@jbrowse/embedded-core 4.3.0 → 5.0.0-beta.2

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 +3329 -0
  2. package/esm/EmbeddedSessionMixin.js +54 -0
  3. package/esm/EmbeddedSessionThemeMixin.d.ts +1725 -0
  4. package/esm/EmbeddedSessionThemeMixin.js +104 -0
  5. package/esm/createEmbeddedRootModel.d.ts +1910 -0
  6. package/esm/createEmbeddedRootModel.js +117 -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 +10 -14
  11. package/esm/ui/VersionAboutDialog.d.ts +1 -1
  12. package/esm/ui/VersionAboutDialog.js +3 -3
  13. package/esm/ui/ViewTitle.d.ts +1 -1
  14. package/esm/ui/ViewTitle.js +26 -8
  15. package/package.json +12 -14
  16. package/esm/ui/ModalWidget.d.ts +0 -5
  17. package/esm/ui/ModalWidget.js +0 -32
  18. package/esm/ui/ViewMenu.d.ts +0 -8
  19. package/esm/ui/ViewMenu.js +0 -8
package/esm/EmbeddedSessionThemeMixin.d.ts ADDED
@@ -0,0 +1,1725 @@
1
+ import type PluginManager from '@jbrowse/core/PluginManager';
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+ import type { SerializableThemeArgs } from '@jbrowse/core/ui';
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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 switching, so the active theme is always `default`; the config
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+ * `theme` slot still applies via `configTheme`.
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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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+ highlightsVisible: 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]>;
16
+ }, 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]>;
26
+ assemblyManager: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
27
+ 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>>;
29
+ }, {
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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>>;
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+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
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+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
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+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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+ loadedGeneticCodes: Record<string, number> | undefined;
38
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
39
+ statusMessage: string | undefined;
40
+ statusProgress: number | undefined;
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+ statusSource: string | undefined;
42
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
43
+ } & {
44
+ getConf(arg: string): any;
45
+ } & {
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+ readonly name: string;
47
+ readonly aliases: string[];
48
+ readonly displayName: string;
49
+ readonly refNameColors: string[];
50
+ } & {
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+ readonly allAliases: string[];
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+ hasName(name: string): boolean;
53
+ } & {
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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;
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+ } & {
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+ 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>;
61
+ }): void;
62
+ setError(e: unknown): void;
63
+ setLoadingP(p?: Promise<void>): void;
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+ loadPre(): Promise<void>;
65
+ } & {
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+ load(): Promise<void>;
67
+ } & {
68
+ afterAttach(): void;
69
+ } & {
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+ readonly initialized: boolean;
71
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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+ readonly allRefNames: string[] | undefined;
73
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
74
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
75
+ } & {
76
+ readonly refNames: string[] | undefined;
77
+ } & {
78
+ readonly refNameToIndex: Map<string, number> | undefined;
79
+ } & {
80
+ getCanonicalRefName(refName: string): string | undefined;
81
+ getRefNameColor(refName: string): string | undefined;
82
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
83
+ getGeneticCodeId(refName: string): number;
84
+ getSeqAdapterRefName(canonicalRefName: string): string;
85
+ } & {
86
+ getCanonicalRefName2(refName: string): string;
87
+ isValidRefName(refName: string): boolean;
88
+ } & {
89
+ getAliasesForRefName(refName: string): string[];
90
+ getRefNameMapForAdapter(adapterConf: {
91
+ [x: string]: unknown;
92
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
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+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
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+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
95
+ }, {
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+ unrecognizedReports: {
97
+ report(session: unknown, name: string, handlerCount: number, fire: () => unknown): void;
98
+ reportFor(session: unknown, name: string): {
99
+ handled: boolean;
100
+ claim?: Promise<void>;
101
+ } | undefined;
102
+ };
103
+ } & {
104
+ readonly assemblyNameMap: Record<string, import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
105
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
106
+ }> & {
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;
117
+ statusProgress: number | undefined;
118
+ statusSource: string | undefined;
119
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
120
+ } & {
121
+ getConf(arg: string): any;
122
+ } & {
123
+ readonly name: string;
124
+ readonly aliases: string[];
125
+ readonly displayName: string;
126
+ readonly refNameColors: string[];
127
+ } & {
128
+ readonly allAliases: string[];
129
+ hasName(name: string): boolean;
130
+ } & {
131
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
132
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
133
+ } & {
134
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
135
+ regions: import("@jbrowse/core/util").Region[];
136
+ cytobands: import("@jbrowse/core/util").Feature[];
137
+ geneticCodes: Record<string, number>;
138
+ }): void;
139
+ setError(e: unknown): void;
140
+ setLoadingP(p?: Promise<void>): void;
141
+ loadPre(): Promise<void>;
142
+ } & {
143
+ load(): Promise<void>;
144
+ } & {
145
+ afterAttach(): void;
146
+ } & {
147
+ 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<{
172
+ 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>>>;
239
+ } & {
240
+ getCanonicalAssemblyName(asmName: string): string | undefined;
241
+ getDisplayName(asmName: string): string;
242
+ get(asmName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
243
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
244
+ }> & {
245
+ error: unknown;
246
+ loadingP: Promise<void> | undefined;
247
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
248
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
249
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
250
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
251
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
252
+ loadedGeneticCodes: Record<string, number> | undefined;
253
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
254
+ statusMessage: string | undefined;
255
+ statusProgress: number | undefined;
256
