@jbrowse/embedded-core 4.3.0 → 5.0.0-beta.10

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 (19) hide show
  1. package/esm/EmbeddedSessionMixin.d.ts +2818 -0
  2. package/esm/EmbeddedSessionMixin.js +61 -0
  3. package/esm/EmbeddedSessionThemeMixin.d.ts +1448 -0
  4. package/esm/EmbeddedSessionThemeMixin.js +113 -0
  5. package/esm/createEmbeddedRootModel.d.ts +1638 -0
  6. package/esm/createEmbeddedRootModel.js +126 -0
  7. package/esm/index.d.ts +4 -1
  8. package/esm/index.js +4 -2
  9. package/esm/ui/EmbeddedViewContainer.d.ts +3 -3
  10. package/esm/ui/EmbeddedViewContainer.js +14 -18
  11. package/package.json +12 -14
  12. package/esm/ui/ModalWidget.d.ts +0 -5
  13. package/esm/ui/ModalWidget.js +0 -32
  14. package/esm/ui/VersionAboutDialog.d.ts +0 -5
  15. package/esm/ui/VersionAboutDialog.js +0 -13
  16. package/esm/ui/ViewMenu.d.ts +0 -8
  17. package/esm/ui/ViewMenu.js +0 -8
  18. package/esm/ui/ViewTitle.d.ts +0 -5
  19. package/esm/ui/ViewTitle.js +0 -47
package/esm/EmbeddedSessionThemeMixin.d.ts ADDED
@@ -0,0 +1,1448 @@
1
+ import type PluginManager from '@jbrowse/core/PluginManager';
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+ import type { SerializableThemeArgs } from '@jbrowse/core/ui';
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+ import type { PaletteMode } from '@jbrowse/core/ui/palette';
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+ /**
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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 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`.
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+ */
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+ export declare function EmbeddedSessionThemeMixin(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<Omit<{
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+ id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
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+ name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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+ focusedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
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+ 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]>;
17
+ highlightsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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+ highlightLabelsVisible: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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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]>;
20
+ }, never>, {
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+ selection: unknown;
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+ hovered: unknown;
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+ queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>][];
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+ preferencesOverrides: import("mobx").ObservableMap<string, unknown>;
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+ } & {
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+ readonly root: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
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+ jbrowse: import("@jbrowse/mobx-state-tree").IAnyType;
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+ session: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IAnyType>;
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+ sessionPath: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
30
+ assemblyManager: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
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+ assemblies: import("@jbrowse/mobx-state-tree").IArrayType<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>>;
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+ }, {
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+ error: unknown;
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+ loadingP: Promise<void> | undefined;
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+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
37
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
38
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
39
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
40
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
41
+ loadedGeneticCodes: Record<string, number> | undefined;
42
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
43
+ statusMessage: string | undefined;
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+ statusProgress: number | undefined;
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+ statusSource: string | undefined;
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+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
47
+ } & {
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+ getConf(arg: string): any;
49
+ } & {
50
+ readonly name: string;
51
+ readonly aliases: string[];
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+ readonly displayName: string;
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+ readonly refNameColors: string[];
54
+ } & {
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+ readonly allAliases: string[];
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+ hasName(name: string): boolean;
57
+ } & {
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+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
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+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
60
+ } & {
61
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
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+ regions: import("@jbrowse/core/util").Region[];
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+ cytobands: import("@jbrowse/core/util").Feature[];
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+ geneticCodes: Record<string, number>;
65
+ }): void;
66
+ setError(e: unknown): void;
67
+ setLoadingP(p?: Promise<void>): void;
68
+ loadPre(): Promise<void>;
69
+ } & {
70
+ load(): Promise<void>;
71
+ } & {
72
+ afterAttach(): void;
73
+ } & {
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+ readonly initialized: boolean;
75
+ readonly allRefNames: string[] | undefined;
76
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
77
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
78
+ } & {
79
+ readonly refNames: string[] | undefined;
80
+ } & {
81
+ readonly refNameToIndex: Map<string, number> | undefined;
82
+ } & {
83
+ getCanonicalRefName(refName: string): string | undefined;
84
+ getRefNameColor(refName: string): string | undefined;
85
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
86
+ getGeneticCodeId(refName: string): number;
87
+ getSeqAdapterRefName(canonicalRefName: string): string;
88
+ } & {
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+ getCanonicalRefName2(refName: string): string;
90
+ isValidRefName(refName: string): boolean;
91
+ } & {
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+ getRefNamePosition(refName: string): number | undefined;
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+ getAliasesForRefName(refName: string): string[];
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+ getRefNameMapForAdapter(adapterConf: {
95
+ [x: string]: unknown;
96
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
97
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
98
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
99
+ }, {
100
+ unrecognizedReports: {
101
+ report(session: unknown, name: string, handlerCount: number, fire: () => unknown): void;
102
+ reportFor(session: unknown, name: string): {
103
+ handled: boolean;
104
+ claim?: Promise<void>;
105
+ } | undefined;
106
+ };
107
+ } & {
108
+ readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
109
+ } & {
110
+ getCanonicalAssemblyName(asmName: string): string | undefined;
111
+ getDisplayName(asmName: string): string;
112
