@jbrowse/react-circular-genome-view2 3.7.0 → 4.0.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (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 +517 -680
  9. package/esm/createModel/createModel.js +5 -5
  10. package/esm/createModel/createSessionModel.d.ts +247 -327
  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 +1305 -1757
  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 -4588
  36. package/dist/createModel/createModel.js +0 -117
  37. package/dist/createModel/createSessionModel.d.ts +0 -1870
  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 -11770
  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 -145
  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;
@@ -98,23 +57,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
98
57
  readonly refNames: string[] | undefined;
99
58
  } & {
100
59
  getCanonicalRefName(refName: string): string | undefined;
101
- getCanonicalRefName2(asmName: string): string;
60
+ getCanonicalRefName2(refName: string): string;
102
61
  getRefNameColor(refName: string): string | undefined;
103
62
  isValidRefName(refName: string): boolean;
63
+ getSeqAdapterRefName(canonicalRefName: string): string;
104
64
  } & {
105
65
  setLoaded({ regions, refNameAliases, cytobands, }: {
106
- regions: import("@jbrowse/core/util/types").Region[];
66
+ regions: import("@jbrowse/core/util").Region[];
107
67
  refNameAliases: {
108
68
  [x: string]: string;
109
69
  };
110
70
  cytobands: import("@jbrowse/core/util").Feature[];
111
71
  }): void;
112
72
  setError(e: unknown): void;
113
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
73
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
114
74
  setRefNameAliases(aliases: {
115
75
  [x: string]: string;
116
76
  }): void;
117
77
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
78
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
118
79
  setLoadingP(p?: Promise<void>): void;
119
80
  load(): Promise<void>;
120
81
  loadPre(): Promise<void>;
@@ -133,8 +94,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
133
94
  [x: string]: string;
134
95
  }>;
135
96
  afterCreate(): void;
136
- }, 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<{
137
- 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>>;
138
99
  }, {
139
100
  error: unknown;
140
101
  loadingP: Promise<void> | undefined;
@@ -142,6 +103,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
142
103
  refNameAliases: {
143
104
  [x: string]: string;
144
105
  } | undefined;
106
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
145
107
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
146
108
  } & {
147
109
  getConf(arg: string): any;
@@ -165,23 +127,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
165
127
  readonly refNames: string[] | undefined;
166
128
  } & {
167
129
  getCanonicalRefName(refName: string): string | undefined;
168
- getCanonicalRefName2(asmName: string): string;
130
+ getCanonicalRefName2(refName: string): string;
169
131
  getRefNameColor(refName: string): string | undefined;
170
132
  isValidRefName(refName: string): boolean;
133
+ getSeqAdapterRefName(canonicalRefName: string): string;
171
134
  } & {
172
135
  setLoaded({ regions, refNameAliases, cytobands, }: {
173
- regions: import("@jbrowse/core/util/types").Region[];
136
+ regions: import("@jbrowse/core/util").Region[];
174
137
  refNameAliases: {
175
138
  [x: string]: string;
176
139
  };
177
140
  cytobands: import("@jbrowse/core/util").Feature[];
178
141
  }): void;
179
142
  setError(e: unknown): void;
180
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
143
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
181
144
  setRefNameAliases(aliases: {
182
145
  [x: string]: string;
183
146
  }): void;
184
147
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
148
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
185
149
  setLoadingP(p?: Promise<void>): void;
186
150
  load(): Promise<void>;
187
151
  loadPre(): Promise<void>;
@@ -200,17 +164,18 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
200
164
  [x: string]: string;
201
165
  }>;
202
166
  afterCreate(): void;
203
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
204
- } & 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 & {
205
169
  readonly assemblyNameMap: Record<string, {
206
170
  configuration: any;
207
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
171
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
208
172
  error: unknown;
209
173
  loadingP: Promise<void> | undefined;
210
174
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
211
175
  refNameAliases: {
212
176
  [x: string]: string;
213
177
  } | undefined;
178
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
214
179
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
215
180
  } & {
216
181
  getConf(arg: string): any;
@@ -234,23 +199,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
234
199
  readonly refNames: string[] | undefined;
235
200
  } & {
236
201
  getCanonicalRefName(refName: string): string | undefined;
237
- getCanonicalRefName2(asmName: string): string;
202
+ getCanonicalRefName2(refName: string): string;
238
203
  getRefNameColor(refName: string): string | undefined;
239
204
  isValidRefName(refName: string): boolean;
205
+ getSeqAdapterRefName(canonicalRefName: string): string;
240
206
  } & {
241
207
  setLoaded({ regions, refNameAliases, cytobands, }: {
242
- regions: import("@jbrowse/core/util/types").Region[];
208
+ regions: import("@jbrowse/core/util").Region[];
243
209
  refNameAliases: {
244
210
  [x: string]: string;
245
211
  };
246
212
  cytobands: import("@jbrowse/core/util").Feature[];
247
213
  }): void;
248
214
  setError(e: unknown): void;
249
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
215
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
250
216
  setRefNameAliases(aliases: {
251
217
  [x: string]: string;
252
218
  }): void;
253
219
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
220
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
254
221
  setLoadingP(p?: Promise<void>): void;
255
222
  load(): Promise<void>;
256
223
  loadPre(): Promise<void>;
@@ -269,8 +236,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
269
236
  [x: string]: string;
270
237
  }>;
271
238
  afterCreate(): void;
272
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
273
- 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>>;
274
241
  }, {
275
242
  error: unknown;
276
243
  loadingP: Promise<void> | undefined;
@@ -278,6 +245,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
278
245
  refNameAliases: {
279
246
  [x: string]: string;
280
247
  } | undefined;
248
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
281
249
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
282
250
  } & {
283
251
  getConf(arg: string): any;
@@ -301,23 +269,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
301
269
  readonly refNames: string[] | undefined;
302
270
  } & {
303
271
  getCanonicalRefName(refName: string): string | undefined;
304
- getCanonicalRefName2(asmName: string): string;
272
+ getCanonicalRefName2(refName: string): string;
305
273
  getRefNameColor(refName: string): string | undefined;
306
274
  isValidRefName(refName: string): boolean;
275
+ getSeqAdapterRefName(canonicalRefName: string): string;
307
276
  } & {
308
277
  setLoaded({ regions, refNameAliases, cytobands, }: {
309
- regions: import("@jbrowse/core/util/types").Region[];
278
+ regions: import("@jbrowse/core/util").Region[];
310
279
  refNameAliases: {
311
280
  [x: string]: string;
312
281
  };
313
282