+ statusSource: string | undefined;
257
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
258
+ } & {
259
+ getConf(arg: string): any;
260
+ } & {
261
+ readonly name: string;
262
+ readonly aliases: string[];
263
+ readonly displayName: string;
264
+ readonly refNameColors: string[];
265
+ } & {
266
+ readonly allAliases: string[];
267
+ hasName(name: string): boolean;
268
+ } & {
269
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
270
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
271
+ } & {
272
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
273
+ regions: import("@jbrowse/core/util").Region[];
274
+ cytobands: import("@jbrowse/core/util").Feature[];
275
+ geneticCodes: Record<string, number>;
276
+ }): void;
277
+ setError(e: unknown): void;
278
+ setLoadingP(p?: Promise<void>): void;
279
+ loadPre(): Promise<void>;
280
+ } & {
281
+ load(): Promise<void>;
282
+ } & {
283
+ afterAttach(): void;
284
+ } & {
285
+ readonly initialized: boolean;
286
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
287
+ readonly allRefNames: string[] | undefined;
288
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
289
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
290
+ } & {
291
+ readonly refNames: string[] | undefined;
292
+ } & {
293
+ readonly refNameToIndex: Map<string, number> | undefined;
294
+ } & {
295
+ getCanonicalRefName(refName: string): string | undefined;
296
+ getRefNameColor(refName: string): string | undefined;
297
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
298
+ getGeneticCodeId(refName: string): number;
299
+ getSeqAdapterRefName(canonicalRefName: string): string;
300
+ } & {
301
+ getCanonicalRefName2(refName: string): string;
302
+ isValidRefName(refName: string): boolean;
303
+ } & {
304
+ getAliasesForRefName(refName: string): string[];
305
+ getRefNameMapForAdapter(adapterConf: {
306
+ [x: string]: unknown;
307
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
308
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
309
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
310
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
311
+ }, {
312
+ error: unknown;
313
+ loadingP: Promise<void> | undefined;
314
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
315
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
316
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
317
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
318
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
319
+ loadedGeneticCodes: Record<string, number> | undefined;
320
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
321
+ statusMessage: string | undefined;
322
+ statusProgress: number | undefined;
323
+ statusSource: string | undefined;
324
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
325
+ } & {
326
+ getConf(arg: string): any;
327
+ } & {
328
+ readonly name: string;
329
+ readonly aliases: string[];
330
+ readonly displayName: string;
331
+ readonly refNameColors: string[];
332
+ } & {
333
+ readonly allAliases: string[];
334
+ hasName(name: string): boolean;
335
+ } & {
336
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
337
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
338
+ } & {
339
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
340
+ regions: import("@jbrowse/core/util").Region[];
341
+ cytobands: import("@jbrowse/core/util").Feature[];
342
+ geneticCodes: Record<string, number>;
343
+ }): void;
344
+ setError(e: unknown): void;
345
+ setLoadingP(p?: Promise<void>): void;
346
+ loadPre(): Promise<void>;
347
+ } & {
348
+ load(): Promise<void>;
349
+ } & {
350
+ afterAttach(): void;
351
+ } & {
352
+ readonly initialized: boolean;
353
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
354
+ readonly allRefNames: string[] | undefined;
355
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
356
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
357
+ } & {
358
+ readonly refNames: string[] | undefined;
359
+ } & {
360
+ readonly refNameToIndex: Map<string, number> | undefined;
361
+ } & {
362
+ getCanonicalRefName(refName: string): string | undefined;
363
+ getRefNameColor(refName: string): string | undefined;
364
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
365
+ getGeneticCodeId(refName: string): number;
366
+ getSeqAdapterRefName(canonicalRefName: string): string;
367
+ } & {
368
+ getCanonicalRefName2(refName: string): string;
369
+ isValidRefName(refName: string): boolean;
370
+ } & {
371
+ getAliasesForRefName(refName: string): string[];
372
+ getRefNameMapForAdapter(adapterConf: {
373
+ [x: string]: unknown;
374
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
375
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
376
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
377
+ has(asmName: string): boolean;
378
+ loadingAssembly(asmNames: string[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
379
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
380
+ }> & {
381
+ error: unknown;
382
+ loadingP: Promise<void> | undefined;
383
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
384
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
385
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
386
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
387
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
388
+ loadedGeneticCodes: Record<string, number> | undefined;
389
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
390
+ statusMessage: string | undefined;
391
+ statusProgress: number | undefined;
392
+ statusSource: string | undefined;
393
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
394
+ } & {
395
+ getConf(arg: string): any;
396
+ } & {
397
+ readonly name: string;
398
+ readonly aliases: string[];
399
+ readonly displayName: string;
400
+ readonly refNameColors: string[];
401
+ } & {
402
+ readonly allAliases: string[];
403
+ hasName(name: string): boolean;
404
+ } & {
405
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
406
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
407
+ } & {
408
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
409
+ regions: import("@jbrowse/core/util").Region[];
410
+ cytobands: import("@jbrowse/core/util").Feature[];
411
+ geneticCodes: Record<string, number>;
412
+ }): void;
413
+ setError(e: unknown): void;
414
+ setLoadingP(p?: Promise<void>): void;
415
+ loadPre(): Promise<void>;
416
+ } & {
417
+ load(): Promise<void>;
418
+ } & {
419
+ afterAttach(): void;
420
+ } & {
421
+ readonly initialized: boolean;
422
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
423
+ readonly allRefNames: string[] | undefined;
424
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
425
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
426
+ } & {
427
+ readonly refNames: string[] | undefined;
428
+ } & {
429
+ readonly refNameToIndex: Map<string, number> | undefined;
430
+ } & {
431
+ getCanonicalRefName(refName: string): string | undefined;
432
+ getRefNameColor(refName: string): string | undefined;
433
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
434
+ getGeneticCodeId(refName: string): number;
435
+ getSeqAdapterRefName(canonicalRefName: string): string;
436
+ } & {
437
+ getCanonicalRefName2(refName: string): string;
438
+ isValidRefName(refName: string): boolean;
439
+ } & {
440
+ getAliasesForRefName(refName: string): string[];
441
+ getRefNameMapForAdapter(adapterConf: {
442
+ [x: string]: unknown;
443