+ get(asmName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
113
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
114
+ }> & {
115
+ error: unknown;
116
+ loadingP: Promise<void> | undefined;
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+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
118
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
119
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
120
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
121
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
122
+ loadedGeneticCodes: Record<string, number> | undefined;
123
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
124
+ statusMessage: string | undefined;
125
+ statusProgress: number | undefined;
126
+ statusSource: string | undefined;
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+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
128
+ } & {
129
+ getConf(arg: string): any;
130
+ } & {
131
+ readonly name: string;
132
+ readonly aliases: string[];
133
+ readonly displayName: string;
134
+ readonly refNameColors: string[];
135
+ } & {
136
+ readonly allAliases: string[];
137
+ hasName(name: string): boolean;
138
+ } & {
139
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
140
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
141
+ } & {
142
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
143
+ regions: import("@jbrowse/core/util").Region[];
144
+ cytobands: import("@jbrowse/core/util").Feature[];
145
+ geneticCodes: Record<string, number>;
146
+ }): void;
147
+ setError(e: unknown): void;
148
+ setLoadingP(p?: Promise<void>): void;
149
+ loadPre(): Promise<void>;
150
+ } & {
151
+ load(): Promise<void>;
152
+ } & {
153
+ afterAttach(): void;
154
+ } & {
155
+ readonly initialized: boolean;
156
+ readonly allRefNames: string[] | undefined;
157
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
158
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
159
+ } & {
160
+ readonly refNames: string[] | undefined;
161
+ } & {
162
+ readonly refNameToIndex: Map<string, number> | undefined;
163
+ } & {
164
+ getCanonicalRefName(refName: string): string | undefined;
165
+ getRefNameColor(refName: string): string | undefined;
166
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
167
+ getGeneticCodeId(refName: string): number;
168
+ getSeqAdapterRefName(canonicalRefName: string): string;
169
+ } & {
170
+ getCanonicalRefName2(refName: string): string;
171
+ isValidRefName(refName: string): boolean;
172
+ } & {
173
+ getRefNamePosition(refName: string): number | undefined;
174
+ getAliasesForRefName(refName: string): string[];
175
+ getRefNameMapForAdapter(adapterConf: {
176
+ [x: string]: unknown;
177
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
178
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
179
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
180
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
181
+ }, {
182
+ error: unknown;
183
+ loadingP: Promise<void> | undefined;
184
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
185
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
186
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
187
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
188
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
189
+ loadedGeneticCodes: Record<string, number> | undefined;
190
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
191
+ statusMessage: string | undefined;
192
+ statusProgress: number | undefined;
193
+ statusSource: string | undefined;
194
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
195
+ } & {
196
+ getConf(arg: string): any;
197
+ } & {
198
+ readonly name: string;
199
+ readonly aliases: string[];
200
+ readonly displayName: string;
201
+ readonly refNameColors: string[];
202
+ } & {
203
+ readonly allAliases: string[];
204
+ hasName(name: string): boolean;
205
+ } & {
206
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
207
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
208
+ } & {
209
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
210
+ regions: import("@jbrowse/core/util").Region[];
211
+ cytobands: import("@jbrowse/core/util").Feature[];
212
+ geneticCodes: Record<string, number>;
213
+ }): void;
214
+ setError(e: unknown): void;
215
+ setLoadingP(p?: Promise<void>): void;
216
+ loadPre(): Promise<void>;
217
+ } & {
218
+ load(): Promise<void>;
219
+ } & {
220
+ afterAttach(): void;
221
+ } & {
222
+ readonly initialized: boolean;
223
+ readonly allRefNames: string[] | undefined;
224
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
225
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
226
+ } & {
227
+ readonly refNames: string[] | undefined;
228
+ } & {
229
+ readonly refNameToIndex: Map<string, number> | undefined;
230
+ } & {
231
+ getCanonicalRefName(refName: string): string | undefined;
232
+ getRefNameColor(refName: string): string | undefined;
233
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
234
+ getGeneticCodeId(refName: string): number;
235
+ getSeqAdapterRefName(canonicalRefName: string): string;
236
+ } & {
237
+ getCanonicalRefName2(refName: string): string;
238
+ isValidRefName(refName: string): boolean;
239
+ } & {
240
+ getRefNamePosition(refName: string): number | undefined;
241
+ getAliasesForRefName(refName: string): string[];
242
+ getRefNameMapForAdapter(adapterConf: {
243
+ [x: string]: unknown;
244
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
245
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
246
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
247
+ has(asmName: string): boolean;
248
+ loadingAssembly(asmNames: string[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
249
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
250
+ }> & {
251
+ error: unknown;
252
+ loadingP: Promise<void> | undefined;
253
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
254
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
255
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
256
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
257
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
258
+ loadedGeneticCodes: Record<string, number> | undefined;
259
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
260
+ statusMessage: string | undefined;
261
+ statusProgress: number | undefined;
262
+ statusSource: string | undefined;
263
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
264
+ } & {
265
+ getConf(arg: string): any;
266
+ } & {
267
+ readonly name: string;
268
+ readonly aliases: string[];
269
+ readonly displayName: string;
270
+ readonly refNameColors: string[];
271
+ } & {
272
+ readonly allAliases: string[];
273
+ hasName(name: string): boolean;
274
+ } & {
275
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
276
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
277
+ } & {
278
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
279
+ regions: import("@jbrowse/core/util").Region[];
280
+ cytobands: import("@jbrowse/core/util").Feature[];
281
+ geneticCodes: Record<string, number>;
282
+ }): void;
283
+ setError(e: unknown): void;
284
+ setLoadingP(p?: Promise<void>): void;
285
+ loadPre(): Promise<void>;
286
+ } & {
287
+ load(): Promise<void>;
288
+ } & {
289
+ afterAttach(): void;
290
+ } & {
291
+ readonly initialized: boolean;
292
+ readonly allRefNames: string[] | undefined;
293
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
294
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
295
+ } & {
296
+ readonly refNames: string[] | undefined;
297
+ } & {
298
+ readonly refNameToIndex: Map<string, number> | undefined;
299
+ } & {
300
+ getCanonicalRefName(refName: string): string | undefined;
301
+ getRefNameColor(refName: string): string | undefined;
302
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
303
+ getGeneticCodeId(refName: string): number;
304
+ getSeqAdapterRefName(canonicalRefName: string): string;
305
+ } & {
306