  cytobands: import("@jbrowse/core/util").Feature[];
314
283
  }): void;
315
284
  setError(e: unknown): void;
316
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
285
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
317
286
  setRefNameAliases(aliases: {
318
287
  [x: string]: string;
319
288
  }): void;
320
289
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
290
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
321
291
  setLoadingP(p?: Promise<void>): void;
322
292
  load(): Promise<void>;
323
293
  loadPre(): Promise<void>;
@@ -336,19 +306,20 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
336
306
  [x: string]: string;
337
307
  }>;
338
308
  afterCreate(): void;
339
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
309
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
340
310
  } & {
341
311
  getCanonicalAssemblyName(asmName: string): string | undefined;
342
312
  getCanonicalAssemblyName2(asmName: string): string;
343
313
  get(asmName: string): ({
344
314
  configuration: any;
345
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
315
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
346
316
  error: unknown;
347
317
  loadingP: Promise<void> | undefined;
348
318
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
349
319
  refNameAliases: {
350
320
  [x: string]: string;
351
321
  } | undefined;
322
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
352
323
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
353
324
  } & {
354
325
  getConf(arg: string): any;
@@ -372,23 +343,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
372
343
  readonly refNames: string[] | undefined;
373
344
  } & {
374
345
  getCanonicalRefName(refName: string): string | undefined;
375
- getCanonicalRefName2(asmName: string): string;
346
+ getCanonicalRefName2(refName: string): string;
376
347
  getRefNameColor(refName: string): string | undefined;
377
348
  isValidRefName(refName: string): boolean;
349
+ getSeqAdapterRefName(canonicalRefName: string): string;
378
350
  } & {
379
351
  setLoaded({ regions, refNameAliases, cytobands, }: {
380
- regions: import("@jbrowse/core/util/types").Region[];
352
+ regions: import("@jbrowse/core/util").Region[];
381
353
  refNameAliases: {
382
354
  [x: string]: string;
383
355
  };
384
356
  cytobands: import("@jbrowse/core/util").Feature[];
385
357
  }): void;
386
358
  setError(e: unknown): void;
387
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
359
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
388
360
  setRefNameAliases(aliases: {
389
361
  [x: string]: string;
390
362
  }): void;
391
363
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
364
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
392
365
  setLoadingP(p?: Promise<void>): void;
393
366
  load(): Promise<void>;
394
367
  loadPre(): Promise<void>;
@@ -407,8 +380,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
407
380
  [x: string]: string;
408
381
  }>;
409
382
  afterCreate(): void;
410
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
411
- 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>>;
412
385
  }, {
413
386
  error: unknown;
414
387
  loadingP: Promise<void> | undefined;
@@ -416,6 +389,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
416
389
  refNameAliases: {
417
390
  [x: string]: string;
418
391
  } | undefined;
392
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
419
393
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
420
394
  } & {
421
395
  getConf(arg: string): any;
@@ -439,23 +413,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
439
413
  readonly refNames: string[] | undefined;
440
414
  } & {
441
415
  getCanonicalRefName(refName: string): string | undefined;
442
- getCanonicalRefName2(asmName: string): string;
416
+ getCanonicalRefName2(refName: string): string;
443
417
  getRefNameColor(refName: string): string | undefined;
444
418
  isValidRefName(refName: string): boolean;
419
+ getSeqAdapterRefName(canonicalRefName: string): string;
445
420
  } & {
446
421
  setLoaded({ regions, refNameAliases, cytobands, }: {
447
- regions: import("@jbrowse/core/util/types").Region[];
422
+ regions: import("@jbrowse/core/util").Region[];
448
423
  refNameAliases: {
449
424
  [x: string]: string;
450
425
  };
451
426
  cytobands: import("@jbrowse/core/util").Feature[];
452
427
  }): void;
453
428
  setError(e: unknown): void;
454
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
429
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
455
430
  setRefNameAliases(aliases: {
456
431
  [x: string]: string;
457
432
  }): void;
458
433
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
434
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
459
435
  setLoadingP(p?: Promise<void>): void;
460
436
  load(): Promise<void>;
461
437
  loadPre(): Promise<void>;
@@ -474,20 +450,21 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
474
450
  [x: string]: string;
475
451
  }>;
476
452
  afterCreate(): void;
477
- }, 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;
478
454
  readonly assemblyNamesList: any[];
479
455
  readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
480
456
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
481
457
  } & {
482
458
  waitForAssembly(assemblyName: string): Promise<({
483
459
  configuration: any;
484
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
460
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
485
461
  error: unknown;
486
462
  loadingP: Promise<void> | undefined;
487
463
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
488
464
  refNameAliases: {
489
465
  [x: string]: string;
490
466
  } | undefined;
467
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
491
468
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
492
469
  } & {
493
470
  getConf(arg: string): any;
@@ -511,23 +488,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
511
488
  readonly refNames: string[] | undefined;
512
489
  } & {
513
490
  getCanonicalRefName(refName: string): string | undefined;
514
- getCanonicalRefName2(asmName: string): string;
491
+ getCanonicalRefName2(refName: string): string;
515
492
  getRefNameColor(refName: string): string | undefined;
516
493
  isValidRefName(refName: string): boolean;
494
+ getSeqAdapterRefName(canonicalRefName: string): string;
517
495
  } & {
518
496
  setLoaded({ regions, refNameAliases, cytobands, }: {
519
- regions: import("@jbrowse/core/util/types").Region[];
497
+ regions: import("@jbrowse/core/util").Region[];
520
498
  refNameAliases: {
521
499
  [x: string]: string;
522
500
  };
523
501
  cytobands: import("@jbrowse/core/util").Feature[];
524
502
  }): void;
525
503
  setError(e: unknown): void;
526
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
504
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
527
505
  setRefNameAliases(aliases: {
528
506
  [x: string]: string;
529
507
  }): void;
530
508
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
509
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
531
510
  setLoadingP(p?: Promise<void>): void;
532
511
  load(): Promise<void>;
533
512
  loadPre(): Promise<void>;
@@ -546,8 +525,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
546
525
  [x: string]: string;
547
526
  }>;
548
527
  afterCreate(): void;
549
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
550
- 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>>;
551
530
  }, {
552
531
  error: unknown;
553
532
  loadingP: Promise<void> | undefined;
@@ -555,6 +534,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
555
534
  refNameAliases: {
556
535
  [x: string]: string;
