@jbrowse/embedded-core 5.0.0-beta.1 → 5.0.0-beta.11

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 (12) hide show
  1. package/esm/EmbeddedSessionMixin.d.ts +250 -759
  2. package/esm/EmbeddedSessionMixin.js +19 -12
  3. package/esm/EmbeddedSessionThemeMixin.d.ts +70 -345
  4. package/esm/EmbeddedSessionThemeMixin.js +31 -22
  5. package/esm/createEmbeddedRootModel.d.ts +192 -454
  6. package/esm/createEmbeddedRootModel.js +29 -16
  7. package/esm/ui/EmbeddedViewContainer.js +8 -8
  8. package/package.json +7 -7
  9. package/esm/ui/VersionAboutDialog.d.ts +0 -5
  10. package/esm/ui/VersionAboutDialog.js +0 -13
  11. package/esm/ui/ViewTitle.d.ts +0 -5
  12. package/esm/ui/ViewTitle.js +0 -65
package/esm/EmbeddedSessionThemeMixin.d.ts CHANGED
@@ -1,17 +1,21 @@
1
1
  import type PluginManager from '@jbrowse/core/PluginManager';
2
2
  import type { SerializableThemeArgs } from '@jbrowse/core/ui';
3
+ import type { PaletteMode } from '@jbrowse/core/ui/palette';
3
4
  /**
4
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  * #stateModel EmbeddedSessionThemeMixin
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  * Theme getters shared by the single-view embedded sessions
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  * (react-linear-genome-view, react-circular-genome-view). Embedded products
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- * have no theme switching, so the active theme is always `default`; the config
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- * `theme` slot still applies via `configTheme`.
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+ * have no theme picker, so the palette is always `default` and the config
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+ * `theme` slot supplies it; light or dark is the host's to drive, through
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+ * `setThemeMode`.
9
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  */
10
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  export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<Omit<{
11
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  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
12
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  name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
13
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  focusedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
16
+ highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType, import("@jbrowse/core/util/highlights").HighlightType>>, [undefined]>;
14
17
  highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
18
+ highlightLabelsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
15
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  heldForMissingPlugins: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/product-core").HeldNode[] | undefined, import("@jbrowse/product-core").HeldNode[] | undefined, import("@jbrowse/product-core").HeldNode[] | undefined>, [undefined]>;
16
20
  }, never>, {
17
21
  selection: unknown;
@@ -30,7 +34,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
30
34
  error: unknown;
31
35
  loadingP: Promise<void> | undefined;
32
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  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
33
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
37
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
34
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  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
35
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  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
36
40
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -68,7 +72,6 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
68
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  afterAttach(): void;
69
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  } & {
70
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  readonly initialized: boolean;
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- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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  readonly allRefNames: string[] | undefined;
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  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
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  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -86,6 +89,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
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  getCanonicalRefName2(refName: string): string;
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  isValidRefName(refName: string): boolean;
88
91
  } & {
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+ getRefNamePosition(refName: string): number | undefined;
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  getAliasesForRefName(refName: string): string[];
90
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  getRefNameMapForAdapter(adapterConf: {
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  [x: string]: unknown;
@@ -101,141 +105,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
101
105
  } | undefined;
102
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  };
103
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  } & {
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- readonly assemblyNameMap: Record<string, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
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- configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
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- }> & {
107
- error: unknown;
108
- loadingP: Promise<void> | undefined;
109
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
110
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
111
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
112
- canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
