@jbrowse/product-core 3.2.0 → 3.4.0

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Files changed (9) hide show
  1. package/dist/Session/MultipleViews.d.ts +1671 -8
  2. package/dist/Session/MultipleViews.js +1 -24
  3. package/dist/Session/SessionTracks.d.ts +1671 -1
  4. package/dist/Session/Tracks.d.ts +1671 -1
  5. package/esm/Session/MultipleViews.d.ts +1671 -8
  6. package/esm/Session/MultipleViews.js +2 -25
  7. package/esm/Session/SessionTracks.d.ts +1671 -1
  8. package/esm/Session/Tracks.d.ts +1671 -1
  9. package/package.json +5 -5
package/dist/Session/MultipleViews.d.ts CHANGED
@@ -1,7 +1,5 @@
1
1
  import type PluginManager from '@jbrowse/core/PluginManager';
2
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  import type { IBaseViewModel } from '@jbrowse/core/pluggableElementTypes';
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- import type { IBaseViewModelWithDisplayedRegions } from '@jbrowse/core/pluggableElementTypes/models/BaseViewModel';
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- import type { Region } from '@jbrowse/core/util';
5
3
  import type { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
6
4
  export declare function MultipleViewsSessionMixin(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
7
5
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -20,7 +18,1677 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
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  selection: unknown;
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  hovered: unknown;
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  } & {
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- readonly root: import("mobx-state-tree").TypeOrStateTreeNodeToStateTreeNode<ROOT_MODEL_TYPE>;
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+ readonly root: {
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+ jbrowse: any;
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+ session: any;
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+ sessionPath: string;
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+ assemblyManager: {
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+ assemblies: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
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+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
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+ }, {
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+ error: unknown;
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+ loadingP: Promise<void> | undefined;
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+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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+ refNameAliases: {
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+ [x: string]: string;
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+ } | undefined;
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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+ } | undefined;
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+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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+ } & {
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+ getConf(arg: string): any;
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+ } & {
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+ readonly initialized: boolean;
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+ readonly name: string;
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+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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+ readonly aliases: string[];
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+ readonly displayName: string | undefined;
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+ hasName(name: string): boolean;
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+ readonly allAliases: string[];
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+ readonly allRefNames: string[] | undefined;
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+ readonly lowerCaseRefNames: string[] | undefined;
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+ readonly allRefNamesWithLowerCase: string[] | undefined;
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+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
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+ readonly refNameColors: string[];
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+ } & {
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+ readonly refNames: string[] | undefined;
56
+ } & {
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+ getCanonicalRefName(refName: string): string | undefined;
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+ getRefNameColor(refName: string): string | undefined;
59
+ isValidRefName(refName: string): boolean;
60
+ } & {
61
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
62
+ regions: import("@jbrowse/core/util").Region[];
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+ refNameAliases: {
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+ [x: string]: string;
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+ };
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
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+ };
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+ cytobands: import("@jbrowse/core/util").Feature[];
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+ }): void;
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+ setError(e: unknown): void;
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+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
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+ setRefNameAliases(aliases: {
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+ [x: string]: string;
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+ }, lowerCaseAliases: {
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+ [x: string]: string;
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+ }): void;
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+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
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+ setLoadingP(p?: Promise<void>): void;
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+ load(): Promise<void>;
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+ loadPre(): Promise<void>;
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+ } & {
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+ getAdapterMapEntry(adapterConf: {
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+ [x: string]: unknown;
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+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
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+ getRefNameMapForAdapter(adapterConf: {
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+ [x: string]: unknown;
88
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
89
+ [x: string]: string;
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+ }>;
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+ getReverseRefNameMapForAdapter(adapterConf: {
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+ [x: string]: unknown;
93
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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+ [x: string]: string;
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+ }>;
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+ }, 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<{
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+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
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+ }, {
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+ error: unknown;
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+ loadingP: Promise<void> | undefined;
101
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
102
+ refNameAliases: {
103
+ [x: string]: string;
104
+ } | undefined;
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
107
+ } | undefined;
108
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
109
+ } & {
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+ getConf(arg: string): any;
111
+ } & {
112
+ readonly initialized: boolean;
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+ readonly name: string;
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+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