557
536
  } | undefined;
537
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
558
538
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
559
539
  } & {
560
540
  getConf(arg: string): any;
@@ -578,23 +558,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
578
558
  readonly refNames: string[] | undefined;
579
559
  } & {
580
560
  getCanonicalRefName(refName: string): string | undefined;
581
- getCanonicalRefName2(asmName: string): string;
561
+ getCanonicalRefName2(refName: string): string;
582
562
  getRefNameColor(refName: string): string | undefined;
583
563
  isValidRefName(refName: string): boolean;
564
+ getSeqAdapterRefName(canonicalRefName: string): string;
584
565
  } & {
585
566
  setLoaded({ regions, refNameAliases, cytobands, }: {
586
- regions: import("@jbrowse/core/util/types").Region[];
567
+ regions: import("@jbrowse/core/util").Region[];
587
568
  refNameAliases: {
588
569
  [x: string]: string;
589
570
  };
590
571
  cytobands: import("@jbrowse/core/util").Feature[];
591
572
  }): void;
592
573
  setError(e: unknown): void;
593
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
574
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
594
575
  setRefNameAliases(aliases: {
595
576
  [x: string]: string;
596
577
  }): void;
597
578
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
579
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
598
580
  setLoadingP(p?: Promise<void>): void;
599
581
  load(): Promise<void>;
600
582
  loadPre(): Promise<void>;
@@ -613,21 +595,15 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
613
595
  [x: string]: string;
614
596
  }>;
615
597
  afterCreate(): void;
616
- }, 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>;
617
599
  getRefNameMapForAdapter(adapterConf: {
618
600
  [x: string]: unknown;
619
- }, assemblyName: string | undefined, opts: {
620
- stopToken?: string;
621
- sessionId: string;
622
- }): Promise<{
601
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
623
602
  [x: string]: string;
624
603
  } | undefined>;
625
604
  getReverseRefNameMapForAdapter(adapterConf: {
626
605
  [x: string]: unknown;
627
- }, assemblyName: string | undefined, opts: {
628
- stopToken?: string;
629
- sessionId: string;
630
- }): Promise<{
606
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
631
607
  [x: string]: string;
632
608
  } | undefined>;
633
609
  isValidRefName(refName: string, assemblyName: string): boolean;
@@ -635,9 +611,9 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
635
611
  afterAttach(): void;
636
612
  removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
637
613
  addAssembly(configuration: any): void;
638
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
639
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
640
- 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>>;
641
617
  }, {
642
618
  error: unknown;
643
619
  loadingP: Promise<void> | undefined;
@@ -645,6 +621,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
645
621
  refNameAliases: {
646
622
  [x: string]: string;
647
623
  } | undefined;
624
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
648
625
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
649
626
  } & {
650
627
  getConf(arg: string): any;
@@ -668,23 +645,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
668
645
  readonly refNames: string[] | undefined;
669
646
  } & {
670
647
  getCanonicalRefName(refName: string): string | undefined;
671
- getCanonicalRefName2(asmName: string): string;
648
+ getCanonicalRefName2(refName: string): string;
672
649
  getRefNameColor(refName: string): string | undefined;
673
650
  isValidRefName(refName: string): boolean;
651
+ getSeqAdapterRefName(canonicalRefName: string): string;
674
652
  } & {
675
653
  setLoaded({ regions, refNameAliases, cytobands, }: {
676
- regions: import("@jbrowse/core/util/types").Region[];
654
+ regions: import("@jbrowse/core/util").Region[];
677
655
  refNameAliases: {
678
656
  [x: string]: string;
679
657
  };
680
658
  cytobands: import("@jbrowse/core/util").Feature[];
681
659
  }): void;
682
660
  setError(e: unknown): void;
683
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
661
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
684
662
  setRefNameAliases(aliases: {
685
663
  [x: string]: string;
686
664
  }): void;
687
665
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
666
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
688
667
  setLoadingP(p?: Promise<void>): void;
689
668
  load(): Promise<void>;
690
669
  loadPre(): Promise<void>;
@@ -703,17 +682,18 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
703
682
  [x: string]: string;
704
683
  }>;
705
684
  afterCreate(): void;
706
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
685
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
707
686
  }, {
708
687
  readonly assemblyNameMap: Record<string, {
709
688
  configuration: any;
710
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
689
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
711
690
  error: unknown;
712
691
  loadingP: Promise<void> | undefined;
713
692
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
714
693
  refNameAliases: {
715
694
  [x: string]: string;
716
695
  } | undefined;
696
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
717
697
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
718
698
  } & {
719
699
  getConf(arg: string): any;
@@ -737,23 +717,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
737
717
  readonly refNames: string[] | undefined;
738
718
  } & {
739
719
  getCanonicalRefName(refName: string): string | undefined;
740
- getCanonicalRefName2(asmName: string): string;
720
+ getCanonicalRefName2(refName: string): string;
741
721
  getRefNameColor(refName: string): string | undefined;
742
722
  isValidRefName(refName: string): boolean;
723
+ getSeqAdapterRefName(canonicalRefName: string): string;
743
724
  } & {
744
725
  setLoaded({ regions, refNameAliases, cytobands, }: {
745
- regions: import("@jbrowse/core/util/types").Region[];
726
+ regions: import("@jbrowse/core/util").Region[];
746
727
  refNameAliases: {
747
728
  [x: string]: string;
748
729
  };
749
730
  cytobands: import("@jbrowse/core/util").Feature[];
750
731
  }): void;
751
732
  setError(e: unknown): void;
752
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
733
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
753
734
  setRefNameAliases(aliases: {
754
735
  [x: string]: string;
755
736
  }): void;
756
737
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
738
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
757
739
  setLoadingP(p?: Promise<void>): void;
758
740
  load(): Promise<void>;
759
741
  loadPre(): Promise<void>;
@@ -772,8 +754,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
772
754
  [x: string]: string;
773
755
  }>;
774
756
  afterCreate(): void;
775
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
776
- 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>>;
777
759
  }, {
778
760
  error: unknown;
779
761
  loadingP: Promise<void> | undefined;
@@ -781,6 +763,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
781
763
  refNameAliases: {
782
764
  [x: string]: string;
783
765
  } | undefined;
766
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
784
767
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
785
768
  } & {
786
769
  getConf(arg: string): any;
@@ -804,23 +787,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
804
787
  readonly refNames: string[] | undefined;
805
788
  } & {
806
789
  getCanonicalRefName(refName: string): string | undefined;