113
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
114
- loadedGeneticCodes: Record<string, number> | undefined;
115
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
116
- statusMessage: string | undefined;
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- statusProgress: number | undefined;
118
- statusSource: string | undefined;
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- refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
120
- } & {
121
- getConf(arg: string): any;
122
- } & {
123
- readonly name: string;
124
- readonly aliases: string[];
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- readonly displayName: string;
126
- readonly refNameColors: string[];
127
- } & {
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- readonly allAliases: string[];
129
- hasName(name: string): boolean;
130
- } & {
131
- setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
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- setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
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- } & {
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- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
135
- regions: import("@jbrowse/core/util").Region[];
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- cytobands: import("@jbrowse/core/util").Feature[];
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- geneticCodes: Record<string, number>;
138
- }): void;
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- setError(e: unknown): void;
140
- setLoadingP(p?: Promise<void>): void;
141
- loadPre(): Promise<void>;
142
- } & {
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- load(): Promise<void>;
144
- } & {
145
- afterAttach(): void;
146
- } & {
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- readonly initialized: boolean;
148
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
149
- readonly allRefNames: string[] | undefined;
150
- readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
151
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
152
- } & {
153
- readonly refNames: string[] | undefined;
154
- } & {
155
- readonly refNameToIndex: Map<string, number> | undefined;
156
- } & {
157
- getCanonicalRefName(refName: string): string | undefined;
158
- getRefNameColor(refName: string): string | undefined;
159
- getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
160
- getGeneticCodeId(refName: string): number;
161
- getSeqAdapterRefName(canonicalRefName: string): string;
162
- } & {
163
- getCanonicalRefName2(refName: string): string;
164
- isValidRefName(refName: string): boolean;
165
- } & {
166
- getAliasesForRefName(refName: string): string[];
167
- getRefNameMapForAdapter(adapterConf: {
168
- [x: string]: unknown;
169
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
170
- getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
171
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
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- configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
173
- }, {
174
- error: unknown;
175
- loadingP: Promise<void> | undefined;
176
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
177
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
178
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
179
- canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
180
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
181
- loadedGeneticCodes: Record<string, number> | undefined;
182
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
183
- statusMessage: string | undefined;
184
- statusProgress: number | undefined;
185
- statusSource: string | undefined;
186
- refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
187
- } & {
188
- getConf(arg: string): any;
189
- } & {
190
- readonly name: string;
191
- readonly aliases: string[];
192
- readonly displayName: string;
193
- readonly refNameColors: string[];
194
- } & {
195
- readonly allAliases: string[];
196
- hasName(name: string): boolean;
197
- } & {
198
- setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
199
- setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
200
- } & {
201
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
202
- regions: import("@jbrowse/core/util").Region[];
203
- cytobands: import("@jbrowse/core/util").Feature[];
204
- geneticCodes: Record<string, number>;
205
- }): void;
206
- setError(e: unknown): void;
207
- setLoadingP(p?: Promise<void>): void;
208
- loadPre(): Promise<void>;
209
- } & {
210
- load(): Promise<void>;
211
- } & {
212
- afterAttach(): void;
213
- } & {
214
- readonly initialized: boolean;
215
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
216
- readonly allRefNames: string[] | undefined;
217
- readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
218
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
219
- } & {
220
- readonly refNames: string[] | undefined;
221
- } & {
222
- readonly refNameToIndex: Map<string, number> | undefined;
223
- } & {
224
- getCanonicalRefName(refName: string): string | undefined;
225
- getRefNameColor(refName: string): string | undefined;
226
- getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
227
- getGeneticCodeId(refName: string): number;
228
- getSeqAdapterRefName(canonicalRefName: string): string;
229
- } & {
230
- getCanonicalRefName2(refName: string): string;
231
- isValidRefName(refName: string): boolean;
232
- } & {
233
- getAliasesForRefName(refName: string): string[];
234
- getRefNameMapForAdapter(adapterConf: {
235
- [x: string]: unknown;
236
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
237
- getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
238
- }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
108
+ readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
239
109
  } & {
240
110
  getCanonicalAssemblyName(asmName: string): string | undefined;