115
+ readonly aliases: string[];
116
+ readonly displayName: string | undefined;
117
+ hasName(name: string): boolean;
118
+ readonly allAliases: string[];
119
+ readonly allRefNames: string[] | undefined;
120
+ readonly lowerCaseRefNames: string[] | undefined;
121
+ readonly allRefNamesWithLowerCase: string[] | undefined;
122
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
123
+ readonly refNameColors: string[];
124
+ } & {
125
+ readonly refNames: string[] | undefined;
126
+ } & {
127
+ getCanonicalRefName(refName: string): string | undefined;
128
+ getRefNameColor(refName: string): string | undefined;
129
+ isValidRefName(refName: string): boolean;
130
+ } & {
131
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
132
+ regions: import("@jbrowse/core/util").Region[];
133
+ refNameAliases: {
134
+ [x: string]: string;
135
+ };
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+ lowerCaseRefNameAliases: {
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+ [x: string]: string;
138
+ };
139
+ cytobands: import("@jbrowse/core/util").Feature[];
140
+ }): void;
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+ setError(e: unknown): void;
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+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
143
+ setRefNameAliases(aliases: {
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+ [x: string]: string;
145
+ }, lowerCaseAliases: {
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+ [x: string]: string;
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+ }): void;
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+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
149
+ setLoadingP(p?: Promise<void>): void;
150
+ load(): Promise<void>;
151
+ loadPre(): Promise<void>;
152
+ } & {
153
+ getAdapterMapEntry(adapterConf: {
154
+ [x: string]: unknown;
155
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
156
+ getRefNameMapForAdapter(adapterConf: {
157
+ [x: string]: unknown;
158
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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+ [x: string]: string;
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+ }>;
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+ getReverseRefNameMapForAdapter(adapterConf: {
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+ [x: string]: unknown;
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+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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+ [x: string]: string;
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+ }>;
166
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
167
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
168
+ readonly assemblyNameMap: Record<string, {
169
+ configuration: any;
170
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
171
+ error: unknown;
172
+ loadingP: Promise<void> | undefined;
173
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
174
+ refNameAliases: {
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+ [x: string]: string;
176
+ } | undefined;
177
+ lowerCaseRefNameAliases: {
178
+ [x: string]: string;
179
+ } | undefined;
180
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
181
+ } & {
182
+ getConf(arg: string): any;
183
+ } & {
184
+ readonly initialized: boolean;
185
+ readonly name: string;
186
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
187
+ readonly aliases: string[];
188
+ readonly displayName: string | undefined;
189
+ hasName(name: string): boolean;
190
+ readonly allAliases: string[];
191
+ readonly allRefNames: string[] | undefined;
192
+ readonly lowerCaseRefNames: string[] | undefined;
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+ readonly allRefNamesWithLowerCase: string[] | undefined;
194
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
195
+ readonly refNameColors: string[];
196
+ } & {
197
+ readonly refNames: string[] | undefined;
198
+ } & {
199
+ getCanonicalRefName(refName: string): string | undefined;
200
+ getRefNameColor(refName: string): string | undefined;
201
+ isValidRefName(refName: string): boolean;
202
+ } & {
203
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
204
+ regions: import("@jbrowse/core/util").Region[];
205
+ refNameAliases: {
206
+ [x: string]: string;
207
+ };
208
+ lowerCaseRefNameAliases: {
209
+ [x: string]: string;
210
+ };
211
+ cytobands: import("@jbrowse/core/util").Feature[];
212
+ }): void;
213
+ setError(e: unknown): void;
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+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
215
+ setRefNameAliases(aliases: {
216
+ [x: string]: string;
217
+ }, lowerCaseAliases: {
218
+ [x: string]: string;
219
+ }): void;
220
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
221
+ setLoadingP(p?: Promise<void>): void;
222
+ load(): Promise<void>;
223
+ loadPre(): Promise<void>;
224
+ } & {
225
+ getAdapterMapEntry(adapterConf: {
226
+ [x: string]: unknown;
227
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
228
+ getRefNameMapForAdapter(adapterConf: {
229
+ [x: string]: unknown;
230
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
231
+ [x: string]: string;
232
+ }>;
233
+ getReverseRefNameMapForAdapter(adapterConf: {
234
+ [x: string]: unknown;
235
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
236
+ [x: string]: string;
237
+ }>;
238
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
239
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
240
+ }, {
241
+ error: unknown;
242
+ loadingP: Promise<void> | undefined;
243
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
244
+ refNameAliases: {
245
+ [x: string]: string;
246
+ } | undefined;
247
+ lowerCaseRefNameAliases: {
248
+ [x: string]: string;
249
+ } | undefined;
250
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
251
+ } & {
252
+ getConf(arg: string): any;
253
+ } & {
254
+ readonly initialized: boolean;
255
+ readonly name: string;
256
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
257
+ readonly aliases: string[];
258
+ readonly displayName: string | undefined;
259
+ hasName(name: string): boolean;
260
+ readonly allAliases: string[];
261
+ readonly allRefNames: string[] | undefined;
262
+ readonly lowerCaseRefNames: string[] | undefined;
263
+ readonly allRefNamesWithLowerCase: string[] | undefined;
264
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
265
+ readonly refNameColors: string[];
266
+ } & {
267
+ readonly refNames: string[] | undefined;
268
+ } & {
269
+ getCanonicalRefName(refName: string): string | undefined;
270
+ getRefNameColor(refName: string): string | undefined;
271
+ isValidRefName(refName: string): boolean;
272
+ } & {
273
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
274
+ regions: import("@jbrowse/core/util").Region[];
275
+ refNameAliases: {
276
+ [x: string]: string;
277
+ };
278
+ lowerCaseRefNameAliases: {
279
+ [x: string]: string;
280
+ };
281
+ cytobands: import("@jbrowse/core/util").Feature[];
282
+ }): void;
283
+ setError(e: unknown): void;
284
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
285
+ setRefNameAliases(aliases: {
286
+ [x: string]: string;
287
+ }, lowerCaseAliases: {
288
+ [x: string]: string;
289
+ }): void;
290
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
291
+ setLoadingP(p?: Promise<void>): void;
292
+ load(): Promise<void>;
293
+ loadPre(): Promise<void>;
294
+ } & {
295
+ getAdapterMapEntry(adapterConf: {
296
+ [x: string]: unknown;
297
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
298
+ getRefNameMapForAdapter(adapterConf: {
299
+ [x: string]: unknown;
300
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
301
+ [x: string]: string;
302
+ }>;
303
+ getReverseRefNameMapForAdapter(adapterConf: {
304
+ [x: string]: unknown;
305
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
306
+ [x: string]: string;
307
+ }>;
308
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
309
+ } & {
310
+ get(asmName: string): ({
311
+ configuration: any;
312
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
313
+ error: unknown;
314
+ loadingP: Promise<void> | undefined;
315
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
316
+ refNameAliases: {
317
+ [x: string]: string;
318
+ } | undefined;
319
+ lowerCaseRefNameAliases: {
320
+ [x: string]: string;
321
+ } | undefined;
322
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
323
+ } & {
324
+ getConf(arg: string): any;