+ getCanonicalRefName2(refName: string): string;
307
+ isValidRefName(refName: string): boolean;
308
+ } & {
309
+ getRefNamePosition(refName: string): number | undefined;
310
+ getAliasesForRefName(refName: string): string[];
311
+ getRefNameMapForAdapter(adapterConf: {
312
+ [x: string]: unknown;
313
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
314
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
315
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
316
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
317
+ }, {
318
+ error: unknown;
319
+ loadingP: Promise<void> | undefined;
320
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
321
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
322
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
323
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
324
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
325
+ loadedGeneticCodes: Record<string, number> | undefined;
326
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
327
+ statusMessage: string | undefined;
328
+ statusProgress: number | undefined;
329
+ statusSource: string | undefined;
330
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
331
+ } & {
332
+ getConf(arg: string): any;
333
+ } & {
334
+ readonly name: string;
335
+ readonly aliases: string[];
336
+ readonly displayName: string;
337
+ readonly refNameColors: string[];
338
+ } & {
339
+ readonly allAliases: string[];
340
+ hasName(name: string): boolean;
341
+ } & {
342
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
343
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
344
+ } & {
345
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
346
+ regions: import("@jbrowse/core/util").Region[];
347
+ cytobands: import("@jbrowse/core/util").Feature[];
348
+ geneticCodes: Record<string, number>;
349
+ }): void;
350
+ setError(e: unknown): void;
351
+ setLoadingP(p?: Promise<void>): void;
352
+ loadPre(): Promise<void>;
353
+ } & {
354
+ load(): Promise<void>;
355
+ } & {
356
+ afterAttach(): void;
357
+ } & {
358
+ readonly initialized: boolean;
359
+ readonly allRefNames: string[] | undefined;
360
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
361
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
362
+ } & {
363
+ readonly refNames: string[] | undefined;
364
+ } & {
365
+ readonly refNameToIndex: Map<string, number> | undefined;
366
+ } & {
367
+ getCanonicalRefName(refName: string): string | undefined;
368
+ getRefNameColor(refName: string): string | undefined;
369
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
370
+ getGeneticCodeId(refName: string): number;
371
+ getSeqAdapterRefName(canonicalRefName: string): string;
372
+ } & {
373
+ getCanonicalRefName2(refName: string): string;
374
+ isValidRefName(refName: string): boolean;
375
+ } & {
376
+ getRefNamePosition(refName: string): number | undefined;
377
+ getAliasesForRefName(refName: string): string[];
378
+ getRefNameMapForAdapter(adapterConf: {
379
+ [x: string]: unknown;
380
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
381
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
382
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
383
+ readonly assemblyNamesList: string[];
384
+ readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
385
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
386
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
387
+ } & {
388
+ settleAssemblyResolution(assemblyName: string): Promise<void>;
389
+ } & {
390
+ waitForAssembly(assemblyName: string): Promise<(import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
391
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
392
+ }> & {
393
+ error: unknown;
394
+ loadingP: Promise<void> | undefined;
395
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
396
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
397
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
398
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
399
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
400
+ loadedGeneticCodes: Record<string, number> | undefined;
401
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
402
+ statusMessage: string | undefined;
403
+ statusProgress: number | undefined;
404
+ statusSource: string | undefined;
405
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
406
+ } & {
407
+ getConf(arg: string): any;
408
+ } & {
409
+ readonly name: string;
410
+ readonly aliases: string[];
411
+ readonly displayName: string;
412
+ readonly refNameColors: string[];
413
+ } & {
414
+ readonly allAliases: string[];
415
+ hasName(name: string): boolean;
416
+ } & {
417
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
418
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
419
+ } & {
420
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
421
+ regions: import("@jbrowse/core/util").Region[];
422
+ cytobands: import("@jbrowse/core/util").Feature[];
423
+ geneticCodes: Record<string, number>;
424
+ }): void;
425
+ setError(e: unknown): void;
426
+ setLoadingP(p?: Promise<void>): void;
427
+ loadPre(): Promise<void>;
428
+ } & {
429
+ load(): Promise<void>;
430
+ } & {
431
+ afterAttach(): void;
432
+ } & {
433
+ readonly initialized: boolean;
434
+ readonly allRefNames: string[] | undefined;
435
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
436
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
437
+ } & {
438
+ readonly refNames: string[] | undefined;
439
+ } & {
440
+ readonly refNameToIndex: Map<string, number> | undefined;
441
+ } & {
442
+ getCanonicalRefName(refName: string): string | undefined;
443
+ getRefNameColor(refName: string): string | undefined;
444
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
445
+ getGeneticCodeId(refName: string): number;
446
+ getSeqAdapterRefName(canonicalRefName: string): string;
447
+ } & {
448
+ getCanonicalRefName2(refName: string): string;
449
+ isValidRefName(refName: string): boolean;
450
+ } & {
451
+ getRefNamePosition(refName: string): number | undefined;
452
+ getAliasesForRefName(refName: string): string[];
453
+ getRefNameMapForAdapter(adapterConf: {
454
+ [x: string]: unknown;
455
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
456
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
457
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
458
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
459
+ }, {
460
+ error: unknown;
461
+ loadingP: Promise<void> | undefined;
462
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
463
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
464
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
465
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
466
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
467
+ loadedGeneticCodes: Record<string, number> | undefined;
468
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
469
+ statusMessage: string | undefined;
470
+ statusProgress: number | undefined;
471
+ statusSource: string | undefined;
472
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
473
+ } & {
474
+ getConf(arg: string): any;
475
+ } & {
476
+ readonly name: string;
477
+ readonly aliases: string[];
478
+ readonly displayName: string;
479
+ readonly refNameColors: string[];
480
+ } & {
481
+ readonly allAliases: string[];
482
+ hasName(name: string): boolean;
483
+ } & {
484
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
485
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
486
+ } & {
487
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
488
+ regions: import("@jbrowse/core/util").Region[];
489
+ cytobands: import("@jbrowse/core/util").Feature[];
490
+ geneticCodes: Record<string, number>;
491
+ }): void;
492
+ setError(e: unknown): void;
493
+ setLoadingP(p?: Promise<void>): void;
494
+ loadPre(): Promise<void>;
495
+ } & {
496
+ load(): Promise<void>;
497
+ } & {
498
+ afterAttach(): void;
499
+ } & {
500
+ readonly initialized: boolean;
501
+ readonly allRefNames: string[] | undefined;