241
111
  getDisplayName(asmName: string): string;
@@ -245,7 +115,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
245
115
  error: unknown;
246
116
  loadingP: Promise<void> | undefined;
247
117
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
248
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
118
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
249
119
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
250
120
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
251
121
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -283,7 +153,6 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
283
153
  afterAttach(): void;
284
154
  } & {
285
155
  readonly initialized: boolean;
286
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
287
156
  readonly allRefNames: string[] | undefined;
288
157
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
289
158
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -301,6 +170,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
301
170
  getCanonicalRefName2(refName: string): string;
302
171
  isValidRefName(refName: string): boolean;
303
172
  } & {
173
+ getRefNamePosition(refName: string): number | undefined;
304
174
  getAliasesForRefName(refName: string): string[];
305
175
  getRefNameMapForAdapter(adapterConf: {
306
176
  [x: string]: unknown;
@@ -312,7 +182,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
312
182
  error: unknown;
313
183
  loadingP: Promise<void> | undefined;
314
184
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
315
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
185
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
316
186
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
317
187
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
318
188
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -350,7 +220,6 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
350
220
  afterAttach(): void;
351
221
  } & {
352
222
  readonly initialized: boolean;
353
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
354
223
  readonly allRefNames: string[] | undefined;
355
224
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
356
225
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -368,6 +237,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
368
237
  getCanonicalRefName2(refName: string): string;
369
238
  isValidRefName(refName: string): boolean;
370
239
  } & {
240
+ getRefNamePosition(refName: string): number | undefined;
371
241
  getAliasesForRefName(refName: string): string[];
372
242
  getRefNameMapForAdapter(adapterConf: {
373
243
  [x: string]: unknown;
@@ -381,7 +251,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
381
251
  error: unknown;
382
252
  loadingP: Promise<void> | undefined;
383
253
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
384
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
254
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
385
255
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
386
256
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
387
257
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -419,7 +289,6 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
419
289
  afterAttach(): void;
420
290
  } & {
421
291
  readonly initialized: boolean;
422
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
423
292
  readonly allRefNames: string[] | undefined;
424
293
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
425
294
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -437,6 +306,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
437
306
  getCanonicalRefName2(refName: string): string;
438
307
  isValidRefName(refName: string): boolean;
439
308
  } & {
309
+ getRefNamePosition(refName: string): number | undefined;
440
310
  getAliasesForRefName(refName: string): string[];
441
311
  getRefNameMapForAdapter(adapterConf: {
442
312
  [x: string]: unknown;
@@ -448,7 +318,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
448
318
  error: unknown;
449
319
  loadingP: Promise<void> | undefined;
450
320
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
451
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
321
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
452
322
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
453
323
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
454
324
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -486,7 +356,6 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
486
356
  afterAttach(): void;
487
357
  } & {
488
358
  readonly initialized: boolean;
489
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
490
359
  readonly allRefNames: string[] | undefined;
491
360
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
492
361
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -504,6 +373,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
504
373
  getCanonicalRefName2(refName: string): string;
505
374
  isValidRefName(refName: string): boolean;
506
375
  } & {
376
+ getRefNamePosition(refName: string): number | undefined;
507
377
  getAliasesForRefName(refName: string): string[];
508
378
  getRefNameMapForAdapter(adapterConf: {
509
379
  [x: string]: unknown;
@@ -511,11 +381,8 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
511
381
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
512
382
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
513
383
  readonly assemblyNamesList: string[];
514
- readonly configuredAssemblyNames: Set<string>;
515
- readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
516
- setSubschema(slotName: string, data: Record<string, unknown>): any;
517
- setSlot(slotName: string, value: unknown): void;
518
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
384
+ readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
385
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
519
386