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
444
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
445
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
446
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
447
+ }, {
448
+ error: unknown;
449
+ loadingP: Promise<void> | undefined;
450
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
451
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
452
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
453
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
454
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
455
+ loadedGeneticCodes: Record<string, number> | undefined;
456
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
457
+ statusMessage: string | undefined;
458
+ statusProgress: number | undefined;
459
+ statusSource: string | undefined;
460
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
461
+ } & {
462
+ getConf(arg: string): any;
463
+ } & {
464
+ readonly name: string;
465
+ readonly aliases: string[];
466
+ readonly displayName: string;
467
+ readonly refNameColors: string[];
468
+ } & {
469
+ readonly allAliases: string[];
470
+ hasName(name: string): boolean;
471
+ } & {
472
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
473
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
474
+ } & {
475
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
476
+ regions: import("@jbrowse/core/util").Region[];
477
+ cytobands: import("@jbrowse/core/util").Feature[];
478
+ geneticCodes: Record<string, number>;
479
+ }): void;
480
+ setError(e: unknown): void;
481
+ setLoadingP(p?: Promise<void>): void;
482
+ loadPre(): Promise<void>;
483
+ } & {
484
+ load(): Promise<void>;
485
+ } & {
486
+ afterAttach(): void;
487
+ } & {
488
+ readonly initialized: boolean;
489
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
490
+ readonly allRefNames: string[] | undefined;
491
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
492
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
493
+ } & {
494
+ readonly refNames: string[] | undefined;
495
+ } & {
496
+ readonly refNameToIndex: Map<string, number> | undefined;
497
+ } & {
498
+ getCanonicalRefName(refName: string): string | undefined;
499
+ getRefNameColor(refName: string): string | undefined;
500
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
501
+ getGeneticCodeId(refName: string): number;
502
+ getSeqAdapterRefName(canonicalRefName: string): string;
503
+ } & {
504
+ getCanonicalRefName2(refName: string): string;
505
+ isValidRefName(refName: string): boolean;
506
+ } & {
507
+ getAliasesForRefName(refName: string): string[];
508
+ getRefNameMapForAdapter(adapterConf: {
509
+ [x: string]: unknown;
510
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
511
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
512
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
513
+ 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>)[];
519
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
520
+ } & {
521
+ settleAssemblyResolution(assemblyName: string): Promise<void>;
522
+ } & {
523
+ waitForAssembly(assemblyName: string): Promise<(import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
524
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
525
+ }> & {
526
+ error: unknown;
527
+ loadingP: Promise<void> | undefined;
528
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
529
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
530
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
531
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
532
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
533
+ loadedGeneticCodes: Record<string, number> | undefined;
534
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
535
+ statusMessage: string | undefined;
536
+ statusProgress: number | undefined;
537
+ statusSource: string | undefined;
538
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
539
+ } & {
540
+ getConf(arg: string): any;
541
+ } & {
542
+ readonly name: string;
543
+ readonly aliases: string[];
544
+ readonly displayName: string;
545
+ readonly refNameColors: string[];
546
+ } & {
547
+ readonly allAliases: string[];
548
+ hasName(name: string): boolean;
549
+ } & {
550
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
551
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
552
+ } & {
553
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
554
+ regions: import("@jbrowse/core/util").Region[];
555
+ cytobands: import("@jbrowse/core/util").Feature[];
556
+ geneticCodes: Record<string, number>;
557
+ }): void;
558
+ setError(e: unknown): void;
559
+ setLoadingP(p?: Promise<void>): void;
560
+ loadPre(): Promise<void>;
561
+ } & {
562
+ load(): Promise<void>;
563
+ } & {
564
+ afterAttach(): void;
565
+ } & {
566
+ readonly initialized: boolean;
567
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
568
+ readonly allRefNames: string[] | undefined;
569
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
570
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
571
+ } & {
572
+ readonly refNames: string[] | undefined;
573
+ } & {
574
+ readonly refNameToIndex: Map<string, number> | undefined;
575
+ } & {
576
+ getCanonicalRefName(refName: string): string | undefined;
577
+ getRefNameColor(refName: string): string | undefined;
578
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
579
+ getGeneticCodeId(refName: string): number;
580
+ getSeqAdapterRefName(canonicalRefName: string): string;
581
+ } & {
582
+ getCanonicalRefName2(refName: string): string;
583
+ isValidRefName(refName: string): boolean;
584
+ } & {
585
+ getAliasesForRefName(refName: string): string[];
586
+ getRefNameMapForAdapter(adapterConf: {
587
+ [x: string]: unknown;
588
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
589
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
590
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
591
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
592
+ }, {
593
+ error: unknown;
594
+ loadingP: Promise<void> | undefined;
595
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
596
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
597
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
598
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
599
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
600
+ loadedGeneticCodes: Record<string, number> | undefined;
601
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
602
+ statusMessage: string | undefined;
603
+ statusProgress: number | undefined;
604
+ statusSource: string | undefined;
605
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
606
+ } & {
607
+ getConf(arg: string): any;
608
+ } & {
609
+ readonly name: string;
610
+ readonly aliases: string[];
611
+ readonly displayName: string;
612
+ readonly refNameColors: string[];
613
+ } & {
614
+ readonly allAliases: string[];
615
+ hasName(name: string): boolean;
616
+ } & {
617
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
618
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
619
+ } & {
620
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
621
+ regions: import("@jbrowse/core/util").Region[];
622
+ cytobands: import("@jbrowse/core/util").Feature[];
623
+ geneticCodes: Record<string, number>;
624
+ }): void;
625
+ setError(e: unknown): void;
626
+ setLoadingP(p?: Promise<void>): void;
627
+ loadPre(): Promise<void>;
628
+ } & {
629
+ load(): Promise<void>;
630
+ } & {
631
+ afterAttach(): void;
632
+ } & {