807
- getCanonicalRefName2(asmName: string): string;
790
+ getCanonicalRefName2(refName: string): string;
808
791
  getRefNameColor(refName: string): string | undefined;
809
792
  isValidRefName(refName: string): boolean;
793
+ getSeqAdapterRefName(canonicalRefName: string): string;
810
794
  } & {
811
795
  setLoaded({ regions, refNameAliases, cytobands, }: {
812
- regions: import("@jbrowse/core/util/types").Region[];
796
+ regions: import("@jbrowse/core/util").Region[];
813
797
  refNameAliases: {
814
798
  [x: string]: string;
815
799
  };
816
800
  cytobands: import("@jbrowse/core/util").Feature[];
817
801
  }): void;
818
802
  setError(e: unknown): void;
819
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
803
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
820
804
  setRefNameAliases(aliases: {
821
805
  [x: string]: string;
822
806
  }): void;
823
807
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
808
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
824
809
  setLoadingP(p?: Promise<void>): void;
825
810
  load(): Promise<void>;
826
811
  loadPre(): Promise<void>;
@@ -839,19 +824,20 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
839
824
  [x: string]: string;
840
825
  }>;
841
826
  afterCreate(): void;
842
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
827
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
843
828
  } & {
844
829
  getCanonicalAssemblyName(asmName: string): string | undefined;
845
830
  getCanonicalAssemblyName2(asmName: string): string;
846
831
  get(asmName: string): ({
847
832
  configuration: any;
848
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
833
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
849
834
  error: unknown;
850
835
  loadingP: Promise<void> | undefined;
851
836
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
852
837
  refNameAliases: {
853
838
  [x: string]: string;
854
839
  } | undefined;
840
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
855
841
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
856
842
  } & {
857
843
  getConf(arg: string): any;
@@ -875,23 +861,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
875
861
  readonly refNames: string[] | undefined;
876
862
  } & {
877
863
  getCanonicalRefName(refName: string): string | undefined;
878
- getCanonicalRefName2(asmName: string): string;
864
+ getCanonicalRefName2(refName: string): string;
879
865
  getRefNameColor(refName: string): string | undefined;
880
866
  isValidRefName(refName: string): boolean;
867
+ getSeqAdapterRefName(canonicalRefName: string): string;
881
868
  } & {
882
869
  setLoaded({ regions, refNameAliases, cytobands, }: {
883
- regions: import("@jbrowse/core/util/types").Region[];
870
+ regions: import("@jbrowse/core/util").Region[];
884
871
  refNameAliases: {
885
872
  [x: string]: string;
886
873
  };
887
874
  cytobands: import("@jbrowse/core/util").Feature[];
888
875
  }): void;
889
876
  setError(e: unknown): void;
890
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
877
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
891
878
  setRefNameAliases(aliases: {
892
879
  [x: string]: string;
893
880
  }): void;
894
881
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
882
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
895
883
  setLoadingP(p?: Promise<void>): void;
896
884
  load(): Promise<void>;
897
885
  loadPre(): Promise<void>;
@@ -910,8 +898,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
910
898
  [x: string]: string;
911
899
  }>;
912
900
  afterCreate(): void;
913
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
914
- 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>>;
915
903
  }, {
916
904
  error: unknown;
917
905
  loadingP: Promise<void> | undefined;
@@ -919,6 +907,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
919
907
  refNameAliases: {
920
908
  [x: string]: string;
921
909
  } | undefined;
910
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
922
911
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
923
912
  } & {
924
913
  getConf(arg: string): any;
@@ -942,23 +931,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
942
931
  readonly refNames: string[] | undefined;
943
932
  } & {
944
933
  getCanonicalRefName(refName: string): string | undefined;
945
- getCanonicalRefName2(asmName: string): string;
934
+ getCanonicalRefName2(refName: string): string;
946
935
  getRefNameColor(refName: string): string | undefined;
947
936
  isValidRefName(refName: string): boolean;
937
+ getSeqAdapterRefName(canonicalRefName: string): string;
948
938
  } & {
949
939
  setLoaded({ regions, refNameAliases, cytobands, }: {
950
- regions: import("@jbrowse/core/util/types").Region[];
940
+ regions: import("@jbrowse/core/util").Region[];
951
941
  refNameAliases: {
952
942
  [x: string]: string;
953
943
  };
954
944
  cytobands: import("@jbrowse/core/util").Feature[];
955
945
  }): void;
956
946
  setError(e: unknown): void;
957
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
947
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
958
948
  setRefNameAliases(aliases: {
959
949
  [x: string]: string;
960
950
  }): void;
961
951
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
952
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
962
953
  setLoadingP(p?: Promise<void>): void;
963
954
  load(): Promise<void>;
964
955
  loadPre(): Promise<void>;
@@ -977,20 +968,21 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
977
968
  [x: string]: string;
978
969
  }>;
979
970
  afterCreate(): void;
980
- }, 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;
981
972
  readonly assemblyNamesList: any[];
982
973
  readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
983
974
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
984
975
  } & {
985
976
  waitForAssembly(assemblyName: string): Promise<({
986
977
  configuration: any;
987
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
978
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
988
979
  error: unknown;
989
980
  loadingP: Promise<void> | undefined;
990
981
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
991
982
  refNameAliases: {
992
983
  [x: string]: string;
993
984
  } | undefined;
985
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
994
986
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
995
987
  } & {
996
988
  getConf(arg: string): any;
@@ -1014,23 +1006,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1014
1006
  readonly refNames: string[] | undefined;
1015
1007
  } & {
1016
1008
  getCanonicalRefName(refName: string): string | undefined;
1017
- getCanonicalRefName2(asmName: string): string;
1009
+ getCanonicalRefName2(refName: string): string;
1018
1010
  getRefNameColor(refName: string): string | undefined;
1019
1011
  isValidRefName(refName: string): boolean;
1012
+ getSeqAdapterRefName(canonicalRefName: string): string;
1020
1013
  } & {
1021
1014
  setLoaded({ regions, refNameAliases, cytobands, }: {
1022
- regions: import("@jbrowse/core/util/types").Region[];
1015
+ regions: import("@jbrowse/core/util").Region[];
1023
1016
  refNameAliases: {
1024
1017
  [x: string]: string;
1025
1018
  };
1026
1019
  cytobands: import("@jbrowse/core/util").Feature[];
1027
1020
  }): void;
1028
1021
  setError(e: unknown): void;
1029
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1022
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1030
1023
  setRefNameAliases(aliases: {
1031
1024
  [x: string]: string;
1032
1025
  }): void;
1033
1026
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1027