502
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
503
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
504
+ } & {
505
+ readonly refNames: string[] | undefined;
506
+ } & {
507
+ readonly refNameToIndex: Map<string, number> | undefined;
508
+ } & {
509
+ getCanonicalRefName(refName: string): string | undefined;
510
+ getRefNameColor(refName: string): string | undefined;
511
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
512
+ getGeneticCodeId(refName: string): number;
513
+ getSeqAdapterRefName(canonicalRefName: string): string;
514
+ } & {
515
+ getCanonicalRefName2(refName: string): string;
516
+ isValidRefName(refName: string): boolean;
517
+ } & {
518
+ getRefNamePosition(refName: string): number | undefined;
519
+ getAliasesForRefName(refName: string): string[];
520
+ getRefNameMapForAdapter(adapterConf: {
521
+ [x: string]: unknown;
522
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
523
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
524
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
525
+ requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
526
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
527
+ }> & {
528
+ error: unknown;
529
+ loadingP: Promise<void> | undefined;
530
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
531
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
532
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
533
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
534
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
535
+ loadedGeneticCodes: Record<string, number> | undefined;
536
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
537
+ statusMessage: string | undefined;
538
+ statusProgress: number | undefined;
539
+ statusSource: string | undefined;
540
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
541
+ } & {
542
+ getConf(arg: string): any;
543
+ } & {
544
+ readonly name: string;
545
+ readonly aliases: string[];
546
+ readonly displayName: string;
547
+ readonly refNameColors: string[];
548
+ } & {
549
+ readonly allAliases: string[];
550
+ hasName(name: string): boolean;
551
+ } & {
552
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
553
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
554
+ } & {
555
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
556
+ regions: import("@jbrowse/core/util").Region[];
557
+ cytobands: import("@jbrowse/core/util").Feature[];
558
+ geneticCodes: Record<string, number>;
559
+ }): void;
560
+ setError(e: unknown): void;
561
+ setLoadingP(p?: Promise<void>): void;
562
+ loadPre(): Promise<void>;
563
+ } & {
564
+ load(): Promise<void>;
565
+ } & {
566
+ afterAttach(): void;
567
+ } & {
568
+ readonly initialized: boolean;
569
+ readonly allRefNames: string[] | undefined;
570
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
571
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
572
+ } & {
573
+ readonly refNames: string[] | undefined;
574
+ } & {
575
+ readonly refNameToIndex: Map<string, number> | undefined;
576
+ } & {
577
+ getCanonicalRefName(refName: string): string | undefined;
578
+ getRefNameColor(refName: string): string | undefined;
579
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
580
+ getGeneticCodeId(refName: string): number;
581
+ getSeqAdapterRefName(canonicalRefName: string): string;
582
+ } & {
583
+ getCanonicalRefName2(refName: string): string;
584
+ isValidRefName(refName: string): boolean;
585
+ } & {
586
+ getRefNamePosition(refName: string): number | undefined;
587
+ getAliasesForRefName(refName: string): string[];
588
+ getRefNameMapForAdapter(adapterConf: {
589
+ [x: string]: unknown;
590
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
591
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
592
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
593
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
594
+ }, {
595
+ error: unknown;
596
+ loadingP: Promise<void> | undefined;
597
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
598
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
599
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
600
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
601
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
602
+ loadedGeneticCodes: Record<string, number> | undefined;
603
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
604
+ statusMessage: string | undefined;
605
+ statusProgress: number | undefined;
606
+ statusSource: string | undefined;
607
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
608
+ } & {
609
+ getConf(arg: string): any;
610
+ } & {
611
+ readonly name: string;
612
+ readonly aliases: string[];
613
+ readonly displayName: string;
614
+ readonly refNameColors: string[];
615
+ } & {
616
+ readonly allAliases: string[];
617
+ hasName(name: string): boolean;
618
+ } & {
619
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
620
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
621
+ } & {
622
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
623
+ regions: import("@jbrowse/core/util").Region[];
624
+ cytobands: import("@jbrowse/core/util").Feature[];
625
+ geneticCodes: Record<string, number>;
626
+ }): void;
627
+ setError(e: unknown): void;
628
+ setLoadingP(p?: Promise<void>): void;
629
+ loadPre(): Promise<void>;
630
+ } & {
631
+ load(): Promise<void>;
632
+ } & {
633
+ afterAttach(): void;
634
+ } & {
635
+ readonly initialized: boolean;
636
+ readonly allRefNames: string[] | undefined;
637
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
638
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
639
+ } & {
640
+ readonly refNames: string[] | undefined;
641
+ } & {
642
+ readonly refNameToIndex: Map<string, number> | undefined;
643
+ } & {
644
+ getCanonicalRefName(refName: string): string | undefined;
645
+ getRefNameColor(refName: string): string | undefined;
646
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
647
+ getGeneticCodeId(refName: string): number;
648
+ getSeqAdapterRefName(canonicalRefName: string): string;
649
+ } & {
650
+ getCanonicalRefName2(refName: string): string;
651
+ isValidRefName(refName: string): boolean;
652
+ } & {
653
+ getRefNamePosition(refName: string): number | undefined;
654
+ getAliasesForRefName(refName: string): string[];
655
+ getRefNameMapForAdapter(adapterConf: {
656
+ [x: string]: unknown;
657
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
658
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
659
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
660
+ getRefNameMapForAdapter(adapterConf: {
661
+ [x: string]: unknown;
662
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
663
+ isValidRefName(refName: string, assemblyName: string): boolean;
664
+ } & {
665
+ afterAttach(): void;
666
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
667
+ addAssembly(configuration: any): void;
668
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
669
+ }> & {
670
+ rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
671
+ adminMode: boolean;
672
+ error: unknown;
673
+ textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
674
+ pluginManager: PluginManager;
675
+ } & {
676
+ setError(error: unknown): void;
677
+ setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
678
+ setDefaultSession(): void;
679
+ setSessionPath(path: string): void;
680
+ renameCurrentSession(newName: string): void;
681
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
682
+ jbrowse: import("@jbrowse/mobx-state-tree").IAnyType;
683
+ session: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IAnyType>;
684
+ sessionPath: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
685
+ assemblyManager: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
686
+ assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
687
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
688
+ }, {
689
+ error: unknown;
690
+ loadingP: Promise<void> | undefined;
