };
1714
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>;
1715
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1716
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1717
- } & {
1718
- afterAttach(): void;
1719
- addTrackConf(trackConf: Record<string, unknown> | ({
1720
- [x: string]: any;
1721
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1722
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
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 & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1728
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1729
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
1730
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
1731
- [x: string]: any;
1732
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1733
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1734
- [x: string]: any;
1735
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1736
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1737
- [x: string]: any;
1738
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1739
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1740
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
1741
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
1742
- clear(): void;
1743
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1744
- name: import("mobx-state-tree").ISimpleType<string>;
1745
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
1746
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1747
- name: {
1748
- type: string;
1749
- defaultValue: string;
1750
- description: string;
1751
- };
1752
- assemblyNames: {
1753
- type: string;
1754
- defaultValue: never[];
1755
- description: string;
1756
- };
1757
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
1758
- }, {
1759
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1760
- } & {
1761
- afterAttach(): void;
1762
- addTrackConf(trackConf: 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 & {
1768
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1769
- [x: string]: any;
1770
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1771
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1772
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
1773
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
1774
- [x: string]: any;
1775
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1776
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1777
- [x: string]: any;
1778
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1779
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1780
- [x: string]: any;
1781
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1782
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1783
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
1784
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
1785
- clear(): void;
1786
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1719
+ makeConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: {}): any;
1787
1720
  prepareToBreakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): (Record<string, number> | (() => void))[] | undefined;
1788
1721
  breakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1789
1722
  deleteConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1790
1723
  addConnectionConf(connectionConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1791
1724
  clearConnections(): void;
1792
1725
  } & {
1793
- queueOfDialogs: [import("@jbrowse/core/util/types").DialogComponentType, unknown][];
1726
+ queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, unknown][];
1794
1727
  } & {
1795
- readonly DialogComponent: import("@jbrowse/core/util/types").DialogComponentType | undefined;
1728
+ readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType | undefined;
1796
1729
  readonly DialogProps: unknown;
1797
1730
  } & {
1798
1731
  removeActiveDialog(): void;
1799
- queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util/types").DialogComponentType, unknown]): void;
1732
+ queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, unknown]): void;
1800
1733
  } & {
1801
- getReferring(object: import("mobx-state-tree").IAnyStateTreeNode): import("@jbrowse/product-core").ReferringNode[];
1734
+ getReferring(object: import("@jbrowse/mobx-state-tree").IAnyStateTreeNode): import("@jbrowse/product-core").ReferringNode[];
1802
1735
  } & {
1803
1736
  removeReferring(referring: import("@jbrowse/product-core").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
1804
1737
  } & {
1805
1738
  readonly tracks: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1739
+ readonly assemblies: {
1740
+ sequence: {
1741
+ trackId: string;
1742
+ };
1743
+ }[];
1744
+ readonly tracksById: Record<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
1806
1745
  } & {
1807
1746
  addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfiguration): any;
1808
1747
  deleteTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
@@ -1811,9 +1750,9 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1811
1750
  } & {
1812
1751
  readonly snackbarMessageSet: Map<string, import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1813
1752
  } & {
1814
- notify(message: string, level?: import("@jbrowse/core/util/types").NotificationLevel, action?: import("@jbrowse/core/util/types").SnackAction): void;
1753
+ notify(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction): void;
1815
1754
  notifyError(errorMessage: string, error?: unknown, extra?: unknown): void;
1816
- pushSnackbarMessage(message: string, level?: import("@jbrowse/core/util/types").NotificationLevel, action?: import("@jbrowse/core/util/types").SnackAction): void;
1755
+ pushSnackbarMessage(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction): void;
1817
1756
  popSnackbarMessage(): import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage | undefined;
1818
1757
  removeSnackbarMessage(message: string): void;
1819
1758
  } & {
@@ -1833,13 +1772,19 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1833
1772
  addView(typeName: string, initialState?: {}): any;
1834
1773
  removeView(): void;
1835
1774
  } & {
1836
- getTrackActionMenuItems(config: any): {
1837
- label: string;
1838
- onClick: () => void;
1839
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
1840
- muiName: string;
1841
- };
1842
- }[];
1843
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
1775
+ getTrackActionMenuItems(config: any, extraTrackActions?: MenuItem[]): MenuItem[];
1776
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
1777
+ id: string;
1778
+ name: string;
1779
+ margin: number;
1780
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
1781
+ drawerPosition: string;
1782
+ drawerWidth: number;
1783
+ widgets: import("mobx").IKeyValueMap<any>;
1784
+ activeWidgets: import("mobx").IKeyValueMap<import("@jbrowse/mobx-state-tree").ReferenceIdentifier | undefined>;
1785
+ minimized: boolean;
1786
+ } & {
1787
+ connectionInstances: any[];
1788
+ } & import("@jbrowse/mobx-state-tree")._NotCustomized>;
1844
1789
  export type SessionStateModel = ReturnType<typeof sessionModelFactory>;
1845
1790
  export type SessionModel = Instance<SessionStateModel>;