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
520
387
  } & {
521
388
  settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -526,7 +393,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
526
393
  error: unknown;
527
394
  loadingP: Promise<void> | undefined;
528
395
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
529
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
396
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
530
397
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
531
398
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
532
399
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -564,7 +431,6 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
564
431
  afterAttach(): void;
565
432
  } & {
566
433
  readonly initialized: boolean;
567
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
568
434
  readonly allRefNames: string[] | undefined;
569
435
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
570
436
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -582,6 +448,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
582
448
  getCanonicalRefName2(refName: string): string;
583
449
  isValidRefName(refName: string): boolean;
584
450
  } & {
451
+ getRefNamePosition(refName: string): number | undefined;
585
452
  getAliasesForRefName(refName: string): string[];
586
453
  getRefNameMapForAdapter(adapterConf: {
587
454
  [x: string]: unknown;
@@ -593,7 +460,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
593
460
  error: unknown;
594
461
  loadingP: Promise<void> | undefined;
595
462
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
596
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
463
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
597
464
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
598
465
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
599
466
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -631,7 +498,6 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
631
498
  afterAttach(): void;
632
499
  } & {
633
500
  readonly initialized: boolean;
634
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
635
501
  readonly allRefNames: string[] | undefined;
636
502
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
637
503
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -649,6 +515,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
649
515
  getCanonicalRefName2(refName: string): string;
650
516
  isValidRefName(refName: string): boolean;
651
517
  } & {
518
+ getRefNamePosition(refName: string): number | undefined;
652
519
  getAliasesForRefName(refName: string): string[];
653
520
  getRefNameMapForAdapter(adapterConf: {
654
521
  [x: string]: unknown;
@@ -661,7 +528,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
661
528
  error: unknown;
662
529
  loadingP: Promise<void> | undefined;
663
530
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
664
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
531
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
665
532
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
666
533
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
667
534
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -699,7 +566,6 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
699
566
  afterAttach(): void;
700
567
  } & {
701
568
  readonly initialized: boolean;
702
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
703
569
  readonly allRefNames: string[] | undefined;
704
570
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
705
571
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -717,6 +583,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
717
583
  getCanonicalRefName2(refName: string): string;
718
584
  isValidRefName(refName: string): boolean;
719
585
  } & {
586
+ getRefNamePosition(refName: string): number | undefined;
720
587
  getAliasesForRefName(refName: string): string[];
721
588
  getRefNameMapForAdapter(adapterConf: {
722
589
  [x: string]: unknown;
@@ -728,7 +595,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
728
595
  error: unknown;
729
596
  loadingP: Promise<void> | undefined;
730
597
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
731
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
598
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
732
599
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
733
600
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
734
601
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -766,7 +633,6 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
766
633
  afterAttach(): void;
767
634
  } & {
768
635
  readonly initialized: boolean;
769
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
770
636
  readonly allRefNames: string[] | undefined;
771
637
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
772
638
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -784,6 +650,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
784
650
  getCanonicalRefName2(refName: string): string;
785
651
  isValidRefName(refName: string): boolean;
786
652
  } & {
653
+ getRefNamePosition(refName: string): number | undefined;
787
654
  getAliasesForRefName(refName: string): string[];
788
655
  getRefNameMapForAdapter(adapterConf: {
789
656
  [x: string]: unknown;
@@ -822,7 +689,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
822
689
  error: unknown;
823
690
  loadingP: Promise<void> | undefined;
824
691
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
825
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
692
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
826
693
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
827
694
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
828
695
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -860,7 +727,6 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
860
727
  afterAttach(): void;
861
728
  } & {
862
729