691
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
692
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
693
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
694
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
695
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
696
+ loadedGeneticCodes: Record<string, number> | undefined;
697
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
698
+ statusMessage: string | undefined;
699
+ statusProgress: number | undefined;
700
+ statusSource: string | undefined;
701
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
702
+ } & {
703
+ getConf(arg: string): any;
704
+ } & {
705
+ readonly name: string;
706
+ readonly aliases: string[];
707
+ readonly displayName: string;
708
+ readonly refNameColors: string[];
709
+ } & {
710
+ readonly allAliases: string[];
711
+ hasName(name: string): boolean;
712
+ } & {
713
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
714
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
715
+ } & {
716
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
717
+ regions: import("@jbrowse/core/util").Region[];
718
+ cytobands: import("@jbrowse/core/util").Feature[];
719
+ geneticCodes: Record<string, number>;
720
+ }): void;
721
+ setError(e: unknown): void;
722
+ setLoadingP(p?: Promise<void>): void;
723
+ loadPre(): Promise<void>;
724
+ } & {
725
+ load(): Promise<void>;
726
+ } & {
727
+ afterAttach(): void;
728
+ } & {
729
+ readonly initialized: boolean;
730
+ readonly allRefNames: string[] | undefined;
731
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
732
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
733
+ } & {
734
+ readonly refNames: string[] | undefined;
735
+ } & {
736
+ readonly refNameToIndex: Map<string, number> | undefined;
737
+ } & {
738
+ getCanonicalRefName(refName: string): string | undefined;
739
+ getRefNameColor(refName: string): string | undefined;
740
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
741
+ getGeneticCodeId(refName: string): number;
742
+ getSeqAdapterRefName(canonicalRefName: string): string;
743
+ } & {
744
+ getCanonicalRefName2(refName: string): string;
745
+ isValidRefName(refName: string): boolean;
746
+ } & {
747
+ getRefNamePosition(refName: string): number | undefined;
748
+ getAliasesForRefName(refName: string): string[];
749
+ getRefNameMapForAdapter(adapterConf: {
750
+ [x: string]: unknown;
751
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
752
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
753
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
754
+ }, {
755
+ unrecognizedReports: {
756
+ report(session: unknown, name: string, handlerCount: number, fire: () => unknown): void;
757
+ reportFor(session: unknown, name: string): {
758
+ handled: boolean;
759
+ claim?: Promise<void>;
760
+ } | undefined;
761
+ };
762
+ } & {
763
+ readonly assemblyNameMap: Record<string, import("@jbrowse/core/assemblyManager/assembly").Assembly>;
764
+ } & {
765
+ getCanonicalAssemblyName(asmName: string): string | undefined;
766
+ getDisplayName(asmName: string): string;
767
+ get(asmName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
768
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
769
+ }> & {
770
+ error: unknown;
771
+ loadingP: Promise<void> | undefined;
772
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
773
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
774
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
775
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
776
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
777
+ loadedGeneticCodes: Record<string, number> | undefined;
778
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
779
+ statusMessage: string | undefined;
780
+ statusProgress: number | undefined;
781
+ statusSource: string | undefined;
782
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
783
+ } & {
784
+ getConf(arg: string): any;
785
+ } & {
786
+ readonly name: string;
787
+ readonly aliases: string[];
788
+ readonly displayName: string;
789
+ readonly refNameColors: string[];
790
+ } & {
791
+ readonly allAliases: string[];
792
+ hasName(name: string): boolean;
793
+ } & {
794
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
795
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
796
+ } & {
797
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
798
+ regions: import("@jbrowse/core/util").Region[];
799
+ cytobands: import("@jbrowse/core/util").Feature[];
800
+ geneticCodes: Record<string, number>;
801
+ }): void;
802
+ setError(e: unknown): void;
803
+ setLoadingP(p?: Promise<void>): void;
804
+ loadPre(): Promise<void>;
805
+ } & {
806
+ load(): Promise<void>;
807
+ } & {
808
+ afterAttach(): void;
809
+ } & {
810
+ readonly initialized: boolean;
811
+ readonly allRefNames: string[] | undefined;
812
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
813
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
814
+ } & {
815
+ readonly refNames: string[] | undefined;
816
+ } & {
817
+ readonly refNameToIndex: Map<string, number> | undefined;
818
+ } & {
819
+ getCanonicalRefName(refName: string): string | undefined;
820
+ getRefNameColor(refName: string): string | undefined;
821
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
822
+ getGeneticCodeId(refName: string): number;
823
+ getSeqAdapterRefName(canonicalRefName: string): string;
824
+ } & {
825
+ getCanonicalRefName2(refName: string): string;
826
+ isValidRefName(refName: string): boolean;
827
+ } & {
828
+ getRefNamePosition(refName: string): number | undefined;
829
+ getAliasesForRefName(refName: string): string[];
830
+ getRefNameMapForAdapter(adapterConf: {
831
+ [x: string]: unknown;
832
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
833
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
834
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
835
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
836
+ }, {
837
+ error: unknown;
838
+ loadingP: Promise<void> | undefined;
839
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
840
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
841
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
842
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
843
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
844
+ loadedGeneticCodes: Record<string, number> | undefined;
845
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
846
+ statusMessage: string | undefined;
847
+ statusProgress: number | undefined;
848
+ statusSource: string | undefined;
849
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
850
+ } & {
851
+ getConf(arg: string): any;
852
+ } & {
853
+ readonly name: string;
854
+ readonly aliases: string[];
855
+ readonly displayName: string;
856
+ readonly refNameColors: string[];
857
+ } & {
858
+ readonly allAliases: string[];
859
+ hasName(name: string): boolean;
860
+ } & {
861
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
862
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
863
+ } & {
864
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
865
+ regions: import("@jbrowse/core/util").Region[];
866
+ cytobands: import("@jbrowse/core/util").Feature[];
867
+ geneticCodes: Record<string, number>;
868
+ }): void;
869
+ setError(e: unknown): void;
870
+ setLoadingP(p?: Promise<void>): void;
871
+ loadPre(): Promise<void>;
872
+ } & {
873
+ load(): Promise<void>;
874
+ } & {
875
+ afterAttach(): void;
876
+ } & {
877
+ readonly initialized: boolean;
878
+ readonly allRefNames: string[] | undefined;
879
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
880
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
881
+ } & {
882
+ readonly refNames: string[] | undefined;
883
+ } & {
884
+ readonly refNameToIndex: Map<string, number> | undefined;
885
+ } & {
886
+ getCanonicalRefName(refName: string): string | undefined;
887
+ getRefNameColor(refName: string): string | undefined;
888