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1034
1028
  setLoadingP(p?: Promise<void>): void;
1035
1029
  load(): Promise<void>;
1036
1030
  loadPre(): Promise<void>;
@@ -1049,8 +1043,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1049
1043
  [x: string]: string;
1050
1044
  }>;
1051
1045
  afterCreate(): void;
1052
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1053
- 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>>;
1054
1048
  }, {
1055
1049
  error: unknown;
1056
1050
  loadingP: Promise<void> | undefined;
@@ -1058,6 +1052,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1058
1052
  refNameAliases: {
1059
1053
  [x: string]: string;
1060
1054
  } | undefined;
1055
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1061
1056
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1062
1057
  } & {
1063
1058
  getConf(arg: string): any;
@@ -1081,23 +1076,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1081
1076
  readonly refNames: string[] | undefined;
1082
1077
  } & {
1083
1078
  getCanonicalRefName(refName: string): string | undefined;
1084
- getCanonicalRefName2(asmName: string): string;
1079
+ getCanonicalRefName2(refName: string): string;
1085
1080
  getRefNameColor(refName: string): string | undefined;
1086
1081
  isValidRefName(refName: string): boolean;
1082
+ getSeqAdapterRefName(canonicalRefName: string): string;
1087
1083
  } & {
1088
1084
  setLoaded({ regions, refNameAliases, cytobands, }: {
1089
- regions: import("@jbrowse/core/util/types").Region[];
1085
+ regions: import("@jbrowse/core/util").Region[];
1090
1086
  refNameAliases: {
1091
1087
  [x: string]: string;
1092
1088
  };
1093
1089
  cytobands: import("@jbrowse/core/util").Feature[];
1094
1090
  }): void;
1095
1091
  setError(e: unknown): void;
1096
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1092
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1097
1093
  setRefNameAliases(aliases: {
1098
1094
  [x: string]: string;
1099
1095
  }): void;
1100
1096
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1097
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1101
1098
  setLoadingP(p?: Promise<void>): void;
1102
1099
  load(): Promise<void>;
1103
1100
  loadPre(): Promise<void>;
@@ -1116,21 +1113,15 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1116
1113
  [x: string]: string;
1117
1114
  }>;
1118
1115
  afterCreate(): void;
1119
- }, 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>;
1120
1117
  getRefNameMapForAdapter(adapterConf: {
1121
1118
  [x: string]: unknown;
1122
- }, assemblyName: string | undefined, opts: {
1123
- stopToken?: string;
1124
- sessionId: string;
1125
- }): Promise<{
1119
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
1126
1120
  [x: string]: string;
1127
1121
  } | undefined>;
1128
1122
  getReverseRefNameMapForAdapter(adapterConf: {
1129
1123
  [x: string]: unknown;
1130
- }, assemblyName: string | undefined, opts: {
1131
- stopToken?: string;
1132
- sessionId: string;
1133
- }): Promise<{
1124
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
1134
1125
  [x: string]: string;
1135
1126
  } | undefined>;
1136
1127
  isValidRefName(refName: string, assemblyName: string): boolean;
@@ -1138,26 +1129,26 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1138
1129
  afterAttach(): void;
1139
1130
  removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1140
1131
  addAssembly(configuration: any): void;
1141
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
1142
- } & 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 & {
1143
1134
  rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1144
1135
  adminMode: boolean;
1145
1136
  error: unknown;
1146
- textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1137
+ textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1147
1138
  pluginManager: PluginManager;
1148
1139
  } & {
1149
1140
  setError(error: unknown): void;
1150
- 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;
1151
1142
  setDefaultSession(): void;
1152
1143
  setSessionPath(path: string): void;
1153
1144
  renameCurrentSession(newName: string): void;
1154
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1155
- jbrowse: import("mobx-state-tree").IAnyType;
1156
- session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
1157
- sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1158
- assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1159
- assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1160
- 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>>;
1161
1152
  }, {
1162
1153
  error: unknown;
1163
1154
  loadingP: Promise<void> | undefined;
@@ -1165,6 +1156,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1165
1156
  refNameAliases: {
1166
1157
  [x: string]: string;
1167
1158
  } | undefined;
1159
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1168
1160
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1169
1161
  } & {
1170
1162
  getConf(arg: string): any;
@@ -1188,23 +1180,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1188
1180
  readonly refNames: string[] | undefined;
1189
1181
  } & {
1190
1182
  getCanonicalRefName(refName: string): string | undefined;
1191
- getCanonicalRefName2(asmName: string): string;
1183
+ getCanonicalRefName2(refName: string): string;
1192
1184
  getRefNameColor(refName: string): string | undefined;
1193
1185
  isValidRefName(refName: string): boolean;
1186
+ getSeqAdapterRefName(canonicalRefName: string): string;
1194
1187
  } & {
1195
1188
  setLoaded({ regions, refNameAliases, cytobands, }: {
1196
- regions: import("@jbrowse/core/util/types").Region[];
1189
+ regions: import("@jbrowse/core/util").Region[];
1197
1190
  refNameAliases: {
1198
1191
  [x: string]: string;
1199
1192
  };
1200
1193
  cytobands: import("@jbrowse/core/util").Feature[];
1201
1194
  }): void;
1202
1195
  setError(e: unknown): void;
1203
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1196
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1204
1197
  setRefNameAliases(aliases: {
1205
1198
  [x: string]: string;
1206
1199
  }): void;
1207
1200
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1201
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1208
1202
  setLoadingP(p?: Promise<void>): void;
1209
1203
  load(): Promise<void>;
1210
1204
  loadPre(): Promise<void>;
@@ -1223,17 +1217,18 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1223
1217
  [x: string]: string;
1224
1218
  }>;
1225
1219
  afterCreate(): void;
1226
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1220
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1227
1221
  }, {
1228
1222
  readonly assemblyNameMap: Record<string, {
1229
1223
  configuration: any;
1230
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1224
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
1231
1225
  error: unknown;
1232
1226
  loadingP: Promise<void> | undefined;
1233
1227
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1234
1228
  refNameAliases: {
1235
1229
  [x: string]: string;
1236
1230
  } | undefined;
1231
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1237
1232
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1238
1233
  } & {
1239
1234
  getConf(arg: string): any;
@@ -1257,23 +1252,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1257
1252
  readonly refNames: string[] | undefined;
1258
1253
  } & {
1259
1254
  getCanonicalRefName(refName: string): string | undefined;
1260
- getCanonicalRefName2(asmName: string): string;
1255
+ getCanonicalRefName2(refName: string): string;
1261
1256
  getRefNameColor(refName: string): string | undefined;
1262
1257