633
+ readonly initialized: boolean;
634
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
635
+ readonly allRefNames: string[] | undefined;
636
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
637
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
638
+ } & {
639
+ readonly refNames: string[] | undefined;
640
+ } & {
641
+ readonly refNameToIndex: Map<string, number> | undefined;
642
+ } & {
643
+ getCanonicalRefName(refName: string): string | undefined;
644
+ getRefNameColor(refName: string): string | undefined;
645
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
646
+ getGeneticCodeId(refName: string): number;
647
+ getSeqAdapterRefName(canonicalRefName: string): string;
648
+ } & {
649
+ getCanonicalRefName2(refName: string): string;
650
+ isValidRefName(refName: string): boolean;
651
+ } & {
652
+ getAliasesForRefName(refName: string): string[];
653
+ getRefNameMapForAdapter(adapterConf: {
654
+ [x: string]: unknown;
655
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
656
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
657
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
658
+ requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
659
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
660
+ }> & {
661
+ error: unknown;
662
+ loadingP: Promise<void> | undefined;
663
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
664
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
665
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
666
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
667
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
668
+ loadedGeneticCodes: Record<string, number> | undefined;
669
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
670
+ statusMessage: string | undefined;
671
+ statusProgress: number | undefined;
672
+ statusSource: string | undefined;
673
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
674
+ } & {
675
+ getConf(arg: string): any;
676
+ } & {
677
+ readonly name: string;
678
+ readonly aliases: string[];
679
+ readonly displayName: string;
680
+ readonly refNameColors: string[];
681
+ } & {
682
+ readonly allAliases: string[];
683
+ hasName(name: string): boolean;
684
+ } & {
685
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
686
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
687
+ } & {
688
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
689
+ regions: import("@jbrowse/core/util").Region[];
690
+ cytobands: import("@jbrowse/core/util").Feature[];
691
+ geneticCodes: Record<string, number>;
692
+ }): void;
693
+ setError(e: unknown): void;
694
+ setLoadingP(p?: Promise<void>): void;
695
+ loadPre(): Promise<void>;
696
+ } & {
697
+ load(): Promise<void>;
698
+ } & {
699
+ afterAttach(): void;
700
+ } & {
701
+ readonly initialized: boolean;
702
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
703
+ readonly allRefNames: string[] | undefined;
704
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
705
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
706
+ } & {
707
+ readonly refNames: string[] | undefined;
708
+ } & {
709
+ readonly refNameToIndex: Map<string, number> | undefined;
710
+ } & {
711
+ getCanonicalRefName(refName: string): string | undefined;
712
+ getRefNameColor(refName: string): string | undefined;
713
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
714
+ getGeneticCodeId(refName: string): number;
715
+ getSeqAdapterRefName(canonicalRefName: string): string;
716
+ } & {
717
+ getCanonicalRefName2(refName: string): string;
718
+ isValidRefName(refName: string): boolean;
719
+ } & {
720
+ getAliasesForRefName(refName: string): string[];
721
+ getRefNameMapForAdapter(adapterConf: {
722
+ [x: string]: unknown;
723
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
724
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
725
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
726
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
727
+ }, {
728
+ error: unknown;
729
+ loadingP: Promise<void> | undefined;
730
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
731
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
732
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
733
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
734
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
735
+ loadedGeneticCodes: Record<string, number> | undefined;
736
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
737
+ statusMessage: string | undefined;
738
+ statusProgress: number | undefined;
739
+ statusSource: string | undefined;
740
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
741
+ } & {
742
+ getConf(arg: string): any;
743
+ } & {
744
+ readonly name: string;
745
+ readonly aliases: string[];
746
+ readonly displayName: string;
747
+ readonly refNameColors: string[];
748
+ } & {
749
+ readonly allAliases: string[];
750
+ hasName(name: string): boolean;
751
+ } & {
752
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
753
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
754
+ } & {
755
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
756
+ regions: import("@jbrowse/core/util").Region[];
757
+ cytobands: import("@jbrowse/core/util").Feature[];
758
+ geneticCodes: Record<string, number>;
759
+ }): void;
760
+ setError(e: unknown): void;
761
+ setLoadingP(p?: Promise<void>): void;
762
+ loadPre(): Promise<void>;
763
+ } & {
764
+ load(): Promise<void>;
765
+ } & {
766
+ afterAttach(): void;
767
+ } & {
768
+ readonly initialized: boolean;
769
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
770
+ readonly allRefNames: string[] | undefined;
771
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
772
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
773
+ } & {
774
+ readonly refNames: string[] | undefined;
775
+ } & {
776
+ readonly refNameToIndex: Map<string, number> | undefined;
777
+ } & {
778
+ getCanonicalRefName(refName: string): string | undefined;
779
+ getRefNameColor(refName: string): string | undefined;
780
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
781
+ getGeneticCodeId(refName: string): number;
782
+ getSeqAdapterRefName(canonicalRefName: string): string;
783
+ } & {
784
+ getCanonicalRefName2(refName: string): string;
785
+ isValidRefName(refName: string): boolean;
786
+ } & {
787
+ getAliasesForRefName(refName: string): string[];
788
+ getRefNameMapForAdapter(adapterConf: {
789
+ [x: string]: unknown;
790
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
791
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
792
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
793
+ getRefNameMapForAdapter(adapterConf: {
794
+ [x: string]: unknown;
795
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
796
+ isValidRefName(refName: string, assemblyName: string): boolean;
797
+ } & {
798
+ afterAttach(): void;
799
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
800
+ addAssembly(configuration: any): void;
801
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
802
+ }> & {
803
+ rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
804
+ adminMode: boolean;
805
+ error: unknown;
806
+ textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
807
+ pluginManager: PluginManager;
808
+ } & {
809
+ setError(error: unknown): void;
810
+ setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
811
+ setDefaultSession(): void;
812
+ setSessionPath(path: string): void;
813
+ renameCurrentSession(newName: string): void;