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
889
+ getGeneticCodeId(refName: string): number;
890
+ getSeqAdapterRefName(canonicalRefName: string): string;
891
+ } & {
892
+ getCanonicalRefName2(refName: string): string;
893
+ isValidRefName(refName: string): boolean;
894
+ } & {
895
+ getRefNamePosition(refName: string): number | undefined;
896
+ getAliasesForRefName(refName: string): string[];
897
+ getRefNameMapForAdapter(adapterConf: {
898
+ [x: string]: unknown;
899
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
900
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
901
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
902
+ has(asmName: string): boolean;
903
+ loadingAssembly(asmNames: string[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
904
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
905
+ }> & {
906
+ error: unknown;
907
+ loadingP: Promise<void> | undefined;
908
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
909
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
910
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
911
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
912
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
913
+ loadedGeneticCodes: Record<string, number> | undefined;
914
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
915
+ statusMessage: string | undefined;
916
+ statusProgress: number | undefined;
917
+ statusSource: string | undefined;
918
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
919
+ } & {
920
+ getConf(arg: string): any;
921
+ } & {
922
+ readonly name: string;
923
+ readonly aliases: string[];
924
+ readonly displayName: string;
925
+ readonly refNameColors: string[];
926
+ } & {
927
+ readonly allAliases: string[];
928
+ hasName(name: string): boolean;
929
+ } & {
930
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
931
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
932
+ } & {
933
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
934
+ regions: import("@jbrowse/core/util").Region[];
935
+ cytobands: import("@jbrowse/core/util").Feature[];
936
+ geneticCodes: Record<string, number>;
937
+ }): void;
938
+ setError(e: unknown): void;
939
+ setLoadingP(p?: Promise<void>): void;
940
+ loadPre(): Promise<void>;
941
+ } & {
942
+ load(): Promise<void>;
943
+ } & {
944
+ afterAttach(): void;
945
+ } & {
946
+ readonly initialized: boolean;
947
+ readonly allRefNames: string[] | undefined;
948
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
949
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
950
+ } & {
951
+ readonly refNames: string[] | undefined;
952
+ } & {
953
+ readonly refNameToIndex: Map<string, number> | undefined;
954
+ } & {
955
+ getCanonicalRefName(refName: string): string | undefined;
956
+ getRefNameColor(refName: string): string | undefined;
957
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
958
+ getGeneticCodeId(refName: string): number;
959
+ getSeqAdapterRefName(canonicalRefName: string): string;
960
+ } & {
961
+ getCanonicalRefName2(refName: string): string;
962
+ isValidRefName(refName: string): boolean;
963
+ } & {
964
+ getRefNamePosition(refName: string): number | undefined;
965
+ getAliasesForRefName(refName: string): string[];
966
+ getRefNameMapForAdapter(adapterConf: {
967
+ [x: string]: unknown;
968
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
969
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
970
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
971
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
972
+ }, {
973
+ error: unknown;
974
+ loadingP: Promise<void> | undefined;
975
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
976
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
977
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
978
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
979
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
980
+ loadedGeneticCodes: Record<string, number> | undefined;
981
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
982
+ statusMessage: string | undefined;
983
+ statusProgress: number | undefined;
984
+ statusSource: string | undefined;
985
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
986
+ } & {
987
+ getConf(arg: string): any;
988
+ } & {
989
+ readonly name: string;
990
+ readonly aliases: string[];
991
+ readonly displayName: string;
992
+ readonly refNameColors: string[];
993
+ } & {
994
+ readonly allAliases: string[];
995
+ hasName(name: string): boolean;
996
+ } & {
997
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
998
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
999
+ } & {
1000
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1001
+ regions: import("@jbrowse/core/util").Region[];
1002
+ cytobands: import("@jbrowse/core/util").Feature[];
1003
+ geneticCodes: Record<string, number>;
1004
+ }): void;
1005
+ setError(e: unknown): void;
1006
+ setLoadingP(p?: Promise<void>): void;
1007
+ loadPre(): Promise<void>;
1008
+ } & {
1009
+ load(): Promise<void>;
1010
+ } & {
1011
+ afterAttach(): void;
1012
+ } & {
1013
+ readonly initialized: boolean;
1014
+ readonly allRefNames: string[] | undefined;
1015
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1016
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1017
+ } & {
1018
+ readonly refNames: string[] | undefined;
1019
+ } & {
1020
+ readonly refNameToIndex: Map<string, number> | undefined;
1021
+ } & {
1022
+ getCanonicalRefName(refName: string): string | undefined;
1023
+ getRefNameColor(refName: string): string | undefined;
1024
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1025
+ getGeneticCodeId(refName: string): number;
1026
+ getSeqAdapterRefName(canonicalRefName: string): string;
1027
+ } & {
1028
+ getCanonicalRefName2(refName: string): string;
1029
+ isValidRefName(refName: string): boolean;
1030
+ } & {
1031
+ getRefNamePosition(refName: string): number | undefined;
1032
+ getAliasesForRefName(refName: string): string[];
1033
+ getRefNameMapForAdapter(adapterConf: {
1034
+ [x: string]: unknown;
1035
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1036
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1037
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1038
+ readonly assemblyNamesList: string[];
1039
+ readonly confByName: Map<string, import("@jbrowse/core/configuration").AnyConfigurationModel>;
1040
+ readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
1041
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1042
+ } & {
1043
+ settleAssemblyResolution(assemblyName: string): Promise<void>;
1044
+ } & {
1045
+ waitForAssembly(assemblyName: string): Promise<(import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1046
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1047
+ }> & {
1048
+ error: unknown;
1049
+ loadingP: Promise<void> | undefined;
1050
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1051
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1052
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1053
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1054
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1055
+ loadedGeneticCodes: Record<string, number> | undefined;
1056
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1057
+ statusMessage: string | undefined;
1058
+ statusProgress: number | undefined;
1059
+ statusSource: string | undefined;
1060
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1061
+ } & {
1062
+ getConf(arg: string): any;
1063
+ } & {
1064
+ readonly name: string;
1065
+ readonly aliases: string[];
1066
+ readonly displayName: string;
1067
+ readonly refNameColors: string[];
1068
+ } & {
1069
+ readonly allAliases: string[];
1070
+ hasName(name: string): boolean;
1071
+ } & {
1072
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1073
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1074
+ } & {
1075
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1076