  isValidRefName(refName: string): boolean;
1258
+ getSeqAdapterRefName(canonicalRefName: string): string;
1263
1259
  } & {
1264
1260
  setLoaded({ regions, refNameAliases, cytobands, }: {
1265
- regions: import("@jbrowse/core/util/types").Region[];
1261
+ regions: import("@jbrowse/core/util").Region[];
1266
1262
  refNameAliases: {
1267
1263
  [x: string]: string;
1268
1264
  };
1269
1265
  cytobands: import("@jbrowse/core/util").Feature[];
1270
1266
  }): void;
1271
1267
  setError(e: unknown): void;
1272
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1268
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1273
1269
  setRefNameAliases(aliases: {
1274
1270
  [x: string]: string;
1275
1271
  }): void;
1276
1272
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1273
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1277
1274
  setLoadingP(p?: Promise<void>): void;
1278
1275
  load(): Promise<void>;
1279
1276
  loadPre(): Promise<void>;
@@ -1292,8 +1289,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1292
1289
  [x: string]: string;
1293
1290
  }>;
1294
1291
  afterCreate(): void;
1295
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1296
- 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>>;
1297
1294
  }, {
1298
1295
  error: unknown;
1299
1296
  loadingP: Promise<void> | undefined;
@@ -1301,6 +1298,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1301
1298
  refNameAliases: {
1302
1299
  [x: string]: string;
1303
1300
  } | undefined;
1301
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1304
1302
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1305
1303
  } & {
1306
1304
  getConf(arg: string): any;
@@ -1324,23 +1322,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1324
1322
  readonly refNames: string[] | undefined;
1325
1323
  } & {
1326
1324
  getCanonicalRefName(refName: string): string | undefined;
1327
- getCanonicalRefName2(asmName: string): string;
1325
+ getCanonicalRefName2(refName: string): string;
1328
1326
  getRefNameColor(refName: string): string | undefined;
1329
1327
  isValidRefName(refName: string): boolean;
1328
+ getSeqAdapterRefName(canonicalRefName: string): string;
1330
1329
  } & {
1331
1330
  setLoaded({ regions, refNameAliases, cytobands, }: {
1332
- regions: import("@jbrowse/core/util/types").Region[];
1331
+ regions: import("@jbrowse/core/util").Region[];
1333
1332
  refNameAliases: {
1334
1333
  [x: string]: string;
1335
1334
  };
1336
1335
  cytobands: import("@jbrowse/core/util").Feature[];
1337
1336
  }): void;
1338
1337
  setError(e: unknown): void;
1339
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1338
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1340
1339
  setRefNameAliases(aliases: {
1341
1340
  [x: string]: string;
1342
1341
  }): void;
1343
1342
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1343
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1344
1344
  setLoadingP(p?: Promise<void>): void;
1345
1345
  load(): Promise<void>;
1346
1346
  loadPre(): Promise<void>;
@@ -1359,19 +1359,20 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1359
1359
  [x: string]: string;
1360
1360
  }>;
1361
1361
  afterCreate(): void;
1362
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
1362
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
1363
1363
  } & {
1364
1364
  getCanonicalAssemblyName(asmName: string): string | undefined;
1365
1365
  getCanonicalAssemblyName2(asmName: string): string;
1366
1366
  get(asmName: string): ({
1367
1367
  configuration: any;
1368
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1368
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
1369
1369
  error: unknown;
1370
1370
  loadingP: Promise<void> | undefined;
1371
1371
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1372
1372
  refNameAliases: {
1373
1373
  [x: string]: string;
1374
1374
  } | undefined;
1375
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1375
1376
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1376
1377
  } & {
1377
1378
  getConf(arg: string): any;
@@ -1395,23 +1396,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1395
1396
  readonly refNames: string[] | undefined;
1396
1397
  } & {
1397
1398
  getCanonicalRefName(refName: string): string | undefined;
1398
- getCanonicalRefName2(asmName: string): string;
1399
+ getCanonicalRefName2(refName: string): string;
1399
1400
  getRefNameColor(refName: string): string | undefined;
1400
1401
  isValidRefName(refName: string): boolean;
1402
+ getSeqAdapterRefName(canonicalRefName: string): string;
1401
1403
  } & {
1402
1404
  setLoaded({ regions, refNameAliases, cytobands, }: {
1403
- regions: import("@jbrowse/core/util/types").Region[];
1405
+ regions: import("@jbrowse/core/util").Region[];
1404
1406
  refNameAliases: {
1405
1407
  [x: string]: string;
1406
1408
  };
1407
1409
  cytobands: import("@jbrowse/core/util").Feature[];
1408
1410
  }): void;
1409
1411
  setError(e: unknown): void;
1410
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1412
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1411
1413
  setRefNameAliases(aliases: {
1412
1414
  [x: string]: string;
1413
1415
  }): void;
1414
1416
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1417
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1415
1418
  setLoadingP(p?: Promise<void>): void;
1416
1419
  load(): Promise<void>;
1417
1420
  loadPre(): Promise<void>;
@@ -1430,8 +1433,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1430
1433
  [x: string]: string;
1431
1434
  }>;
1432
1435
  afterCreate(): void;
1433
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1434
- 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>>;
1435
1438
  }, {
1436
1439
  error: unknown;
1437
1440
  loadingP: Promise<void> | undefined;
@@ -1439,6 +1442,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1439
1442
  refNameAliases: {
1440
1443
  [x: string]: string;
1441
1444
  } | undefined;
1445
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1442
1446
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1443
1447
  } & {
1444
1448
  getConf(arg: string): any;
@@ -1462,23 +1466,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1462
1466
  readonly refNames: string[] | undefined;
1463
1467
  } & {
1464
1468
  getCanonicalRefName(refName: string): string | undefined;
1465
- getCanonicalRefName2(asmName: string): string;
1469
+ getCanonicalRefName2(refName: string): string;
1466
1470
  getRefNameColor(refName: string): string | undefined;
1467
1471
  isValidRefName(refName: string): boolean;
1472
+ getSeqAdapterRefName(canonicalRefName: string): string;
1468
1473
  } & {
1469
1474
  setLoaded({ regions, refNameAliases, cytobands, }: {
1470
- regions: import("@jbrowse/core/util/types").Region[];
1475
+ regions: import("@jbrowse/core/util").Region[];
1471
1476
  refNameAliases: {
1472
1477
  [x: string]: string;
1473
1478
  };
1474
1479
  cytobands: import("@jbrowse/core/util").Feature[];
1475
1480
  }): void;
1476
1481
  setError(e: unknown): void;
1477
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1482
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1478
1483
  setRefNameAliases(aliases: {
1479
1484
  [x: string]: string;
1480
1485
  }): void;
1481
1486
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1487
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1482
1488
  setLoadingP(p?: Promise<void>): void;
1483
1489
  load(): Promise<void>;
1484
1490
  loadPre(): Promise<void>;
@@ -1497,20 +1503,21 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1497
1503
  [x: string]: string;
1498
1504
  }>;
1499
1505
  afterCreate(): void;
1500