814
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
815
+ jbrowse: import("@jbrowse/mobx-state-tree").IAnyType;
816
+ session: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IAnyType>;
817
+ sessionPath: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
818
+ assemblyManager: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
819
+ assemblies: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
820
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
821
+ }, {
822
+ error: unknown;
823
+ loadingP: Promise<void> | undefined;
824
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
825
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
826
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
827
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
828
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
829
+ loadedGeneticCodes: Record<string, number> | undefined;
830
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
831
+ statusMessage: string | undefined;
832
+ statusProgress: number | undefined;
833
+ statusSource: string | undefined;
834
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
835
+ } & {
836
+ getConf(arg: string): any;
837
+ } & {
838
+ readonly name: string;
839
+ readonly aliases: string[];
840
+ readonly displayName: string;
841
+ readonly refNameColors: string[];
842
+ } & {
843
+ readonly allAliases: string[];
844
+ hasName(name: string): boolean;
845
+ } & {
846
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
847
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
848
+ } & {
849
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
850
+ regions: import("@jbrowse/core/util").Region[];
851
+ cytobands: import("@jbrowse/core/util").Feature[];
852
+ geneticCodes: Record<string, number>;
853
+ }): void;
854
+ setError(e: unknown): void;
855
+ setLoadingP(p?: Promise<void>): void;
856
+ loadPre(): Promise<void>;
857
+ } & {
858
+ load(): Promise<void>;
859
+ } & {
860
+ afterAttach(): void;
861
+ } & {
862
+ readonly initialized: boolean;
863
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
864
+ readonly allRefNames: string[] | undefined;
865
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
866
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
867
+ } & {
868
+ readonly refNames: string[] | undefined;
869
+ } & {
870
+ readonly refNameToIndex: Map<string, number> | undefined;
871
+ } & {
872
+ getCanonicalRefName(refName: string): string | undefined;
873
+ getRefNameColor(refName: string): string | undefined;
874
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
875
+ getGeneticCodeId(refName: string): number;
876
+ getSeqAdapterRefName(canonicalRefName: string): string;
877
+ } & {
878
+ getCanonicalRefName2(refName: string): string;
879
+ isValidRefName(refName: string): boolean;
880
+ } & {
881
+ getAliasesForRefName(refName: string): string[];
882
+ getRefNameMapForAdapter(adapterConf: {
883
+ [x: string]: unknown;
884
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
885
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
886
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
887
+ }, {
888
+ unrecognizedReports: {
889
+ report(session: unknown, name: string, handlerCount: number, fire: () => unknown): void;
890
+ reportFor(session: unknown, name: string): {
891
+ handled: boolean;
892
+ claim?: Promise<void>;
893
+ } | undefined;
894
+ };
895
+ } & {
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>>>;
1031
+ } & {
1032
+ getCanonicalAssemblyName(asmName: string): string | undefined;
1033
+ getDisplayName(asmName: string): string;
1034
+ get(asmName: string): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1035
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1036
+ }> & {
1037
+ error: unknown;
1038
+ loadingP: Promise<void> | undefined;
1039
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1040
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1041
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1042
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1043
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1044
+ loadedGeneticCodes: Record<string, number> | undefined;
1045
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1046
+ statusMessage: string | undefined;
1047
+ statusProgress: number | undefined;
1048
+ statusSource: string | undefined;
1049
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1050
+ } & {
1051
+ getConf(arg: string): any;
1052
+ } & {
1053
+ readonly name: string;
1054
+ readonly aliases: string[];
1055
+ readonly displayName: string;
1056
+ readonly refNameColors: string[];
1057
+ } & {
1058
+ readonly allAliases: string[];
1059
+ hasName(name: string): boolean;
1060
+ } & {
1061
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1062
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1063
+ } & {
1064
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1065
+ regions: import("@jbrowse/core/util").Region[];
1066
+ cytobands: import("@jbrowse/core/util").Feature[];
1067
+ geneticCodes: Record<string, number>;
1068
+ }): void;
1069
+ setError(e: unknown): void;
1070
+ setLoadingP(p?: Promise<void>): void;
1071
+ loadPre(): Promise<void>;
1072
+ } & {
1073
+ load(): Promise<void>;
1074
+ } & {
1075
+ afterAttach(): void;
1076
+ } & {
1077
+ readonly initialized: boolean;
1078
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1079
+ readonly allRefNames: string[] | undefined;
1080
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1081
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1082
+ } & {
1083
+ readonly refNames: string[] | undefined;
1084
+ } & {
1085
+ readonly refNameToIndex: Map<string, number> | undefined;
1086
+ } & {
1087
+ getCanonicalRefName(refName: string): string | undefined;
1088
+ getRefNameColor(refName: string): string | undefined;
1089
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1090
+ getGeneticCodeId(refName: string): number;
1091
+ getSeqAdapterRefName(canonicalRefName: string): string;
1092
+ } & {
1093
+ getCanonicalRefName2(refName: string): string;
1094
+ isValidRefName(refName: string): boolean;
1095
+ } & {
1096
+ getAliasesForRefName(refName: string): string[];
1097
+ getRefNameMapForAdapter(adapterConf: {
1098
+ [x: string]: unknown;
1099
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1100
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1101
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1102
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1103
+ }, {
1104
+ error: unknown;
1105
+ loadingP: Promise<void> | undefined;
1106
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1107
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1108
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1109
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1110
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1111
+ loadedGeneticCodes: Record<string, number> | undefined;
1112
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1113
+ statusMessage: string | undefined;
1114
+ statusProgress: number | undefined;
1115
+ statusSource: string | undefined;
1116
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1117
+ } & {
1118
+ getConf(arg: string): any;
1119
+ } & {
1120
+ readonly name: string;
1121
+ readonly aliases: string[];
1122
+ readonly displayName: string;
1123
+ readonly refNameColors: string[];
1124
+ } & {
1125
+ readonly allAliases: string[];
1126
+ hasName(name: string): boolean;
1127
+ } & {