  readonly initialized: boolean;
863
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
864
730
  readonly allRefNames: string[] | undefined;
865
731
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
866
732
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -878,6 +744,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
878
744
  getCanonicalRefName2(refName: string): string;
879
745
  isValidRefName(refName: string): boolean;
880
746
  } & {
747
+ getRefNamePosition(refName: string): number | undefined;
881
748
  getAliasesForRefName(refName: string): string[];
882
749
  getRefNameMapForAdapter(adapterConf: {
883
750
  [x: string]: unknown;
@@ -893,141 +760,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
893
760
  } | undefined;
894
761
  };
895
762
  } & {
896
- readonly assemblyNameMap: Record<string, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
897
- configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
898
- }> & {
899
- error: unknown;
900
- loadingP: Promise<void> | undefined;
901
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
902
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
903
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
904
- canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
905
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
906
- loadedGeneticCodes: Record<string, number> | undefined;
907
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
908
- statusMessage: string | undefined;
909
- statusProgress: number | undefined;
910
- statusSource: string | undefined;
911
- refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
912
- } & {
913
- getConf(arg: string): any;
914
- } & {
915
- readonly name: string;
916
- readonly aliases: string[];
917
- readonly displayName: string;
918
- readonly refNameColors: string[];
919
- } & {
920
- readonly allAliases: string[];
921
- hasName(name: string): boolean;
922
- } & {
923
- setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
924
- setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
925
- } & {
926
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
927
- regions: import("@jbrowse/core/util").Region[];
928
- cytobands: import("@jbrowse/core/util").Feature[];
929
- geneticCodes: Record<string, number>;
930
- }): void;
931
- setError(e: unknown): void;
932
- setLoadingP(p?: Promise<void>): void;
933
- loadPre(): Promise<void>;
934
- } & {
935
- load(): Promise<void>;
936
- } & {
937
- afterAttach(): void;
938
- } & {
939
- readonly initialized: boolean;
940
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
941
- readonly allRefNames: string[] | undefined;
942
- readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
943
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
944
- } & {
945
- readonly refNames: string[] | undefined;
946
- } & {
947
- readonly refNameToIndex: Map<string, number> | undefined;
948
- } & {
949
- getCanonicalRefName(refName: string): string | undefined;
950
- getRefNameColor(refName: string): string | undefined;
951
- getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
952
- getGeneticCodeId(refName: string): number;
953
- getSeqAdapterRefName(canonicalRefName: string): string;
954
- } & {
955
- getCanonicalRefName2(refName: string): string;
956
- isValidRefName(refName: string): boolean;
957
- } & {
958
- getAliasesForRefName(refName: string): string[];
959
- getRefNameMapForAdapter(adapterConf: {
960
- [x: string]: unknown;
961
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
962
- getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
963
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
964
- configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
965
- }, {
966
- error: unknown;
967
- loadingP: Promise<void> | undefined;
968
- adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
969
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
970
- refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
971
- canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
972
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
973
- loadedGeneticCodes: Record<string, number> | undefined;
974
- lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
975
- statusMessage: string | undefined;
976
- statusProgress: number | undefined;
977
- statusSource: string | undefined;
978
- refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
979
- } & {
980
- getConf(arg: string): any;
981
- } & {
982
- readonly name: string;
983
- readonly aliases: string[];
984
- readonly displayName: string;
985
- readonly refNameColors: string[];
986
- } & {
987
- readonly allAliases: string[];
988
- hasName(name: string): boolean;
989
- } & {
990
- setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
991
- setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
992
- } & {
993
- setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
994
- regions: import("@jbrowse/core/util").Region[];
995
- cytobands: import("@jbrowse/core/util").Feature[];
996
- geneticCodes: Record<string, number>;
997
- }): void;
998
- setError(e: unknown): void;
999
- setLoadingP(p?: Promise<void>): void;
1000
- loadPre(): Promise<void>;
1001
- } & {
1002
- load(): Promise<void>;
1003
- } & {
1004
- afterAttach(): void;
1005
- } & {
1006
- readonly initialized: boolean;
1007
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1008
- readonly allRefNames: string[] | undefined;
1009
- readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1010
- readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1011
- } & {
1012
- readonly refNames: string[] | undefined;
1013
- } & {
1014
- readonly refNameToIndex: Map<string, number> | undefined;
1015
- } & {
1016
- getCanonicalRefName(refName: string): string | undefined;
1017
- getRefNameColor(refName: string): string | undefined;
1018
- getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1019
- getGeneticCodeId(refName: string): number;