- }, 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;
1501
1507
  readonly assemblyNamesList: any[];
1502
1508
  readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1503
1509
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1504
1510
  } & {
1505
1511
  waitForAssembly(assemblyName: string): Promise<({
1506
1512
  configuration: any;
1507
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1513
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
1508
1514
  error: unknown;
1509
1515
  loadingP: Promise<void> | undefined;
1510
1516
  volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1511
1517
  refNameAliases: {
1512
1518
  [x: string]: string;
1513
1519
  } | undefined;
1520
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1514
1521
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1515
1522
  } & {
1516
1523
  getConf(arg: string): any;
@@ -1534,23 +1541,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1534
1541
  readonly refNames: string[] | undefined;
1535
1542
  } & {
1536
1543
  getCanonicalRefName(refName: string): string | undefined;
1537
- getCanonicalRefName2(asmName: string): string;
1544
+ getCanonicalRefName2(refName: string): string;
1538
1545
  getRefNameColor(refName: string): string | undefined;
1539
1546
  isValidRefName(refName: string): boolean;
1547
+ getSeqAdapterRefName(canonicalRefName: string): string;
1540
1548
  } & {
1541
1549
  setLoaded({ regions, refNameAliases, cytobands, }: {
1542
- regions: import("@jbrowse/core/util/types").Region[];
1550
+ regions: import("@jbrowse/core/util").Region[];
1543
1551
  refNameAliases: {
1544
1552
  [x: string]: string;
1545
1553
  };
1546
1554
  cytobands: import("@jbrowse/core/util").Feature[];
1547
1555
  }): void;
1548
1556
  setError(e: unknown): void;
1549
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1557
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1550
1558
  setRefNameAliases(aliases: {
1551
1559
  [x: string]: string;
1552
1560
  }): void;
1553
1561
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1562
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1554
1563
  setLoadingP(p?: Promise<void>): void;
1555
1564
  load(): Promise<void>;
1556
1565
  loadPre(): Promise<void>;
@@ -1569,8 +1578,8 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1569
1578
  [x: string]: string;
1570
1579
  }>;
1571
1580
  afterCreate(): void;
1572
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1573
- 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>>;
1574
1583
  }, {
1575
1584
  error: unknown;
1576
1585
  loadingP: Promise<void> | undefined;
@@ -1578,6 +1587,7 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1578
1587
  refNameAliases: {
1579
1588
  [x: string]: string;
1580
1589
  } | undefined;
1590
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1581
1591
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1582
1592
  } & {
1583
1593
  getConf(arg: string): any;
@@ -1601,23 +1611,25 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1601
1611
  readonly refNames: string[] | undefined;
1602
1612
  } & {
1603
1613
  getCanonicalRefName(refName: string): string | undefined;
1604
- getCanonicalRefName2(asmName: string): string;
1614
+ getCanonicalRefName2(refName: string): string;
1605
1615
  getRefNameColor(refName: string): string | undefined;
1606
1616
  isValidRefName(refName: string): boolean;
1617
+ getSeqAdapterRefName(canonicalRefName: string): string;
1607
1618
  } & {
1608
1619
  setLoaded({ regions, refNameAliases, cytobands, }: {
1609
- regions: import("@jbrowse/core/util/types").Region[];
1620
+ regions: import("@jbrowse/core/util").Region[];
1610
1621
  refNameAliases: {
1611
1622
  [x: string]: string;
1612
1623
  };
1613
1624
  cytobands: import("@jbrowse/core/util").Feature[];
1614
1625
  }): void;
1615
1626
  setError(e: unknown): void;
1616
- setRegions(regions: import("@jbrowse/core/util/types").Region[]): void;
1627
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1617
1628
  setRefNameAliases(aliases: {
1618
1629
  [x: string]: string;
1619
1630
  }): void;
1620
1631
  setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1632
+ setCanonicalToSeqAdapterRefNames(map: Record<string, string>): void;
1621
1633
  setLoadingP(p?: Promise<void>): void;
1622
1634
  load(): Promise<void>;
1623
1635
  loadPre(): Promise<void>;
@@ -1636,21 +1648,15 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1636
1648
  [x: string]: string;
1637
1649
  }>;
1638
1650
  afterCreate(): void;
1639
- }, 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>;
1640
1652
  getRefNameMapForAdapter(adapterConf: {
1641
1653
  [x: string]: unknown;
1642
- }, assemblyName: string | undefined, opts: {
1643
- stopToken?: string;
1644
- sessionId: string;
1645
- }): Promise<{
1654
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
1646
1655
  [x: string]: string;
1647
1656
  } | undefined>;
1648
1657
  getReverseRefNameMapForAdapter(adapterConf: {
1649
1658
  [x: string]: unknown;
1650
- }, assemblyName: string | undefined, opts: {
1651
- stopToken?: string;
1652
- sessionId: string;
1653
- }): Promise<{
1659
+ }, assemblyName: string | undefined, opts: import("node_modules/@jbrowse/core/src/assemblyManager/assemblyManager.ts").AssemblyBaseOpts): Promise<{
1654
1660
  [x: string]: string;
1655
1661
  } | undefined>;
1656
1662
  isValidRefName(refName: string, assemblyName: string): boolean;
@@ -1658,36 +1664,32 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1658
1664
  afterAttach(): void;
1659
1665
  removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1660
1666
  addAssembly(configuration: any): void;
1661
- }, 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]>;
1662
1668
  }, {
1663
1669
  rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1664
1670
  adminMode: boolean;
1665
1671
  error: unknown;
1666
- textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1672
+ textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1667
1673
  pluginManager: PluginManager;
1668
1674
  } & {
1669
1675
  setError(error: unknown): void;
1670
- 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;
1671
1677
  setDefaultSession(): void;
1672
1678
  setSessionPath(path: string): void;
1673
1679
  renameCurrentSession(newName: string): void;
1674
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1680
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1675
1681
  } & {
1676
1682
  readonly jbrowse: any;
1677
1683
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1678
1684
  readonly configuration: {
1679
1685
  [x: string]: any;
1680
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1686
+ } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
1681
1687
  setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1682
1688
  [x: string]: any;
1683
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1684
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1685
- [x: string]: any;
1686
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1687
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1688
- } & 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>;
1689
1691
  readonly adminMode: boolean;
1690
- readonly textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1692
+ readonly textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1691
1693
  } & {
1692
1694
  readonly assemblies: Instance<import("@jbrowse/core/assemblyManager").BaseAssemblyConfigSchema>[];
1693
1695
  } & {
@@ -1707,127 +1709,39 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1707
1709
  minimizeWidgetDrawer(): void;
1708
1710
  showWidgetDrawer(): void;
1709
1711