1128
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1129
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1130
+ } & {
1131
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1132
+ regions: import("@jbrowse/core/util").Region[];
1133
+ cytobands: import("@jbrowse/core/util").Feature[];
1134
+ geneticCodes: Record<string, number>;
1135
+ }): void;
1136
+ setError(e: unknown): void;
1137
+ setLoadingP(p?: Promise<void>): void;
1138
+ loadPre(): Promise<void>;
1139
+ } & {
1140
+ load(): Promise<void>;
1141
+ } & {
1142
+ afterAttach(): void;
1143
+ } & {
1144
+ readonly initialized: boolean;
1145
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1146
+ readonly allRefNames: string[] | undefined;
1147
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1148
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1149
+ } & {
1150
+ readonly refNames: string[] | undefined;
1151
+ } & {
1152
+ readonly refNameToIndex: Map<string, number> | undefined;
1153
+ } & {
1154
+ getCanonicalRefName(refName: string): string | undefined;
1155
+ getRefNameColor(refName: string): string | undefined;
1156
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1157
+ getGeneticCodeId(refName: string): number;
1158
+ getSeqAdapterRefName(canonicalRefName: string): string;
1159
+ } & {
1160
+ getCanonicalRefName2(refName: string): string;
1161
+ isValidRefName(refName: string): boolean;
1162
+ } & {
1163
+ getAliasesForRefName(refName: string): string[];
1164
+ getRefNameMapForAdapter(adapterConf: {
1165
+ [x: string]: unknown;
1166
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1167
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1168
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1169
+ has(asmName: string): boolean;
1170
+ loadingAssembly(asmNames: string[]): (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1171
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1172
+ }> & {
1173
+ error: unknown;
1174
+ loadingP: Promise<void> | undefined;
1175
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1176
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1177
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1178
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1179
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1180
+ loadedGeneticCodes: Record<string, number> | undefined;
1181
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1182
+ statusMessage: string | undefined;
1183
+ statusProgress: number | undefined;
1184
+ statusSource: string | undefined;
1185
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1186
+ } & {
1187
+ getConf(arg: string): any;
1188
+ } & {
1189
+ readonly name: string;
1190
+ readonly aliases: string[];
1191
+ readonly displayName: string;
1192
+ readonly refNameColors: string[];
1193
+ } & {
1194
+ readonly allAliases: string[];
1195
+ hasName(name: string): boolean;
1196
+ } & {
1197
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1198
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1199
+ } & {
1200
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1201
+ regions: import("@jbrowse/core/util").Region[];
1202
+ cytobands: import("@jbrowse/core/util").Feature[];
1203
+ geneticCodes: Record<string, number>;
1204
+ }): void;
1205
+ setError(e: unknown): void;
1206
+ setLoadingP(p?: Promise<void>): void;
1207
+ loadPre(): Promise<void>;
1208
+ } & {
1209
+ load(): Promise<void>;
1210
+ } & {
1211
+ afterAttach(): void;
1212
+ } & {
1213
+ readonly initialized: boolean;
1214
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1215
+ readonly allRefNames: string[] | undefined;
1216
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1217
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1218
+ } & {
1219
+ readonly refNames: string[] | undefined;
1220
+ } & {
1221
+ readonly refNameToIndex: Map<string, number> | undefined;
1222
+ } & {
1223
+ getCanonicalRefName(refName: string): string | undefined;
1224
+ getRefNameColor(refName: string): string | undefined;
1225
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1226
+ getGeneticCodeId(refName: string): number;
1227
+ getSeqAdapterRefName(canonicalRefName: string): string;
1228
+ } & {
1229
+ getCanonicalRefName2(refName: string): string;
1230
+ isValidRefName(refName: string): boolean;
1231
+ } & {
1232
+ getAliasesForRefName(refName: string): string[];
1233
+ getRefNameMapForAdapter(adapterConf: {
1234
+ [x: string]: unknown;
1235
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1236
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1237
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1238
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1239
+ }, {
1240
+ error: unknown;
1241
+ loadingP: Promise<void> | undefined;
1242
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1243
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1244
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1245
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1246
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1247
+ loadedGeneticCodes: Record<string, number> | undefined;
1248
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1249
+ statusMessage: string | undefined;
1250
+ statusProgress: number | undefined;
1251
+ statusSource: string | undefined;
1252
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1253
+ } & {
1254
+ getConf(arg: string): any;
1255
+ } & {
1256
+ readonly name: string;
1257
+ readonly aliases: string[];
1258
+ readonly displayName: string;
1259
+ readonly refNameColors: string[];
1260
+ } & {
1261
+ readonly allAliases: string[];
1262
+ hasName(name: string): boolean;
1263
+ } & {
1264
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1265
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1266
+ } & {
1267
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1268
+ regions: import("@jbrowse/core/util").Region[];
1269
+ cytobands: import("@jbrowse/core/util").Feature[];
1270
+ geneticCodes: Record<string, number>;
1271
+ }): void;
1272
+ setError(e: unknown): void;
1273
+ setLoadingP(p?: Promise<void>): void;
1274
+ loadPre(): Promise<void>;
1275
+ } & {
1276
+ load(): Promise<void>;
1277
+ } & {
1278
+ afterAttach(): void;
1279
+ } & {
1280
+ readonly initialized: boolean;
1281
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1282
+ readonly allRefNames: string[] | undefined;
1283
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1284
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1285
+ } & {
1286
+ readonly refNames: string[] | undefined;
1287
+ } & {
1288
+ readonly refNameToIndex: Map<string, number> | undefined;
1289
+ } & {
1290
+ getCanonicalRefName(refName: string): string | undefined;
1291
+ getRefNameColor(refName: string): string | undefined;
1292
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1293
+ getGeneticCodeId(refName: string): number;
1294
+ getSeqAdapterRefName(canonicalRefName: string): string;
1295
+ } & {
1296
+ getCanonicalRefName2(refName: string): string;
1297
+ isValidRefName(refName: string): boolean;
1298
+ } & {
1299
+ getAliasesForRefName(refName: string): string[];
1300
+ getRefNameMapForAdapter(adapterConf: {
1301
+ [x: string]: unknown;
1302
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1303
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1304
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
1305
+ 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>)[];
1311