1020
- getSeqAdapterRefName(canonicalRefName: string): string;
1021
- } & {
1022
- getCanonicalRefName2(refName: string): string;
1023
- isValidRefName(refName: string): boolean;
1024
- } & {
1025
- getAliasesForRefName(refName: string): string[];
1026
- getRefNameMapForAdapter(adapterConf: {
1027
- [x: string]: unknown;
1028
- }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1029
- getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1030
- }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
763
+ readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
1031
764
  } & {
1032
765
  getCanonicalAssemblyName(asmName: string): string | undefined;
1033
766
  getDisplayName(asmName: string): string;
@@ -1037,7 +770,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1037
770
  error: unknown;
1038
771
  loadingP: Promise<void> | undefined;
1039
772
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1040
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
773
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1041
774
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1042
775
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1043
776
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1075,7 +808,6 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1075
808
  afterAttach(): void;
1076
809
  } & {
1077
810
  readonly initialized: boolean;
1078
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1079
811
  readonly allRefNames: string[] | undefined;
1080
812
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1081
813
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1093,6 +825,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1093
825
  getCanonicalRefName2(refName: string): string;
1094
826
  isValidRefName(refName: string): boolean;
1095
827
  } & {
828
+ getRefNamePosition(refName: string): number | undefined;
1096
829
  getAliasesForRefName(refName: string): string[];
1097
830
  getRefNameMapForAdapter(adapterConf: {
1098
831
  [x: string]: unknown;
@@ -1104,7 +837,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1104
837
  error: unknown;
1105
838
  loadingP: Promise<void> | undefined;
1106
839
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1107
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
840
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1108
841
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1109
842
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1110
843
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1142,7 +875,6 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1142
875
  afterAttach(): void;
1143
876
  } & {
1144
877
  readonly initialized: boolean;
1145
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1146
878
  readonly allRefNames: string[] | undefined;
1147
879
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1148
880
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1160,6 +892,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1160
892
  getCanonicalRefName2(refName: string): string;
1161
893
  isValidRefName(refName: string): boolean;
1162
894
  } & {
895
+ getRefNamePosition(refName: string): number | undefined;
1163
896
  getAliasesForRefName(refName: string): string[];
1164
897
  getRefNameMapForAdapter(adapterConf: {
1165
898
  [x: string]: unknown;
@@ -1173,7 +906,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1173
906
  error: unknown;
1174
907
  loadingP: Promise<void> | undefined;
1175
908
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1176
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
909
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1177
910
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1178
911
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1179
912
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1211,7 +944,6 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1211
944
  afterAttach(): void;
1212
945
  } & {
1213
946
  readonly initialized: boolean;
1214
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1215
947
  readonly allRefNames: string[] | undefined;
1216
948
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1217
949
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1229,6 +961,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1229
961
  getCanonicalRefName2(refName: string): string;
1230
962
  isValidRefName(refName: string): boolean;
1231
963
  } & {
964
+ getRefNamePosition(refName: string): number | undefined;
1232
965
  getAliasesForRefName(refName: string): string[];
1233
966
  getRefNameMapForAdapter(adapterConf: {
1234
967
  [x: string]: unknown;
@@ -1240,7 +973,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1240
973
  error: unknown;
1241
974
  loadingP: Promise<void> | undefined;
1242
975
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1243
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
976
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1244
977
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1245
978
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1246
979
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1278,7 +1011,6 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1278
1011
  afterAttach(): void;
1279
1012
  } & {
1280
1013
  readonly initialized: boolean;
1281
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1282
1014
  readonly allRefNames: string[] | undefined;
1283
1015
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1284
1016
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1296,6 +1028,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1296
1028
  getCanonicalRefName2(refName: string): string;
1297
1029
  isValidRefName(refName: string): boolean;
1298
1030
  } & {
1031
+ getRefNamePosition(refName: string): number | undefined;
1299
1032
  getAliasesForRefName(refName: string): string[];
1300
1033
  getRefNameMapForAdapter(adapterConf: {