325
+ } & {
326
+ readonly initialized: boolean;
327
+ readonly name: string;
328
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
329
+ readonly aliases: string[];
330
+ readonly displayName: string | undefined;
331
+ hasName(name: string): boolean;
332
+ readonly allAliases: string[];
333
+ readonly allRefNames: string[] | undefined;
334
+ readonly lowerCaseRefNames: string[] | undefined;
335
+ readonly allRefNamesWithLowerCase: string[] | undefined;
336
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
337
+ readonly refNameColors: string[];
338
+ } & {
339
+ readonly refNames: string[] | undefined;
340
+ } & {
341
+ getCanonicalRefName(refName: string): string | undefined;
342
+ getRefNameColor(refName: string): string | undefined;
343
+ isValidRefName(refName: string): boolean;
344
+ } & {
345
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
346
+ regions: import("@jbrowse/core/util").Region[];
347
+ refNameAliases: {
348
+ [x: string]: string;
349
+ };
350
+ lowerCaseRefNameAliases: {
351
+ [x: string]: string;
352
+ };
353
+ cytobands: import("@jbrowse/core/util").Feature[];
354
+ }): void;
355
+ setError(e: unknown): void;
356
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
357
+ setRefNameAliases(aliases: {
358
+ [x: string]: string;
359
+ }, lowerCaseAliases: {
360
+ [x: string]: string;
361
+ }): void;
362
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
363
+ setLoadingP(p?: Promise<void>): void;
364
+ load(): Promise<void>;
365
+ loadPre(): Promise<void>;
366
+ } & {
367
+ getAdapterMapEntry(adapterConf: {
368
+ [x: string]: unknown;
369
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
370
+ getRefNameMapForAdapter(adapterConf: {
371
+ [x: string]: unknown;
372
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
373
+ [x: string]: string;
374
+ }>;
375
+ getReverseRefNameMapForAdapter(adapterConf: {
376
+ [x: string]: unknown;
377
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
378
+ [x: string]: string;
379
+ }>;
380
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
381
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
382
+ }, {
383
+ error: unknown;
384
+ loadingP: Promise<void> | undefined;
385
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
386
+ refNameAliases: {
387
+ [x: string]: string;
388
+ } | undefined;
389
+ lowerCaseRefNameAliases: {
390
+ [x: string]: string;
391
+ } | undefined;
392
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
393
+ } & {
394
+ getConf(arg: string): any;
395
+ } & {
396
+ readonly initialized: boolean;
397
+ readonly name: string;
398
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
399
+ readonly aliases: string[];
400
+ readonly displayName: string | undefined;
401
+ hasName(name: string): boolean;
402
+ readonly allAliases: string[];
403
+ readonly allRefNames: string[] | undefined;
404
+ readonly lowerCaseRefNames: string[] | undefined;
405
+ readonly allRefNamesWithLowerCase: string[] | undefined;
406
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
407
+ readonly refNameColors: string[];
408
+ } & {
409
+ readonly refNames: string[] | undefined;
410
+ } & {
411
+ getCanonicalRefName(refName: string): string | undefined;
412
+ getRefNameColor(refName: string): string | undefined;
413
+ isValidRefName(refName: string): boolean;
414
+ } & {
415
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
416
+ regions: import("@jbrowse/core/util").Region[];
417
+ refNameAliases: {
418
+ [x: string]: string;
419
+ };
420
+ lowerCaseRefNameAliases: {
421
+ [x: string]: string;
422
+ };
423
+ cytobands: import("@jbrowse/core/util").Feature[];
424
+ }): void;
425
+ setError(e: unknown): void;
426
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
427
+ setRefNameAliases(aliases: {
428
+ [x: string]: string;
429
+ }, lowerCaseAliases: {
430
+ [x: string]: string;
431
+ }): void;
432
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
433
+ setLoadingP(p?: Promise<void>): void;
434
+ load(): Promise<void>;
435
+ loadPre(): Promise<void>;
436
+ } & {
437
+ getAdapterMapEntry(adapterConf: {
438
+ [x: string]: unknown;
439
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
440
+ getRefNameMapForAdapter(adapterConf: {
441
+ [x: string]: unknown;
442
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
443
+ [x: string]: string;
444
+ }>;
445
+ getReverseRefNameMapForAdapter(adapterConf: {
446
+ [x: string]: unknown;
447
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
448
+ [x: string]: string;
449
+ }>;
450
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
451
+ readonly assemblyNamesList: any[];
452
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
453
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
454
+ } & {
455
+ waitForAssembly(assemblyName: string): Promise<({
456
+ configuration: any;
457
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
458
+ error: unknown;
459
+ loadingP: Promise<void> | undefined;
460
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
461
+ refNameAliases: {
462
+ [x: string]: string;
463
+ } | undefined;
464
+ lowerCaseRefNameAliases: {
465
+ [x: string]: string;
466
+ } | undefined;
467
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
468
+ } & {
469
+ getConf(arg: string): any;
470
+ } & {
471
+ readonly initialized: boolean;
472
+ readonly name: string;
473
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
474
+ readonly aliases: string[];
475
+ readonly displayName: string | undefined;
476
+ hasName(name: string): boolean;
477
+ readonly allAliases: string[];
478
+ readonly allRefNames: string[] | undefined;
479
+ readonly lowerCaseRefNames: string[] | undefined;
480
+ readonly allRefNamesWithLowerCase: string[] | undefined;
481
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
482
+ readonly refNameColors: string[];
483
+ } & {
484
+ readonly refNames: string[] | undefined;
485
+ } & {
486
+ getCanonicalRefName(refName: string): string | undefined;
487
+ getRefNameColor(refName: string): string | undefined;
488
+ isValidRefName(refName: string): boolean;
489
+ } & {
490
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
491
+ regions: import("@jbrowse/core/util").Region[];
492
+ refNameAliases: {
493
+ [x: string]: string;
494
+ };
495
+ lowerCaseRefNameAliases: {
496
+ [x: string]: string;
497
+ };
498
+ cytobands: import("@jbrowse/core/util").Feature[];
499
+ }): void;
500
+ setError(e: unknown): void;
501
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
502
+ setRefNameAliases(aliases: {
503
+ [x: string]: string;
504
+ }, lowerCaseAliases: {
505
+ [x: string]: string;
506
+ }): void;
507
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
508
+ setLoadingP(p?: Promise<void>): void;
509
+ load(): Promise<void>;
510
+ loadPre(): Promise<void>;
511
+ } & {
512
+ getAdapterMapEntry(adapterConf: {
513
+ [x: string]: unknown;
514
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
515
+ getRefNameMapForAdapter(adapterConf: {
516
+ [x: string]: unknown;
517
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
518
+ [x: string]: string;
519
+ }>;
520
+ getReverseRefNameMapForAdapter(adapterConf: {
521
+ [x: string]: unknown;
522
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
523
+ [x: string]: string;
524
+ }>;
525
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
526
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
527
+ }, {
528
+ error: unknown;
529
+ loadingP: Promise<void> | undefined;
530
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
531
+ refNameAliases: {
532
+ [x: string]: string;
533
+ } | undefined;
534
+ lowerCaseRefNameAliases: {
535
+ [x: string]: string;
536
+ } | undefined;
537
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
538
+ } & {
539
+ getConf(arg: string): any;
540
+ } & {
541
+ readonly initialized: boolean;
542
+ readonly name: string;
543
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
544
+ readonly aliases: string[];
545
+ readonly displayName: string | undefined;
546
+ hasName(name: string): boolean;
547
+ readonly allAliases: string[];
548
+ readonly allRefNames: string[] | undefined;
549
+ readonly lowerCaseRefNames: string[] | undefined;
550
+ readonly allRefNamesWithLowerCase: string[] | undefined;
551
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
552
+ readonly refNameColors: string[];
553
+ } & {
554
+ readonly refNames: string[] | undefined;
555
+ } & {
556
+ getCanonicalRefName(refName: string): string | undefined;
557