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1312
+ } & {
1313
+ settleAssemblyResolution(assemblyName: string): Promise<void>;
1314
+ } & {
1315
+ waitForAssembly(assemblyName: string): Promise<(import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1316
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1317
+ }> & {
1318
+ error: unknown;
1319
+ loadingP: Promise<void> | undefined;
1320
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1321
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1322
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1323
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1324
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1325
+ loadedGeneticCodes: Record<string, number> | undefined;
1326
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1327
+ statusMessage: string | undefined;
1328
+ statusProgress: number | undefined;
1329
+ statusSource: string | undefined;
1330
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1331
+ } & {
1332
+ getConf(arg: string): any;
1333
+ } & {
1334
+ readonly name: string;
1335
+ readonly aliases: string[];
1336
+ readonly displayName: string;
1337
+ readonly refNameColors: string[];
1338
+ } & {
1339
+ readonly allAliases: string[];
1340
+ hasName(name: string): boolean;
1341
+ } & {
1342
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1343
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1344
+ } & {
1345
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1346
+ regions: import("@jbrowse/core/util").Region[];
1347
+ cytobands: import("@jbrowse/core/util").Feature[];
1348
+ geneticCodes: Record<string, number>;
1349
+ }): void;
1350
+ setError(e: unknown): void;
1351
+ setLoadingP(p?: Promise<void>): void;
1352
+ loadPre(): Promise<void>;
1353
+ } & {
1354
+ load(): Promise<void>;
1355
+ } & {
1356
+ afterAttach(): void;
1357
+ } & {
1358
+ readonly initialized: boolean;
1359
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1360
+ readonly allRefNames: string[] | undefined;
1361
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1362
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1363
+ } & {
1364
+ readonly refNames: string[] | undefined;
1365
+ } & {
1366
+ readonly refNameToIndex: Map<string, number> | undefined;
1367
+ } & {
1368
+ getCanonicalRefName(refName: string): string | undefined;
1369
+ getRefNameColor(refName: string): string | undefined;
1370
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1371
+ getGeneticCodeId(refName: string): number;
1372
+ getSeqAdapterRefName(canonicalRefName: string): string;
1373
+ } & {
1374
+ getCanonicalRefName2(refName: string): string;
1375
+ isValidRefName(refName: string): boolean;
1376
+ } & {
1377
+ getAliasesForRefName(refName: string): string[];
1378
+ getRefNameMapForAdapter(adapterConf: {
1379
+ [x: string]: unknown;
1380
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1381
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1382
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1383
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1384
+ }, {
1385
+ error: unknown;
1386
+ loadingP: Promise<void> | undefined;
1387
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1388
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1389
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1390
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1391
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1392
+ loadedGeneticCodes: Record<string, number> | undefined;
1393
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1394
+ statusMessage: string | undefined;
1395
+ statusProgress: number | undefined;
1396
+ statusSource: string | undefined;
1397
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1398
+ } & {
1399
+ getConf(arg: string): any;
1400
+ } & {
1401
+ readonly name: string;
1402
+ readonly aliases: string[];
1403
+ readonly displayName: string;
1404
+ readonly refNameColors: string[];
1405
+ } & {
1406
+ readonly allAliases: string[];
1407
+ hasName(name: string): boolean;
1408
+ } & {
1409
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1410
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1411
+ } & {
1412
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1413
+ regions: import("@jbrowse/core/util").Region[];
1414
+ cytobands: import("@jbrowse/core/util").Feature[];
1415
+ geneticCodes: Record<string, number>;
1416
+ }): void;
1417
+ setError(e: unknown): void;
1418
+ setLoadingP(p?: Promise<void>): void;
1419
+ loadPre(): Promise<void>;
1420
+ } & {
1421
+ load(): Promise<void>;
1422
+ } & {
1423
+ afterAttach(): void;
1424
+ } & {
1425
+ readonly initialized: boolean;
1426
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1427
+ readonly allRefNames: string[] | undefined;
1428
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1429
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1430
+ } & {
1431
+ readonly refNames: string[] | undefined;
1432
+ } & {
1433
+ readonly refNameToIndex: Map<string, number> | undefined;
1434
+ } & {
1435
+ getCanonicalRefName(refName: string): string | undefined;
1436
+ getRefNameColor(refName: string): string | undefined;
1437
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1438
+ getGeneticCodeId(refName: string): number;
1439
+ getSeqAdapterRefName(canonicalRefName: string): string;
1440
+ } & {
1441
+ getCanonicalRefName2(refName: string): string;
1442
+ isValidRefName(refName: string): boolean;
1443
+ } & {
1444
+ getAliasesForRefName(refName: string): string[];
1445
+ getRefNameMapForAdapter(adapterConf: {
1446
+ [x: string]: unknown;
1447
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1448
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1449
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined>;
1450
+ requireAssembly(assemblyName: string): Promise<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
1451
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1452
+ }> & {
1453
+ error: unknown;
1454
+ loadingP: Promise<void> | undefined;
1455
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1456
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1457
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1458
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1459
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1460
+ loadedGeneticCodes: Record<string, number> | undefined;
1461
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1462
+ statusMessage: string | undefined;
1463
+ statusProgress: number | undefined;
1464
+ statusSource: string | undefined;
1465
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1466
+ } & {
1467
+ getConf(arg: string): any;
1468
+ } & {
1469
+ readonly name: string;
1470
+ readonly aliases: string[];
1471
+ readonly displayName: string;
1472
+ readonly refNameColors: string[];
1473
+ } & {
1474
+ readonly allAliases: string[];
1475
+ hasName(name: string): boolean;
1476
+ } & {
1477
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1478
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1479
+ } & {
1480
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1481
+ regions: import("@jbrowse/core/util").Region[];
1482
+ cytobands: import("@jbrowse/core/util").Feature[];
1483
+ geneticCodes: Record<string, number>;
1484
+ }): void;
1485
+ setError(e: unknown): void;
1486
+ setLoadingP(p?: Promise<void>): void;
1487
+ loadPre(): Promise<void>;
1488
+ } & {
1489
+ load(): Promise<void>;
1490
+ } & {
1491
+ afterAttach(): void;
1492