+ regions: import("@jbrowse/core/util").Region[];
1077
+ cytobands: import("@jbrowse/core/util").Feature[];
1078
+ geneticCodes: Record<string, number>;
1079
+ }): void;
1080
+ setError(e: unknown): void;
1081
+ setLoadingP(p?: Promise<void>): void;
1082
+ loadPre(): Promise<void>;
1083
+ } & {
1084
+ load(): Promise<void>;
1085
+ } & {
1086
+ afterAttach(): void;
1087
+ } & {
1088
+ readonly initialized: boolean;
1089
+ readonly allRefNames: string[] | undefined;
1090
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1091
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1092
+ } & {
1093
+ readonly refNames: string[] | undefined;
1094
+ } & {
1095
+ readonly refNameToIndex: Map<string, number> | undefined;
1096
+ } & {
1097
+ getCanonicalRefName(refName: string): string | undefined;
1098
+ getRefNameColor(refName: string): string | undefined;
1099
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1100
+ getGeneticCodeId(refName: string): number;
1101
+ getSeqAdapterRefName(canonicalRefName: string): string;
1102
+ } & {
1103
+ getCanonicalRefName2(refName: string): string;
1104
+ isValidRefName(refName: string): boolean;
1105
+ } & {
1106
+ getRefNamePosition(refName: string): number | undefined;
1107
+ getAliasesForRefName(refName: string): string[];
1108
+ getRefNameMapForAdapter(adapterConf: {
1109
+ [x: string]: unknown;
1110
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1111
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1112
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1113
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1114
+ }, {
1115
+ error: unknown;
1116
+ loadingP: Promise<void> | undefined;
1117
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1118
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1119
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1120
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1121
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1122
+ loadedGeneticCodes: Record<string, number> | undefined;
1123
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1124
+ statusMessage: string | undefined;
1125
+ statusProgress: number | undefined;
1126
+ statusSource: string | undefined;
1127
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1128
+ } & {
1129
+ getConf(arg: string): any;
1130
+ } & {
1131
+ readonly name: string;
1132
+ readonly aliases: string[];
1133
+ readonly displayName: string;
1134
+ readonly refNameColors: string[];
1135
+ } & {
1136
+ readonly allAliases: string[];
1137
+ hasName(name: string): boolean;
1138
+ } & {
1139
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1140
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1141
+ } & {
1142
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1143
+ regions: import("@jbrowse/core/util").Region[];
1144
+ cytobands: import("@jbrowse/core/util").Feature[];
1145
+ geneticCodes: Record<string, number>;
1146
+ }): void;
1147
+ setError(e: unknown): void;
1148
+ setLoadingP(p?: Promise<void>): void;
1149
+ loadPre(): Promise<void>;
1150
+ } & {
1151
+ load(): Promise<void>;
1152
+ } & {
1153
+ afterAttach(): void;
1154
+ } & {
1155
+ readonly initialized: boolean;
1156
+ readonly allRefNames: string[] | undefined;
1157
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1158
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1159
+ } & {
1160
+ readonly refNames: string[] | undefined;
1161
+ } & {
1162
+ readonly refNameToIndex: Map<string, number> | undefined;
1163
+ } & {
1164
+ getCanonicalRefName(refName: string): string | undefined;
1165
+ getRefNameColor(refName: string): string | undefined;
1166
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1167
+ getGeneticCodeId(refName: string): number;
1168
+ getSeqAdapterRefName(canonicalRefName: string): string;
1169
+ } & {
1170
+ getCanonicalRefName2(refName: string): string;
1171
+ isValidRefName(refName: string): boolean;
1172
+ } & {
1173
+ getRefNamePosition(refName: string): number | undefined;
1174
+ getAliasesForRefName(refName: string): string[];
1175
+ getRefNameMapForAdapter(adapterConf: {
1176
+ [x: string]: unknown;
1177
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1178
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1179
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
1180
+ requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1181
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1182
+ }> & {
1183
+ error: unknown;
1184
+ loadingP: Promise<void> | undefined;
1185
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1186
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1187
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1188
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1189
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1190
+ loadedGeneticCodes: Record<string, number> | undefined;
1191
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1192
+ statusMessage: string | undefined;
1193
+ statusProgress: number | undefined;
1194
+ statusSource: string | undefined;
1195
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1196
+ } & {
1197
+ getConf(arg: string): any;
1198
+ } & {
1199
+ readonly name: string;
1200
+ readonly aliases: string[];
1201
+ readonly displayName: string;
1202
+ readonly refNameColors: string[];
1203
+ } & {
1204
+ readonly allAliases: string[];
1205
+ hasName(name: string): boolean;
1206
+ } & {
1207
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1208
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1209
+ } & {
1210
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1211
+ regions: import("@jbrowse/core/util").Region[];
1212
+ cytobands: import("@jbrowse/core/util").Feature[];
1213
+ geneticCodes: Record<string, number>;
1214
+ }): void;
1215
+ setError(e: unknown): void;
1216
+ setLoadingP(p?: Promise<void>): void;
1217
+ loadPre(): Promise<void>;
1218
+ } & {
1219
+ load(): Promise<void>;
1220
+ } & {
1221
+ afterAttach(): void;
1222
+ } & {
1223
+ readonly initialized: boolean;
1224
+ readonly allRefNames: string[] | undefined;
1225
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1226
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1227
+ } & {
1228
+ readonly refNames: string[] | undefined;
1229
+ } & {
1230
+ readonly refNameToIndex: Map<string, number> | undefined;
1231
+ } & {
1232
+ getCanonicalRefName(refName: string): string | undefined;
1233
+ getRefNameColor(refName: string): string | undefined;
1234
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1235
+ getGeneticCodeId(refName: string): number;
1236
+ getSeqAdapterRefName(canonicalRefName: string): string;
1237
+ } & {
1238
+ getCanonicalRefName2(refName: string): string;
1239
+ isValidRefName(refName: string): boolean;
1240
+ } & {
1241
+ getRefNamePosition(refName: string): number | undefined;
1242
+ getAliasesForRefName(refName: string): string[];
1243
+ getRefNameMapForAdapter(adapterConf: {
1244
+ [x: string]: unknown;
1245
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1246
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1247
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1248
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1249
+ }, {
1250
+ error: unknown;
1251
+ loadingP: Promise<void> | undefined;
1252
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1253
+ regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1254
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1255
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1256
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1257
+ loadedGeneticCodes: Record<string, number> | undefined;
1258
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1259
+ statusMessage: string | undefined;
1260
+ statusProgress: number | undefined;
1261
+ statusSource: string | undefined;
1262
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1263
+ } & {
1264
+ getConf(arg: string): any;
1265
+ } & {
1266
+ readonly name: string;
1267
+ readonly aliases: string[];