+ getRefNameColor(refName: string): string | undefined;
558
+ isValidRefName(refName: string): boolean;
559
+ } & {
560
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
561
+ regions: import("@jbrowse/core/util").Region[];
562
+ refNameAliases: {
563
+ [x: string]: string;
564
+ };
565
+ lowerCaseRefNameAliases: {
566
+ [x: string]: string;
567
+ };
568
+ cytobands: import("@jbrowse/core/util").Feature[];
569
+ }): void;
570
+ setError(e: unknown): void;
571
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
572
+ setRefNameAliases(aliases: {
573
+ [x: string]: string;
574
+ }, lowerCaseAliases: {
575
+ [x: string]: string;
576
+ }): void;
577
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
578
+ setLoadingP(p?: Promise<void>): void;
579
+ load(): Promise<void>;
580
+ loadPre(): Promise<void>;
581
+ } & {
582
+ getAdapterMapEntry(adapterConf: {
583
+ [x: string]: unknown;
584
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
585
+ getRefNameMapForAdapter(adapterConf: {
586
+ [x: string]: unknown;
587
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
588
+ [x: string]: string;
589
+ }>;
590
+ getReverseRefNameMapForAdapter(adapterConf: {
591
+ [x: string]: unknown;
592
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
593
+ [x: string]: string;
594
+ }>;
595
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
596
+ getRefNameMapForAdapter(adapterConf: {
597
+ [x: string]: unknown;
598
+ }, assemblyName: string | undefined, opts: {
599
+ stopToken?: string;
600
+ sessionId: string;
601
+ }): Promise<{
602
+ [x: string]: string;
603
+ } | undefined>;
604
+ getReverseRefNameMapForAdapter(adapterConf: {
605
+ [x: string]: unknown;
606
+ }, assemblyName: string | undefined, opts: {
607
+ stopToken?: string;
608
+ sessionId: string;
609
+ }): Promise<{
610
+ [x: string]: string;
611
+ } | undefined>;
612
+ isValidRefName(refName: string, assemblyName: string): boolean;
613
+ } & {
614
+ afterAttach(): void;
615
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
616
+ addAssembly(configuration: any): void;
617
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
618
+ assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
619
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
620
+ }, {
621
+ error: unknown;
622
+ loadingP: Promise<void> | undefined;
623
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
624
+ refNameAliases: {
625
+ [x: string]: string;
626
+ } | undefined;
627
+ lowerCaseRefNameAliases: {
628
+ [x: string]: string;
629
+ } | undefined;
630
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
631
+ } & {
632
+ getConf(arg: string): any;
633
+ } & {
634
+ readonly initialized: boolean;
635
+ readonly name: string;
636
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
637
+ readonly aliases: string[];
638
+ readonly displayName: string | undefined;
639
+ hasName(name: string): boolean;
640
+ readonly allAliases: string[];
641
+ readonly allRefNames: string[] | undefined;
642
+ readonly lowerCaseRefNames: string[] | undefined;
643
+ readonly allRefNamesWithLowerCase: string[] | undefined;
644
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
645
+ readonly refNameColors: string[];
646
+ } & {
647
+ readonly refNames: string[] | undefined;
648
+ } & {
649
+ getCanonicalRefName(refName: string): string | undefined;
650
+ getRefNameColor(refName: string): string | undefined;
651
+ isValidRefName(refName: string): boolean;
652
+ } & {
653
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
654
+ regions: import("@jbrowse/core/util").Region[];
655
+ refNameAliases: {
656
+ [x: string]: string;
657
+ };
658
+ lowerCaseRefNameAliases: {
659
+ [x: string]: string;
660
+ };
661
+ cytobands: import("@jbrowse/core/util").Feature[];
662
+ }): void;
663
+ setError(e: unknown): void;
664
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
665
+ setRefNameAliases(aliases: {
666
+ [x: string]: string;
667
+ }, lowerCaseAliases: {
668
+ [x: string]: string;
669
+ }): void;
670
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
671
+ setLoadingP(p?: Promise<void>): void;
672
+ load(): Promise<void>;
673
+ loadPre(): Promise<void>;
674
+ } & {
675
+ getAdapterMapEntry(adapterConf: {
676
+ [x: string]: unknown;
677
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
678
+ getRefNameMapForAdapter(adapterConf: {
679
+ [x: string]: unknown;
680
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
681
+ [x: string]: string;
682
+ }>;
683
+ getReverseRefNameMapForAdapter(adapterConf: {
684
+ [x: string]: unknown;
685
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
686
+ [x: string]: string;
687
+ }>;
688
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
689
+ }, {
690
+ readonly assemblyNameMap: Record<string, {
691
+ configuration: any;
692
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
693
+ error: unknown;
694
+ loadingP: Promise<void> | undefined;
695
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
696
+ refNameAliases: {
697
+ [x: string]: string;
698
+ } | undefined;
699
+ lowerCaseRefNameAliases: {
700
+ [x: string]: string;
701
+ } | undefined;
702
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
703
+ } & {
704
+ getConf(arg: string): any;
705
+ } & {
706
+ readonly initialized: boolean;
707
+ readonly name: string;
708
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
709
+ readonly aliases: string[];
710
+ readonly displayName: string | undefined;
711
+ hasName(name: string): boolean;
712
+ readonly allAliases: string[];
713
+ readonly allRefNames: string[] | undefined;
714
+ readonly lowerCaseRefNames: string[] | undefined;
715
+ readonly allRefNamesWithLowerCase: string[] | undefined;
716
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
717
+ readonly refNameColors: string[];
718
+ } & {
719
+ readonly refNames: string[] | undefined;
720
+ } & {
721
+ getCanonicalRefName(refName: string): string | undefined;
722
+ getRefNameColor(refName: string): string | undefined;
723
+ isValidRefName(refName: string): boolean;
724
+ } & {
725
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
726
+ regions: import("@jbrowse/core/util").Region[];
727
+ refNameAliases: {
728
+ [x: string]: string;
729
+ };
730
+ lowerCaseRefNameAliases: {
731
+ [x: string]: string;
732
+ };
733
+ cytobands: import("@jbrowse/core/util").Feature[];
734
+ }): void;
735
+ setError(e: unknown): void;
736
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
737
+ setRefNameAliases(aliases: {
738
+ [x: string]: string;
739
+ }, lowerCaseAliases: {
740
+ [x: string]: string;
741
+ }): void;
742
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
743
+ setLoadingP(p?: Promise<void>): void;
744
+ load(): Promise<void>;
745
+ loadPre(): Promise<void>;
746
+ } & {
747
+ getAdapterMapEntry(adapterConf: {
748
+ [x: string]: unknown;
749
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
750
+ getRefNameMapForAdapter(adapterConf: {
751
+ [x: string]: unknown;
752
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
753
+ [x: string]: string;
754
+ }>;
755
+ getReverseRefNameMapForAdapter(adapterConf: {
756
+ [x: string]: unknown;
757
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
758
+ [x: string]: string;
759
+ }>;
760
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
761
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
762
+ }, {
763
+ error: unknown;
764
+ loadingP: Promise<void> | undefined;
765
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
766
+ refNameAliases: {
767
+ [x: string]: string;
768
+ } | undefined;
769
+ lowerCaseRefNameAliases: {
770
+ [x: string]: string;
771
+ } | undefined;
772
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
773
+ } & {
774
+ getConf(arg: string): any;
775
+ } & {
776
+ readonly initialized: boolean;
777
+ readonly name: string;
778
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
779
+ readonly aliases: string[];
780
+ readonly displayName: string | undefined;
781
+ hasName(name: string): boolean;
782
+ readonly allAliases: string[];
783
+ readonly allRefNames: string[] | undefined;
784
+ readonly lowerCaseRefNames: string[] | undefined;
785
+ readonly allRefNamesWithLowerCase: string[] | undefined;
786
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
787
+ readonly refNameColors: string[];
788
+ } & {
789
+ readonly refNames: string[] | undefined;
790
+ } & {
791
+ getCanonicalRefName(refName: string): string | undefined;
792
+ getRefNameColor(refName: string): string | undefined;
793