1301
1034
  [x: string]: unknown;
@@ -1303,11 +1036,8 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1303
1036
  getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1304
1037
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1305
1038
  readonly assemblyNamesList: string[];
1306
- readonly configuredAssemblyNames: Set<string>;
1307
- readonly assemblyList: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
1308
- setSubschema(slotName: string, data: Record<string, unknown>): any;
1309
- setSlot(slotName: string, value: unknown): void;
1310
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
1039
+ readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
1040
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1311
1041
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1312
1042
  } & {
1313
1043
  settleAssemblyResolution(assemblyName: string): Promise<void>;
@@ -1318,7 +1048,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1318
1048
  error: unknown;
1319
1049
  loadingP: Promise<void> | undefined;
1320
1050
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1321
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1051
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1322
1052
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1323
1053
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1324
1054
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1356,7 +1086,6 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1356
1086
  afterAttach(): void;
1357
1087
  } & {
1358
1088
  readonly initialized: boolean;
1359
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1360
1089
  readonly allRefNames: string[] | undefined;
1361
1090
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1362
1091
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1374,6 +1103,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1374
1103
  getCanonicalRefName2(refName: string): string;
1375
1104
  isValidRefName(refName: string): boolean;
1376
1105
  } & {
1106
+ getRefNamePosition(refName: string): number | undefined;
1377
1107
  getAliasesForRefName(refName: string): string[];
1378
1108
  getRefNameMapForAdapter(adapterConf: {
1379
1109
  [x: string]: unknown;
@@ -1385,7 +1115,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1385
1115
  error: unknown;
1386
1116
  loadingP: Promise<void> | undefined;
1387
1117
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1388
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1118
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1389
1119
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1390
1120
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1391
1121
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1423,7 +1153,6 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1423
1153
  afterAttach(): void;
1424
1154
  } & {
1425
1155
  readonly initialized: boolean;
1426
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1427
1156
  readonly allRefNames: string[] | undefined;
1428
1157
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1429
1158
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1441,6 +1170,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1441
1170
  getCanonicalRefName2(refName: string): string;
1442
1171
  isValidRefName(refName: string): boolean;
1443
1172
  } & {
1173
+ getRefNamePosition(refName: string): number | undefined;
1444
1174
  getAliasesForRefName(refName: string): string[];
1445
1175
  getRefNameMapForAdapter(adapterConf: {
1446
1176
  [x: string]: unknown;
@@ -1453,7 +1183,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1453
1183
  error: unknown;
1454
1184
  loadingP: Promise<void> | undefined;
1455
1185
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1456
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1186
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1457
1187
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1458
1188
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1459
1189
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1491,7 +1221,6 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1491
1221
  afterAttach(): void;
1492
1222
  } & {
1493
1223
  readonly initialized: boolean;
1494
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1495
1224
  readonly allRefNames: string[] | undefined;
1496
1225
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1497
1226
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1509,6 +1238,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1509
1238
  getCanonicalRefName2(refName: string): string;
1510
1239
  isValidRefName(refName: string): boolean;
1511
1240
  } & {
1241
+ getRefNamePosition(refName: string): number | undefined;
1512
1242
  getAliasesForRefName(refName: string): string[];
1513
1243
  getRefNameMapForAdapter(adapterConf: {
1514
1244
  [x: string]: unknown;
@@ -1520,7 +1250,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1520
1250
  error: unknown;
1521
1251
  loadingP: Promise<void> | undefined;
1522
1252
  adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1523
- volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1253
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1524
1254
  refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1525
1255
  canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1526
1256
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
@@ -1558,7 +1288,6 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1558
1288
  afterAttach(): void;
1559
1289
  } & {
1560
1290
  readonly initialized: boolean;
1561
- readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1562
1291
  readonly allRefNames: string[] | undefined;
1563
1292
  readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1564
1293
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
@@ -1576,6 +1305,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1576
1305