1268
+ readonly displayName: string;
1269
+ readonly refNameColors: string[];
1270
+ } & {
1271
+ readonly allAliases: string[];
1272
+ hasName(name: string): boolean;
1273
+ } & {
1274
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1275
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1276
+ } & {
1277
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1278
+ regions: import("@jbrowse/core/util").Region[];
1279
+ cytobands: import("@jbrowse/core/util").Feature[];
1280
+ geneticCodes: Record<string, number>;
1281
+ }): void;
1282
+ setError(e: unknown): void;
1283
+ setLoadingP(p?: Promise<void>): void;
1284
+ loadPre(): Promise<void>;
1285
+ } & {
1286
+ load(): Promise<void>;
1287
+ } & {
1288
+ afterAttach(): void;
1289
+ } & {
1290
+ readonly initialized: boolean;
1291
+ readonly allRefNames: string[] | undefined;
1292
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1293
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1294
+ } & {
1295
+ readonly refNames: string[] | undefined;
1296
+ } & {
1297
+ readonly refNameToIndex: Map<string, number> | undefined;
1298
+ } & {
1299
+ getCanonicalRefName(refName: string): string | undefined;
1300
+ getRefNameColor(refName: string): string | undefined;
1301
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1302
+ getGeneticCodeId(refName: string): number;
1303
+ getSeqAdapterRefName(canonicalRefName: string): string;
1304
+ } & {
1305
+ getCanonicalRefName2(refName: string): string;
1306
+ isValidRefName(refName: string): boolean;
1307
+ } & {
1308
+ getRefNamePosition(refName: string): number | undefined;
1309
+ getAliasesForRefName(refName: string): string[];
1310
+ getRefNameMapForAdapter(adapterConf: {
1311
+ [x: string]: unknown;
1312
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1313
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1314
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
1315
+ getRefNameMapForAdapter(adapterConf: {
1316
+ [x: string]: unknown;
1317
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1318
+ isValidRefName(refName: string, assemblyName: string): boolean;
1319
+ } & {
1320
+ afterAttach(): void;
1321
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1322
+ addAssembly(configuration: any): void;
1323
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
1324
+ }, {
1325
+ rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1326
+ adminMode: boolean;
1327
+ error: unknown;
1328
+ textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1329
+ pluginManager: PluginManager;
1330
+ } & {
1331
+ setError(error: unknown): void;
1332
+ setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
1333
+ setDefaultSession(): void;
1334
+ setSessionPath(path: string): void;
1335
+ renameCurrentSession(newName: string): void;
1336
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1337
+ } & {
1338
+ readonly jbrowse: any;
1339
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1340
+ readonly configuration: import("@jbrowse/core/configuration").ConfigNodeProps<any> & import("@jbrowse/core/configuration").ConfigNodeActions & import("@jbrowse/core/configuration").ConfigNodeBrand<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
1341
+ readonly adminMode: boolean;
1342
+ readonly textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1343
+ } & {
1344
+ readonly assemblies: import("@jbrowse/core/assemblyManager").BaseAssemblyConfigModel[];
1345
+ readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType | undefined;
1346
+ readonly DialogProps: Record<string, unknown> | undefined;
1347
+ } & {
1348
+ getPreferenceDefault(key: string): unknown;
1349
+ getPreference(key: string): unknown;
1350
+ getPreferenceChanges(): import("@jbrowse/core/util").TrackConfigChange[];
1351
+ } & {
1352
+ readonly animationMode: import("@jbrowse/core/util").AnimationMode;
1353
+ readonly scrollZoom: boolean;
1354
+ readonly numberGrouping: boolean;
1355
+ } & {
1356
+ afterAttach(): void;
1357
+ setSelection(thing: unknown): void;
1358
+ clearSelection(): void;
1359
+ setHovered(thing: unknown): void;
1360
+ setHighlightsVisible(arg: boolean): 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;
1366
+ setPreferenceOverride(key: string, value: unknown): void;
1367
+ clearPreferenceOverrides(): void;
1368
+ clearPreferenceOverride(key: string): void;
1369
+ setScrollZoom(flag: boolean): void;
1370
+ setName(str: string): void;
1371
+ setFocusedViewId(viewId: string | undefined): void;
1372
+ removeActiveDialog(): void;
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;
1375
+ } & {
1376
+ snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1377
+ errorDialog: import("@jbrowse/core/ui/SnackbarModel").ErrorDialogState | undefined;
1378
+ } & {
1379
+ readonly snackbarMessageSet: Map<string, import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1380
+ } & {
1381
+ notify(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction | import("@jbrowse/core/util").SnackAction[]): void;
1382
+ notifyError(errorMessage: string, error?: unknown, extra?: unknown, action?: import("@jbrowse/core/util").SnackAction): void;
1383
+ setErrorDialog(state: import("@jbrowse/core/ui/SnackbarModel").ErrorDialogState | undefined): void;
1384
+ pushSnackbarMessage(message: string, level?: import("@jbrowse/core/util").NotificationLevel, actions?: import("@jbrowse/core/util").SnackAction[]): void;
1385
+ popSnackbarMessage(): import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage | undefined;
1386
+ removeSnackbarMessage(message: string): void;
1387
+ } & {
1388
+ afterAttach(): void;
1389
+ } & {
1390
+ sessionThemeMode: PaletteMode | undefined;
1391
+ } & {
1392
+ /**
1393
+ * #getter
1394
+ * Serializable theme description (the canonical `themeOptions` contract
1395
+ * shared with the app-core/web sessions). This is what crosses the RPC
1396
+ * worker boundary — e.g. the canvas display reads
1397
+ * `getSession(self).themeOptions` in its rpcProps so worker-baked colors
1398
+ * (CDS frames, stroke fallback) honor the config `theme` slot.
1399
+ */
1400
+ readonly themeOptions: SerializableThemeArgs;
1401
+ /**
1402
+ * #getter
1403
+ * Every color JBrowse renders, resolved to plain strings and free of any UI
1404
+ * toolkit. This is what rendering reads. See the canonical
1405
+ * `ThemeManagerSessionMixin` getter of the same name.
1406
+ */
1407
+ readonly palette: import("@jbrowse/core/ui/palette").JBrowsePalette;
1408
+ /**
1409
+ * #getter
1410
+ * The palette plus the sizing tokens `makeStyles` reads. See the
1411
+ * canonical `ThemeManagerSessionMixin` getter of the same name.
1412
+ */
1413
+ readonly styleTheme: import("@jbrowse/core/ui/styleTheme").JBrowseStyleTheme;
1414
+ /**
1415
+ * #getter
1416
+ * Resolved MUI theme, mirroring the product's ThemeProvider. Lets
1417
+ * headless/RPC consumers derive theme-dependent state without a mounted
1418
+ * component. Shares its colors with `palette` by construction.
1419
+ */
1420
+ readonly theme: import("@mui/material").Theme;
1421
+ /**
1422
+ * #method
1423
+ * Raw `ThemeOptions` for the active theme, which every view's SVG export
1424
+ * threads into each display's `renderSvg` as a `configTheme` and rebuilds
1425
+ * outside React. The config slot is the whole answer here because it is
1426
+ * the whole of an embedded product's theming: no picker, no `allThemes`,
1427
+ * and it is what `setThemeMode` writes and `palette` resolves from. `name`
1428
+ * is accepted and ignored — the app session's counterpart looks a named
1429
+ * preset up in `allThemes()`.
1430
+ */
1431
+ getActiveThemeOptions(_name?: string): import("@mui/material").ThemeOptions | undefined;
1432
+ } & {
1433
+ /**
1434
+ * #action
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.
1441
+ *
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.
1446
+ */
1447
+ setThemeMode(mode: PaletteMode): void;
1448
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;