+ isValidRefName(refName: string): boolean;
794
+ } & {
795
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
796
+ regions: import("@jbrowse/core/util").Region[];
797
+ refNameAliases: {
798
+ [x: string]: string;
799
+ };
800
+ lowerCaseRefNameAliases: {
801
+ [x: string]: string;
802
+ };
803
+ cytobands: import("@jbrowse/core/util").Feature[];
804
+ }): void;
805
+ setError(e: unknown): void;
806
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
807
+ setRefNameAliases(aliases: {
808
+ [x: string]: string;
809
+ }, lowerCaseAliases: {
810
+ [x: string]: string;
811
+ }): void;
812
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
813
+ setLoadingP(p?: Promise<void>): void;
814
+ load(): Promise<void>;
815
+ loadPre(): Promise<void>;
816
+ } & {
817
+ getAdapterMapEntry(adapterConf: {
818
+ [x: string]: unknown;
819
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
820
+ getRefNameMapForAdapter(adapterConf: {
821
+ [x: string]: unknown;
822
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
823
+ [x: string]: string;
824
+ }>;
825
+ getReverseRefNameMapForAdapter(adapterConf: {
826
+ [x: string]: unknown;
827
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
828
+ [x: string]: string;
829
+ }>;
830
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
831
+ } & {
832
+ get(asmName: string): ({
833
+ configuration: any;
834
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
835
+ error: unknown;
836
+ loadingP: Promise<void> | undefined;
837
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
838
+ refNameAliases: {
839
+ [x: string]: string;
840
+ } | undefined;
841
+ lowerCaseRefNameAliases: {
842
+ [x: string]: string;
843
+ } | undefined;
844
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
845
+ } & {
846
+ getConf(arg: string): any;
847
+ } & {
848
+ readonly initialized: boolean;
849
+ readonly name: string;
850
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
851
+ readonly aliases: string[];
852
+ readonly displayName: string | undefined;
853
+ hasName(name: string): boolean;
854
+ readonly allAliases: string[];
855
+ readonly allRefNames: string[] | undefined;
856
+ readonly lowerCaseRefNames: string[] | undefined;
857
+ readonly allRefNamesWithLowerCase: string[] | undefined;
858
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
859
+ readonly refNameColors: string[];
860
+ } & {
861
+ readonly refNames: string[] | undefined;
862
+ } & {
863
+ getCanonicalRefName(refName: string): string | undefined;
864
+ getRefNameColor(refName: string): string | undefined;
865
+ isValidRefName(refName: string): boolean;
866
+ } & {
867
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
868
+ regions: import("@jbrowse/core/util").Region[];
869
+ refNameAliases: {
870
+ [x: string]: string;
871
+ };
872
+ lowerCaseRefNameAliases: {
873
+ [x: string]: string;
874
+ };
875
+ cytobands: import("@jbrowse/core/util").Feature[];
876
+ }): void;
877
+ setError(e: unknown): void;
878
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
879
+ setRefNameAliases(aliases: {
880
+ [x: string]: string;
881
+ }, lowerCaseAliases: {
882
+ [x: string]: string;
883
+ }): void;
884
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
885
+ setLoadingP(p?: Promise<void>): void;
886
+ load(): Promise<void>;
887
+ loadPre(): Promise<void>;
888
+ } & {
889
+ getAdapterMapEntry(adapterConf: {
890
+ [x: string]: unknown;
891
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
892
+ getRefNameMapForAdapter(adapterConf: {
893
+ [x: string]: unknown;
894
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
895
+ [x: string]: string;
896
+ }>;
897
+ getReverseRefNameMapForAdapter(adapterConf: {
898
+ [x: string]: unknown;
899
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
900
+ [x: string]: string;
901
+ }>;
902
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
903
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
904
+ }, {
905
+ error: unknown;
906
+ loadingP: Promise<void> | undefined;
907
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
908
+ refNameAliases: {
909
+ [x: string]: string;
910
+ } | undefined;
911
+ lowerCaseRefNameAliases: {
912
+ [x: string]: string;
913
+ } | undefined;
914
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
915
+ } & {
916
+ getConf(arg: string): any;
917
+ } & {
918
+ readonly initialized: boolean;
919
+ readonly name: string;
920
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
921
+ readonly aliases: string[];
922
+ readonly displayName: string | undefined;
923
+ hasName(name: string): boolean;
924
+ readonly allAliases: string[];
925
+ readonly allRefNames: string[] | undefined;
926
+ readonly lowerCaseRefNames: string[] | undefined;
927
+ readonly allRefNamesWithLowerCase: string[] | undefined;
928
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
929
+ readonly refNameColors: string[];
930
+ } & {
931
+ readonly refNames: string[] | undefined;
932
+ } & {
933
+ getCanonicalRefName(refName: string): string | undefined;
934
+ getRefNameColor(refName: string): string | undefined;
935
+ isValidRefName(refName: string): boolean;
936
+ } & {
937
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
938
+ regions: import("@jbrowse/core/util").Region[];
939
+ refNameAliases: {
940
+ [x: string]: string;
941
+ };
942
+ lowerCaseRefNameAliases: {
943
+ [x: string]: string;
944
+ };
945
+ cytobands: import("@jbrowse/core/util").Feature[];
946
+ }): void;
947
+ setError(e: unknown): void;
948
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
949
+ setRefNameAliases(aliases: {
950
+ [x: string]: string;
951
+ }, lowerCaseAliases: {
952
+ [x: string]: string;
953
+ }): void;
954
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
955
+ setLoadingP(p?: Promise<void>): void;
956
+ load(): Promise<void>;
957
+ loadPre(): Promise<void>;
958
+ } & {
959
+ getAdapterMapEntry(adapterConf: {
960
+ [x: string]: unknown;
961
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
962
+ getRefNameMapForAdapter(adapterConf: {
963
+ [x: string]: unknown;
964
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
965
+ [x: string]: string;
966
+ }>;
967
+ getReverseRefNameMapForAdapter(adapterConf: {
968
+ [x: string]: unknown;
969
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
970
+ [x: string]: string;
971
+ }>;
972
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
973
+ readonly assemblyNamesList: any[];
974
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
975
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
976
+ } & {
977
+ waitForAssembly(assemblyName: string): Promise<({
978
+ configuration: any;
979
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
980
+ error: unknown;
981
+ loadingP: Promise<void> | undefined;
982
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
983
+ refNameAliases: {
984
+ [x: string]: string;
985
+ } | undefined;
986
+ lowerCaseRefNameAliases: {
987
+ [x: string]: string;
988
+ } | undefined;
989
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
990
+ } & {
991
+ getConf(arg: string): any;
992
+ } & {
993
+ readonly initialized: boolean;
994
+ readonly name: string;
995
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
996
+ readonly aliases: string[];
997
+ readonly displayName: string | undefined;
998
+ hasName(name: string): boolean;
999
+ readonly allAliases: string[];
1000
+ readonly allRefNames: string[] | undefined;
1001
+ readonly lowerCaseRefNames: string[] | undefined;
1002
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1003
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1004
+ readonly refNameColors: string[];
1005
+ } & {
1006
+ readonly refNames: string[] | undefined;
1007
+ } & {
1008
+ getCanonicalRefName(refName: string): string | undefined;
1009
+ getRefNameColor(refName: string): string | undefined;
1010
+ isValidRefName(refName: string): boolean;
1011
+ } & {
1012
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1013
+ regions: import("@jbrowse/core/util").Region[];
1014
+ refNameAliases: {
1015
+ [x: string]: string;
1016
+ };
1017
+ lowerCaseRefNameAliases: {
1018
+ [x: string]: string;
1019
+ };
1020
+ cytobands: import("@jbrowse/core/util").Feature[];
1021
+ }): void;
1022
+ setError(e: unknown): void;
1023
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1024
+ setRefNameAliases(aliases: {
1025
+ [x: string]: string;
1026
+ }, lowerCaseAliases: {
1027
+ [x: string]: string;
1028
+ }): void;
1029
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1030