  getCanonicalRefName2(refName: string): string;
1577
1306
  isValidRefName(refName: string): boolean;
1578
1307
  } & {
1308
+ getRefNamePosition(refName: string): number | undefined;
1579
1309
  getAliasesForRefName(refName: string): string[];
1580
1310
  getRefNameMapForAdapter(adapterConf: {
1581
1311
  [x: string]: unknown;
@@ -1607,10 +1337,7 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1607
1337
  } & {
1608
1338
  readonly jbrowse: any;
1609
1339
  readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1610
- readonly configuration: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
1611
- setSubschema(slotName: string, data: Record<string, unknown>): any;
1612
- setSlot(slotName: string, value: unknown): void;
1613
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1340
+ readonly configuration: import("@jbrowse/core/configuration").ConfigNodeProps<any> & import("@jbrowse/core/configuration").ConfigNodeActions & import("@jbrowse/core/configuration").ConfigNodeBrand<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1614
1341
  readonly adminMode: boolean;
1615
1342
  readonly textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1616
1343
  } & {
@@ -1620,12 +1347,6 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1620
1347
  } & {
1621
1348
  getPreferenceDefault(key: string): unknown;
1622
1349
  getPreference(key: string): unknown;
1623
- getDisplayTypeDefault(displayType: string, slot: string): unknown;
1624
- getDisplayTypeDefaults(): {
1625
- displayType: string;
1626
- slot: string;
1627
- value: unknown;
1628
- }[];
1629
1350
  getPreferenceChanges(): import("@jbrowse/core/util").TrackConfigChange[];
1630
1351
  } & {
1631
1352
  readonly animationMode: import("@jbrowse/core/util").AnimationMode;
@@ -1637,17 +1358,20 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1637
1358
  clearSelection(): void;
1638
1359
  setHovered(thing: unknown): void;
1639
1360
  setHighlightsVisible(arg: boolean): void;
1640
- revealHighlights(): void;
1361
+ setHighlightLabelsVisible(arg: boolean): void;
1362
+ addHighlight(highlight: import("@jbrowse/core/util/highlights").HighlightType): void;
1363
+ removeHighlight(highlight: import("@jbrowse/core/util/highlights").HighlightType): void;
1364
+ updateHighlight(old: import("@jbrowse/core/util/highlights").HighlightType, updates: Partial<import("@jbrowse/core/util/highlights").HighlightType>): void;
1365
+ setHighlights(highlights: import("@jbrowse/core/util/highlights").HighlightType[]): void;
1641
1366
  setPreferenceOverride(key: string, value: unknown): void;
1642
1367
  clearPreferenceOverrides(): void;
1643
1368
  clearPreferenceOverride(key: string): void;
1644
- resetPreferenceChange(path: string[]): void;
1645
1369
  setScrollZoom(flag: boolean): void;
1646
- setDisplayTypeDefault(displayType: string, slot: string, value: unknown): void;
1647
1370
  setName(str: string): void;
1648
1371
  setFocusedViewId(viewId: string | undefined): void;
1649
1372
  removeActiveDialog(): void;
1650
1373
  queueDialog(doneCallback: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
1374
+ removeDialog(entry: [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
1651
1375
  } & {
1652
1376
  snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1653
1377
  errorDialog: import("@jbrowse/core/ui/SnackbarModel").ErrorDialogState | undefined;
@@ -1660,6 +1384,10 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1660
1384
  pushSnackbarMessage(message: string, level?: import("@jbrowse/core/util").NotificationLevel, actions?: import("@jbrowse/core/util").SnackAction[]): void;
1661
1385
  popSnackbarMessage(): import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage | undefined;
1662
1386
  removeSnackbarMessage(message: string): void;
1387
+ } & {
1388
+ afterAttach(): void;
1389
+ } & {
1390
+ sessionThemeMode: PaletteMode | undefined;
1663
1391
  } & {
1664
1392
  /**
1665
1393
  * #getter
@@ -1704,20 +1432,17 @@ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager):
1704
1432
  } & {
1705
1433
  /**
1706
1434
  * #action
1707
- * Point the session at light or dark. One write, not two: the `theme`
1708
- * slot is what `themeOptions` ships to the renderer, so the labels baked
1709
- * in the worker follow it, and `palette` is derived from the same slot,
1710
- * so what React draws follows it too. An embedder who sets only a
1711
- * React-side palette leaves the baked labels behind.
1435
+ * Switch the session to light or dark, leaving the host's configured
1436
+ * colours alone. `themeOptions` carries the mode to the renderer, so
1437
+ * labels drawn in the worker follow it, and `palette` is derived from
1438
+ * the same args, so React-drawn elements follow it too. An embedder who
1439
+ * sets only a React-side palette leaves the worker-drawn labels in the
1440
+ * old mode.
1712
1441
  *
1713
- * Merges rather than replaces, at both levels. `theme` is a frozen slot,
1714
- * so a bare `setConf(session, 'theme', { palette: { mode } })` — the
1715
- * obvious form, and what the build-your-own examples each wrote — drops
1716
- * every other key in it. That silently discards whatever the host passed
1717
- * as `createViewState`'s `configuration.theme` (a brand `primary`, say)
1718
- * the first time their dark-mode toggle fires. `resolvePalette` spreads
1719
- * `configTheme.palette` over the preset shallowly, so `mode` and
1720
- * `primary` are siblings and both levels have to survive.
1442
+ * This used to write `palette.mode` into the config `theme` slot, which
1443
+ * meant merging at two levels to avoid discarding the brand the host had
1444
+ * passed to `createViewState`. Mode is its own axis now, so there is
1445
+ * nothing to merge and nothing to discard.
1721
1446
  */
1722
- setThemeMode(mode: 'light' | 'dark'): void;
1447
+ setThemeMode(mode: PaletteMode): void;
1723
1448
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;