  hideAllWidgets(): void;
1710
- editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1712
+ editConfiguration(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel | {
1713
+ trackId: string;
1714
+ }): void;
1711
1715
  afterAttach(): void;
1712
1716
  } & {
1713
1717
  readonly connections: import("@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig").BaseConnectionConfigModel[];
1714
1718
  } & {
1715
- makeConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: {}): ({
1716
- name: string;
1717
- 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>>;
1718
- configuration: {
1719
- [x: string]: any;
1720
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1721
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1722
- [x: string]: any;
1723
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1724
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1725
- [x: string]: any;
1726
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1727
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1728
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1729
- name: {
1730
- type: string;
1731
- defaultValue: string;
1732
- description: string;
1733
- };
1734
- assemblyNames: {
1735
- type: string;
1736
- defaultValue: never[];
1737
- description: string;
1738
- };
1739
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>;
1740
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1741
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1742
- } & {
1743
- afterAttach(): void;
1744
- addTrackConf(trackConf: Record<string, unknown> | ({
1745
- [x: string]: any;
1746
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1747
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1748
- [x: string]: any;
1749
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1750
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1751
- [x: string]: any;
1752
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1753
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1754
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
1755
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
1756
- [x: string]: any;
1757
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1758
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1759
- [x: string]: any;
1760
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1761
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1762
- [x: string]: any;
1763
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1764
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1765
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
1766
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
1767
- clear(): void;
1768
- } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1769
- name: import("mobx-state-tree").ISimpleType<string>;
1770
- tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
1771
- configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
1772
- name: {
1773
- type: string;
1774
- defaultValue: string;
1775
- description: string;
1776
- };
1777
- assemblyNames: {
1778
- type: string;
1779
- defaultValue: never[];
1780
- description: string;
1781
- };
1782
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
1783
- }, {
1784
- connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1785
- } & {
1786
- afterAttach(): void;
1787
- addTrackConf(trackConf: Record<string, unknown> | ({
1788
- [x: string]: any;
1789
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1790
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1791
- [x: string]: any;
1792
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1793
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1794
- [x: string]: any;
1795
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1796
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1797
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
1798
- addTrackConfs(trackConfs: (Record<string, unknown> | ({
1799
- [x: string]: any;
1800
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1801
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1802
- [x: string]: any;
1803
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1804
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
1805
- [x: string]: any;
1806
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1807
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
1808
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
1809
- setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
1810
- clear(): void;
1811
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1719
+ makeConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel, initialSnapshot?: {}): any;
1812
1720
  prepareToBreakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): (Record<string, number> | (() => void))[] | undefined;
1813
1721
  breakConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
1814
1722
  deleteConnection(configuration: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1815
1723
  addConnectionConf(connectionConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
1816
1724
  clearConnections(): void;
1817
1725
  } & {
1818
- queueOfDialogs: [import("@jbrowse/core/util/types").DialogComponentType, unknown][];
1726
+ queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, unknown][];
1819
1727
  } & {
1820
- readonly DialogComponent: import("@jbrowse/core/util/types").DialogComponentType | undefined;
1728
+ readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType | undefined;
1821
1729
  readonly DialogProps: unknown;
1822
1730
  } & {
1823
1731
  removeActiveDialog(): void;
1824
- queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util/types").DialogComponentType, unknown]): void;
1732
+ queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, unknown]): void;
1825
1733
  } & {
1826
- 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[];
1827
1735
  } & {
1828
1736
  removeReferring(referring: import("@jbrowse/product-core").ReferringNode[], track: import("@jbrowse/core/pluggableElementTypes").BaseTrackConfig, callbacks: ((arg: string) => void)[], dereferenceTypeCount: Record<string, number>): void;
1829
1737
  } & {
1830
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>;
1831
1745
  } & {
1832
1746
  addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfiguration): any;
1833
1747
  deleteTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
@@ -1836,9 +1750,9 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1836
1750
  } & {
1837
1751
  readonly snackbarMessageSet: Map<string, import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1838
1752
  } & {
1839
- 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;
1840
1754
  notifyError(errorMessage: string, error?: unknown, extra?: unknown): void;
1841
- 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;
1842
1756
  popSnackbarMessage(): import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage | undefined;
1843
1757
  removeSnackbarMessage(message: string): void;
1844
1758
  } & {
@@ -1858,13 +1772,19 @@ export default function sessionModelFactory(pluginManager: PluginManager): impor
1858
1772
  addView(typeName: string, initialState?: {}): any;
1859
1773
  removeView(): void;
1860
1774
  } & {
1861
- getTrackActionMenuItems(config: any): {
1862
- label: string;
1863
- onClick: () => void;
1864
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
1865
- muiName: string;
1866
- };
1867
- }[];
1868
- }, 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>;
1869
1789
  export type SessionStateModel = ReturnType<typeof sessionModelFactory>;
1870
1790
  export type SessionModel = Instance<SessionStateModel>;