+ setLoadingP(p?: Promise<void>): void;
1031
+ load(): Promise<void>;
1032
+ loadPre(): Promise<void>;
1033
+ } & {
1034
+ getAdapterMapEntry(adapterConf: {
1035
+ [x: string]: unknown;
1036
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1037
+ getRefNameMapForAdapter(adapterConf: {
1038
+ [x: string]: unknown;
1039
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1040
+ [x: string]: string;
1041
+ }>;
1042
+ getReverseRefNameMapForAdapter(adapterConf: {
1043
+ [x: string]: unknown;
1044
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1045
+ [x: string]: string;
1046
+ }>;
1047
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1048
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1049
+ }, {
1050
+ error: unknown;
1051
+ loadingP: Promise<void> | undefined;
1052
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1053
+ refNameAliases: {
1054
+ [x: string]: string;
1055
+ } | undefined;
1056
+ lowerCaseRefNameAliases: {
1057
+ [x: string]: string;
1058
+ } | undefined;
1059
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1060
+ } & {
1061
+ getConf(arg: string): any;
1062
+ } & {
1063
+ readonly initialized: boolean;
1064
+ readonly name: string;
1065
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1066
+ readonly aliases: string[];
1067
+ readonly displayName: string | undefined;
1068
+ hasName(name: string): boolean;
1069
+ readonly allAliases: string[];
1070
+ readonly allRefNames: string[] | undefined;
1071
+ readonly lowerCaseRefNames: string[] | undefined;
1072
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1073
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1074
+ readonly refNameColors: string[];
1075
+ } & {
1076
+ readonly refNames: string[] | undefined;
1077
+ } & {
1078
+ getCanonicalRefName(refName: string): string | undefined;
1079
+ getRefNameColor(refName: string): string | undefined;
1080
+ isValidRefName(refName: string): boolean;
1081
+ } & {
1082
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1083
+ regions: import("@jbrowse/core/util").Region[];
1084
+ refNameAliases: {
1085
+ [x: string]: string;
1086
+ };
1087
+ lowerCaseRefNameAliases: {
1088
+ [x: string]: string;
1089
+ };
1090
+ cytobands: import("@jbrowse/core/util").Feature[];
1091
+ }): void;
1092
+ setError(e: unknown): void;
1093
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1094
+ setRefNameAliases(aliases: {
1095
+ [x: string]: string;
1096
+ }, lowerCaseAliases: {
1097
+ [x: string]: string;
1098
+ }): void;
1099
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1100
+ setLoadingP(p?: Promise<void>): void;
1101
+ load(): Promise<void>;
1102
+ loadPre(): Promise<void>;
1103
+ } & {
1104
+ getAdapterMapEntry(adapterConf: {
1105
+ [x: string]: unknown;
1106
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1107
+ getRefNameMapForAdapter(adapterConf: {
1108
+ [x: string]: unknown;
1109
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1110
+ [x: string]: string;
1111
+ }>;
1112
+ getReverseRefNameMapForAdapter(adapterConf: {
1113
+ [x: string]: unknown;
1114
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1115
+ [x: string]: string;
1116
+ }>;
1117
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1118
+ getRefNameMapForAdapter(adapterConf: {
1119
+ [x: string]: unknown;
1120
+ }, assemblyName: string | undefined, opts: {
1121
+ stopToken?: string;
1122
+ sessionId: string;
1123
+ }): Promise<{
1124
+ [x: string]: string;
1125
+ } | undefined>;
1126
+ getReverseRefNameMapForAdapter(adapterConf: {
1127
+ [x: string]: unknown;
1128
+ }, assemblyName: string | undefined, opts: {
1129
+ stopToken?: string;
1130
+ sessionId: string;
1131
+ }): Promise<{
1132
+ [x: string]: string;
1133
+ } | undefined>;
1134
+ isValidRefName(refName: string, assemblyName: string): boolean;
1135
+ } & {
1136
+ afterAttach(): void;
1137
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1138
+ addAssembly(configuration: any): void;
1139
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>;
1140
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1141
+ rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1142
+ adminMode: boolean;
1143
+ error: unknown;
1144
+ textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1145
+ pluginManager: PluginManager;
1146
+ } & {
1147
+ setError(error: unknown): void;
1148
+ setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1149
+ setDefaultSession(): void;
1150
+ setSessionPath(path: string): void;
1151
+ renameCurrentSession(newName: string): void;
1152
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1153
+ jbrowse: import("mobx-state-tree").IAnyType;
1154
+ session: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
1155
+ sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
1156
+ assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
1157
+ assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1158
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1159
+ }, {
1160
+ error: unknown;
1161
+ loadingP: Promise<void> | undefined;
1162
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1163
+ refNameAliases: {
1164
+ [x: string]: string;
1165
+ } | undefined;
1166
+ lowerCaseRefNameAliases: {
1167
+ [x: string]: string;
1168
+ } | undefined;
1169
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1170
+ } & {
1171
+ getConf(arg: string): any;
1172
+ } & {
1173
+ readonly initialized: boolean;
1174
+ readonly name: string;
1175
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1176
+ readonly aliases: string[];
1177
+ readonly displayName: string | undefined;
1178
+ hasName(name: string): boolean;
1179
+ readonly allAliases: string[];
1180
+ readonly allRefNames: string[] | undefined;
1181
+ readonly lowerCaseRefNames: string[] | undefined;
1182
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1183
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1184
+ readonly refNameColors: string[];
1185
+ } & {
1186
+ readonly refNames: string[] | undefined;
1187
+ } & {
1188
+ getCanonicalRefName(refName: string): string | undefined;
1189
+ getRefNameColor(refName: string): string | undefined;
1190
+ isValidRefName(refName: string): boolean;
1191
+ } & {
1192
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1193
+ regions: import("@jbrowse/core/util").Region[];
1194
+ refNameAliases: {
1195
+ [x: string]: string;
1196
+ };
1197
+ lowerCaseRefNameAliases: {
1198
+ [x: string]: string;
1199
+ };
1200
+ cytobands: import("@jbrowse/core/util").Feature[];
1201
+ }): void;
1202
+ setError(e: unknown): void;
1203
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1204
+ setRefNameAliases(aliases: {
1205
+ [x: string]: string;
1206
+ }, lowerCaseAliases: {
1207
+ [x: string]: string;
1208
+ }): void;
1209
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1210
+ setLoadingP(p?: Promise<void>): void;
1211
+ load(): Promise<void>;
1212
+ loadPre(): Promise<void>;
1213
+ } & {
1214
+ getAdapterMapEntry(adapterConf: {
1215
+ [x: string]: unknown;
1216
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1217
+ getRefNameMapForAdapter(adapterConf: {
1218
+ [x: string]: unknown;
1219
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1220
+ [x: string]: string;
1221
+ }>;
1222
+ getReverseRefNameMapForAdapter(adapterConf: {
1223
+ [x: string]: unknown;
1224
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1225
+ [x: string]: string;
1226
+ }>;
1227
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1228
+ }, {
1229
+ readonly assemblyNameMap: Record<string, {
1230
+ configuration: any;
1231
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1232
+ error: unknown;
1233
+ loadingP: Promise<void> | undefined;
1234
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1235
+ refNameAliases: {
1236
+ [x: string]: string;
1237
+ } | undefined;
1238
+ lowerCaseRefNameAliases: {
1239
+ [x: string]: string;
1240
+ } | undefined;
1241
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1242
+ } & {
1243
+ getConf(arg: string): any;
1244
+ } & {
1245
+ readonly initialized: boolean;
1246
+ readonly name: string;
1247
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1248
+ readonly aliases: string[];
1249
+ readonly displayName: string | undefined;
1250
+ hasName(name: string): boolean;
1251
+ readonly allAliases: string[];
1252
+ readonly allRefNames: string[] | undefined;
1253
+ readonly lowerCaseRefNames: string[] | undefined;
1254
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1255
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1256
+ readonly refNameColors: string[];
1257
+ } & {
1258
+ readonly refNames: string[] | undefined;
1259
+ } & {
1260
+ getCanonicalRefName(refName: string): string | undefined;
1261
+ getRefNameColor(refName: string): string | undefined;
1262
+ isValidRefName(refName: string): boolean;
1263
+ } & {
1264
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1265
+ regions: import("@jbrowse/core/util").Region[];
1266
+ refNameAliases: {
1267
+ [x: string]: string;
1268
+ };
1269
+ lowerCaseRefNameAliases: {
1270
+ [x: string]: string;
1271
+ };
1272
+ cytobands: import("@jbrowse/core/util").Feature[];
1273
+ }): void;
1274
+ setError(e: unknown): void;
1275
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1276
+ setRefNameAliases(aliases: {
1277
+ [x: string]: string;
1278
+ }, lowerCaseAliases: {
1279
+ [x: string]: string;
1280
+ }): void;
1281
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1282
+ setLoadingP(p?: Promise<void>): void;
1283
+ load(): Promise<void>;
1284
+ loadPre(): Promise<void>;
1285
+ } & {
1286
+ getAdapterMapEntry(adapterConf: {
1287
+ [x: string]: unknown;
1288
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1289
+ getRefNameMapForAdapter(adapterConf: {
1290
+ [x: string]: unknown;
1291
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1292
+ [x: string]: string;
1293
+ }>;
1294
+ getReverseRefNameMapForAdapter(adapterConf: {
1295
+ [x: string]: unknown;
1296
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1297
+ [x: string]: string;
1298
+ }>;
1299
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1300
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1301
+ }, {
1302
+ error: unknown;
1303
+ loadingP: Promise<void> | undefined;
1304
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1305
+ refNameAliases: {
1306
+ [x: string]: string;
1307
+ } | undefined;
1308
+ lowerCaseRefNameAliases: {
1309
+ [x: string]: string;
1310
+ } | undefined;
1311
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1312
+ } & {
1313
+ getConf(arg: string): any;
1314
+ } & {
1315
+ readonly initialized: boolean;
1316
+ readonly name: string;
1317
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1318
+ readonly aliases: string[];
1319
+ readonly displayName: string | undefined;
1320
+ hasName(name: string): boolean;
1321
+ readonly allAliases: string[];
1322
+ readonly allRefNames: string[] | undefined;
1323
+ readonly lowerCaseRefNames: string[] | undefined;
1324
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1325
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1326
+ readonly refNameColors: string[];
1327
+ } & {
1328
+ readonly refNames: string[] | undefined;
1329
+ } & {
1330
+ getCanonicalRefName(refName: string): string | undefined;
1331
+ getRefNameColor(refName: string): string | undefined;
1332
+ isValidRefName(refName: string): boolean;
1333
+ } & {
1334
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1335
+ regions: import("@jbrowse/core/util").Region[];
1336
+ refNameAliases: {
1337
+ [x: string]: string;
1338
+ };
1339
+ lowerCaseRefNameAliases: {
1340
+ [x: string]: string;
1341
+ };
1342
+ cytobands: import("@jbrowse/core/util").Feature[];
1343
+ }): void;
1344
+ setError(e: unknown): void;
1345
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1346
+ setRefNameAliases(aliases: {
1347
+ [x: string]: string;
1348
+ }, lowerCaseAliases: {
1349
+ [x: string]: string;
1350
+ }): void;
1351
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1352
+ setLoadingP(p?: Promise<void>): void;
1353
+ load(): Promise<void>;
1354
+ loadPre(): Promise<void>;
1355
+ } & {
1356
+ getAdapterMapEntry(adapterConf: {
1357
+ [x: string]: unknown;
1358
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1359
+ getRefNameMapForAdapter(adapterConf: {
1360
+ [x: string]: unknown;
1361
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1362
+ [x: string]: string;
1363
+ }>;
1364
+ getReverseRefNameMapForAdapter(adapterConf: {
1365
+ [x: string]: unknown;
1366
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1367
+ [x: string]: string;
1368
+ }>;
1369
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
1370
+ } & {
1371
+ get(asmName: string): ({
1372
+ configuration: any;
1373
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1374
+ error: unknown;
1375
+ loadingP: Promise<void> | undefined;
1376
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1377
+ refNameAliases: {
1378
+ [x: string]: string;
1379
+ } | undefined;
1380
+ lowerCaseRefNameAliases: {
1381
+ [x: string]: string;
1382
+ } | undefined;
1383
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1384
+ } & {
1385
+ getConf(arg: string): any;
1386
+ } & {
1387
+ readonly initialized: boolean;
1388
+ readonly name: string;
1389
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1390
+ readonly aliases: string[];
1391
+ readonly displayName: string | undefined;
1392
+ hasName(name: string): boolean;
1393
+ readonly allAliases: string[];
1394
+ readonly allRefNames: string[] | undefined;
1395
+ readonly lowerCaseRefNames: string[] | undefined;
1396
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1397
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1398
+ readonly refNameColors: string[];
1399
+ } & {
1400
+ readonly refNames: string[] | undefined;
1401
+ } & {
1402
+ getCanonicalRefName(refName: string): string | undefined;
1403
+ getRefNameColor(refName: string): string | undefined;
1404
+ isValidRefName(refName: string): boolean;
1405
+ } & {
1406
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1407
+ regions: import("@jbrowse/core/util").Region[];
1408
+ refNameAliases: {
1409
+ [x: string]: string;
1410
+ };
1411
+ lowerCaseRefNameAliases: {
1412
+ [x: string]: string;
1413
+ };
1414
+ cytobands: import("@jbrowse/core/util").Feature[];
1415
+ }): void;
1416
+ setError(e: unknown): void;
1417
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1418
+ setRefNameAliases(aliases: {
1419
+ [x: string]: string;
1420
+ }, lowerCaseAliases: {
1421
+ [x: string]: string;
1422
+ }): void;
1423
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1424
+ setLoadingP(p?: Promise<void>): void;
1425
+ load(): Promise<void>;
1426
+ loadPre(): Promise<void>;
1427
+ } & {
1428
+ getAdapterMapEntry(adapterConf: {
1429
+ [x: string]: unknown;
1430
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1431
+ getRefNameMapForAdapter(adapterConf: {
1432
+ [x: string]: unknown;
1433
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1434
+ [x: string]: string;
1435
+ }>;
1436
+ getReverseRefNameMapForAdapter(adapterConf: {
1437
+ [x: string]: unknown;
1438
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1439
+ [x: string]: string;
1440
+ }>;
1441
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1442
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1443
+ }, {
1444
+ error: unknown;
1445
+ loadingP: Promise<void> | undefined;
1446
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1447
+ refNameAliases: {
1448
+ [x: string]: string;
1449
+ } | undefined;
1450
+ lowerCaseRefNameAliases: {
1451
+ [x: string]: string;
1452
+ } | undefined;
1453
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1454
+ } & {
1455
+ getConf(arg: string): any;
1456
+ } & {
1457
+ readonly initialized: boolean;
1458
+ readonly name: string;
1459
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1460
+ readonly aliases: string[];
1461
+ readonly displayName: string | undefined;
1462
+ hasName(name: string): boolean;
1463
+ readonly allAliases: string[];
1464
+ readonly allRefNames: string[] | undefined;
1465
+ readonly lowerCaseRefNames: string[] | undefined;
1466
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1467
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1468
+ readonly refNameColors: string[];
1469
+ } & {
1470
+ readonly refNames: string[] | undefined;
1471
+ } & {
1472
+ getCanonicalRefName(refName: string): string | undefined;
1473
+ getRefNameColor(refName: string): string | undefined;
1474
+ isValidRefName(refName: string): boolean;
1475
+ } & {
1476
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1477
+ regions: import("@jbrowse/core/util").Region[];
1478
+ refNameAliases: {
1479
+ [x: string]: string;
1480
+ };
1481
+ lowerCaseRefNameAliases: {
1482
+ [x: string]: string;
1483
+ };
1484
+ cytobands: import("@jbrowse/core/util").Feature[];
1485
+ }): void;
1486
+ setError(e: unknown): void;
1487
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1488
+ setRefNameAliases(aliases: {
1489
+ [x: string]: string;
1490
+ }, lowerCaseAliases: {
1491
+ [x: string]: string;
1492
+ }): void;
1493
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1494
+ setLoadingP(p?: Promise<void>): void;
1495
+ load(): Promise<void>;
1496
+ loadPre(): Promise<void>;
1497
+ } & {
1498
+ getAdapterMapEntry(adapterConf: {
1499
+ [x: string]: unknown;
1500
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1501
+ getRefNameMapForAdapter(adapterConf: {
1502
+ [x: string]: unknown;
1503
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1504
+ [x: string]: string;
1505
+ }>;
1506
+ getReverseRefNameMapForAdapter(adapterConf: {
1507
+ [x: string]: unknown;
1508
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1509
+ [x: string]: string;
1510
+ }>;
1511
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
1512
+ readonly assemblyNamesList: any[];
1513
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1514
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1515
+ } & {
1516
+ waitForAssembly(assemblyName: string): Promise<({
1517
+ configuration: any;
1518
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
1519
+ error: unknown;
1520
+ loadingP: Promise<void> | undefined;
1521
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1522
+ refNameAliases: {
1523
+ [x: string]: string;
1524
+ } | undefined;
1525
+ lowerCaseRefNameAliases: {
1526
+ [x: string]: string;
1527
+ } | undefined;
1528
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1529
+ } & {
1530
+ getConf(arg: string): any;
1531
+ } & {
1532
+ readonly initialized: boolean;
1533
+ readonly name: string;
1534
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1535
+ readonly aliases: string[];
1536
+ readonly displayName: string | undefined;
1537
+ hasName(name: string): boolean;
1538
+ readonly allAliases: string[];
1539
+ readonly allRefNames: string[] | undefined;
1540
+ readonly lowerCaseRefNames: string[] | undefined;
1541
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1542
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1543
+ readonly refNameColors: string[];
1544
+ } & {
1545
+ readonly refNames: string[] | undefined;
1546
+ } & {
1547
+ getCanonicalRefName(refName: string): string | undefined;
1548
+ getRefNameColor(refName: string): string | undefined;
1549
+ isValidRefName(refName: string): boolean;
1550
+ } & {
1551
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1552
+ regions: import("@jbrowse/core/util").Region[];
1553
+ refNameAliases: {
1554
+ [x: string]: string;
1555
+ };
1556
+ lowerCaseRefNameAliases: {
1557
+ [x: string]: string;
1558
+ };
1559
+ cytobands: import("@jbrowse/core/util").Feature[];
1560
+ }): void;
1561
+ setError(e: unknown): void;
1562
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1563
+ setRefNameAliases(aliases: {
1564
+ [x: string]: string;
1565
+ }, lowerCaseAliases: {
1566
+ [x: string]: string;
1567
+ }): void;
1568
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1569
+ setLoadingP(p?: Promise<void>): void;
1570
+ load(): Promise<void>;
1571
+ loadPre(): Promise<void>;
1572
+ } & {
1573
+ getAdapterMapEntry(adapterConf: {
1574
+ [x: string]: unknown;
1575
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1576
+ getRefNameMapForAdapter(adapterConf: {
1577
+ [x: string]: unknown;
1578
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1579
+ [x: string]: string;
1580
+ }>;
1581
+ getReverseRefNameMapForAdapter(adapterConf: {
1582
+ [x: string]: unknown;
1583
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1584
+ [x: string]: string;
1585
+ }>;
1586
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
1587
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
1588
+ }, {
1589
+ error: unknown;
1590
+ loadingP: Promise<void> | undefined;
1591
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1592
+ refNameAliases: {
1593
+ [x: string]: string;
1594
+ } | undefined;
1595
+ lowerCaseRefNameAliases: {
1596
+ [x: string]: string;
1597
+ } | undefined;
1598
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1599
+ } & {
1600
+ getConf(arg: string): any;
1601
+ } & {
1602
+ readonly initialized: boolean;
1603
+ readonly name: string;
1604
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1605
+ readonly aliases: string[];
1606
+ readonly displayName: string | undefined;
1607
+ hasName(name: string): boolean;
1608
+ readonly allAliases: string[];
1609
+ readonly allRefNames: string[] | undefined;
1610
+ readonly lowerCaseRefNames: string[] | undefined;
1611
+ readonly allRefNamesWithLowerCase: string[] | undefined;
1612
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1613
+ readonly refNameColors: string[];
1614
+ } & {
1615
+ readonly refNames: string[] | undefined;
1616
+ } & {
1617
+ getCanonicalRefName(refName: string): string | undefined;
1618
+ getRefNameColor(refName: string): string | undefined;
1619
+ isValidRefName(refName: string): boolean;
1620
+ } & {
1621
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
1622
+ regions: import("@jbrowse/core/util").Region[];
1623
+ refNameAliases: {
1624
+ [x: string]: string;
1625
+ };
1626
+ lowerCaseRefNameAliases: {
1627
+ [x: string]: string;
1628
+ };
1629
+ cytobands: import("@jbrowse/core/util").Feature[];
1630
+ }): void;
1631
+ setError(e: unknown): void;
1632
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
1633
+ setRefNameAliases(aliases: {
1634
+ [x: string]: string;
1635
+ }, lowerCaseAliases: {
1636
+ [x: string]: string;
1637
+ }): void;
1638
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
1639
+ setLoadingP(p?: Promise<void>): void;
1640
+ load(): Promise<void>;
1641
+ loadPre(): Promise<void>;
1642
+ } & {
1643
+ getAdapterMapEntry(adapterConf: {
1644
+ [x: string]: unknown;
1645
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
1646
+ getRefNameMapForAdapter(adapterConf: {
1647
+ [x: string]: unknown;
1648
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1649
+ [x: string]: string;
1650
+ }>;
1651
+ getReverseRefNameMapForAdapter(adapterConf: {
1652
+ [x: string]: unknown;
1653
+ }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
1654
+ [x: string]: string;
1655
+ }>;
1656
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
1657
+ getRefNameMapForAdapter(adapterConf: {
1658
+ [x: string]: unknown;
1659
+ }, assemblyName: string | undefined, opts: {
1660
+ stopToken?: string;
1661
+ sessionId: string;
1662
+ }): Promise<{
1663
+ [x: string]: string;
1664
+ } | undefined>;
1665
+ getReverseRefNameMapForAdapter(adapterConf: {
1666
+ [x: string]: unknown;
1667
+ }, assemblyName: string | undefined, opts: {
1668
+ stopToken?: string;
1669
+ sessionId: string;
1670
+ }): Promise<{
1671
+ [x: string]: string;
1672
+ } | undefined>;
1673
+ isValidRefName(refName: string, assemblyName: string): boolean;
1674
+ } & {
1675
+ afterAttach(): void;
1676
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1677
+ addAssembly(configuration: any): void;
1678
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
1679
+ }, {
1680
+ rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1681
+ adminMode: boolean;
1682
+ error: unknown;
1683
+ textSearchManager: import("@jbrowse/core/util").TextSearchManager;
1684
+ pluginManager: PluginManager;
1685
+ } & {
1686
+ setError(error: unknown): void;
1687
+ setSession(sessionSnapshot?: import("mobx-state-tree").SnapshotIn<import("mobx-state-tree").IAnyType>): void;
1688
+ setDefaultSession(): void;
1689
+ setSessionPath(path: string): void;
1690
+ renameCurrentSession(newName: string): void;
1691
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
24
1692
  } & {
25
1693
  readonly jbrowse: any;
26
1694
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -65,11 +1733,6 @@ export declare function MultipleViewsSessionMixin(pluginManager: PluginManager):
65
1733
  moveViewToBottom(id: string): void;
66
1734
  addView(typeName: string, initialState?: {}): any;
67
1735
  removeView(view: IBaseViewModel): void;
68
- addLinearGenomeViewOfAssembly(assemblyName: string, initialState?: {}): any;
69
- addViewOfAssembly(viewType: string, assemblyName: string, initialState?: Record<string, unknown>): any;
70
- addViewFromAnotherView(viewType: string, otherView: IBaseViewModelWithDisplayedRegions, initialState?: {
71
- displayedRegions?: Region[];
72
- }): any;
73
1736
  setStickyViewHeaders(sticky: boolean): void;
74
1737
  afterAttach(): void;
75
1738
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;