+ } & {
1493
+ readonly initialized: boolean;
1494
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1495
+ readonly allRefNames: string[] | undefined;
1496
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1497
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1498
+ } & {
1499
+ readonly refNames: string[] | undefined;
1500
+ } & {
1501
+ readonly refNameToIndex: Map<string, number> | undefined;
1502
+ } & {
1503
+ getCanonicalRefName(refName: string): string | undefined;
1504
+ getRefNameColor(refName: string): string | undefined;
1505
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1506
+ getGeneticCodeId(refName: string): number;
1507
+ getSeqAdapterRefName(canonicalRefName: string): string;
1508
+ } & {
1509
+ getCanonicalRefName2(refName: string): string;
1510
+ isValidRefName(refName: string): boolean;
1511
+ } & {
1512
+ getAliasesForRefName(refName: string): string[];
1513
+ getRefNameMapForAdapter(adapterConf: {
1514
+ [x: string]: unknown;
1515
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1516
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1517
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
1518
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
1519
+ }, {
1520
+ error: unknown;
1521
+ loadingP: Promise<void> | undefined;
1522
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>>;
1523
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1524
+ refNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1525
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
1526
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1527
+ loadedGeneticCodes: Record<string, number> | undefined;
1528
+ lowerCaseRefNameAliases: import("@jbrowse/core/assemblyManager/assembly").RefNameAliases | undefined;
1529
+ statusMessage: string | undefined;
1530
+ statusProgress: number | undefined;
1531
+ statusSource: string | undefined;
1532
+ refNameMismatches: Map<string, import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch>;
1533
+ } & {
1534
+ getConf(arg: string): any;
1535
+ } & {
1536
+ readonly name: string;
1537
+ readonly aliases: string[];
1538
+ readonly displayName: string;
1539
+ readonly refNameColors: string[];
1540
+ } & {
1541
+ readonly allAliases: string[];
1542
+ hasName(name: string): boolean;
1543
+ } & {
1544
+ setStatus(status?: import("@jbrowse/core/util").RpcStatus): void;
1545
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch): void;
1546
+ } & {
1547
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes }: import("@jbrowse/core/assemblyManager/assembly").RefNameMaps & {
1548
+ regions: import("@jbrowse/core/util").Region[];
1549
+ cytobands: import("@jbrowse/core/util").Feature[];
1550
+ geneticCodes: Record<string, number>;
1551
+ }): void;
1552
+ setError(e: unknown): void;
1553
+ setLoadingP(p?: Promise<void>): void;
1554
+ loadPre(): Promise<void>;
1555
+ } & {
1556
+ load(): Promise<void>;
1557
+ } & {
1558
+ afterAttach(): void;
1559
+ } & {
1560
+ readonly initialized: boolean;
1561
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1562
+ readonly allRefNames: string[] | undefined;
1563
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
1564
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1565
+ } & {
1566
+ readonly refNames: string[] | undefined;
1567
+ } & {
1568
+ readonly refNameToIndex: Map<string, number> | undefined;
1569
+ } & {
1570
+ getCanonicalRefName(refName: string): string | undefined;
1571
+ getRefNameColor(refName: string): string | undefined;
1572
+ getRegionForRefName(refName: string): import("@jbrowse/core/assemblyManager/assembly").BasicRegion | undefined;
1573
+ getGeneticCodeId(refName: string): number;
1574
+ getSeqAdapterRefName(canonicalRefName: string): string;
1575
+ } & {
1576
+ getCanonicalRefName2(refName: string): string;
1577
+ isValidRefName(refName: string): boolean;
1578
+ } & {
1579
+ getAliasesForRefName(refName: string): string[];
1580
+ getRefNameMapForAdapter(adapterConf: {
1581
+ [x: string]: unknown;
1582
+ }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1583
+ getRefNameMismatch(adapterCacheKey: string): import("@jbrowse/core/assemblyManager/assembly").RefNameMismatch | undefined;
1584
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
1585
+ getRefNameMapForAdapter(adapterConf: {
1586
+ [x: string]: unknown;
1587
+ }, assemblyName: string | undefined, opts: import("@jbrowse/core/assemblyManager").AssemblyBaseOpts): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameAliases>;
1588
+ isValidRefName(refName: string, assemblyName: string): boolean;
1589
+ } & {
1590
+ afterAttach(): void;
1591
+ removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
1592
+ addAssembly(configuration: any): void;
1593
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
1594
+ }, {
1595
+ rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
1596
+ adminMode: boolean;
1597
+ error: unknown;
1598
+ textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1599
+ pluginManager: PluginManager;
1600
+ } & {
1601
+ setError(error: unknown): void;
1602
+ setSession(sessionSnapshot?: import("@jbrowse/mobx-state-tree").SnapshotIn<import("@jbrowse/mobx-state-tree").IAnyType>): void;
1603
+ setDefaultSession(): void;
1604
+ setSessionPath(path: string): void;
1605
+ renameCurrentSession(newName: string): void;
1606
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
1607
+ } & {
1608
+ readonly jbrowse: any;
1609
+ 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>;
1614
+ readonly adminMode: boolean;
1615
+ readonly textSearchManager: import("@jbrowse/core/TextSearch/TextSearchManager").default;
1616
+ } & {
1617
+ readonly assemblies: import("@jbrowse/core/assemblyManager").BaseAssemblyConfigModel[];
1618
+ readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType | undefined;
1619
+ readonly DialogProps: Record<string, unknown> | undefined;
1620
+ } & {
1621
+ getPreferenceDefault(key: string): unknown;
1622
+ getPreference(key: string): unknown;
1623
+ getDisplayTypeDefault(displayType: string, slot: string): unknown;
1624
+ getDisplayTypeDefaults(): {
1625
+ displayType: string;
1626
+ slot: string;
1627
+ value: unknown;
1628
+ }[];
1629
+ getPreferenceChanges(): import("@jbrowse/core/util").TrackConfigChange[];
1630
+ } & {
1631
+ readonly animationMode: import("@jbrowse/core/util").AnimationMode;
1632
+ readonly scrollZoom: boolean;
1633
+ readonly numberGrouping: boolean;
1634
+ } & {
1635
+ afterAttach(): void;
1636
+ setSelection(thing: unknown): void;
1637
+ clearSelection(): void;
1638
+ setHovered(thing: unknown): void;
1639
+ setHighlightsVisible(arg: boolean): void;
1640
+ revealHighlights(): void;
1641
+ setPreferenceOverride(key: string, value: unknown): void;
1642
+ clearPreferenceOverrides(): void;
1643
+ clearPreferenceOverride(key: string): void;
1644
+ resetPreferenceChange(path: string[]): void;
1645
+ setScrollZoom(flag: boolean): void;
1646
+ setDisplayTypeDefault(displayType: string, slot: string, value: unknown): void;
1647
+ setName(str: string): void;
1648
+ setFocusedViewId(viewId: string | undefined): void;
1649
+ removeActiveDialog(): void;
1650
+ queueDialog(doneCallback: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, Record<string, unknown>]): void;
1651
+ } & {
1652
+ snackbarMessages: import("mobx").IObservableArray<import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1653
+ errorDialog: import("@jbrowse/core/ui/SnackbarModel").ErrorDialogState | undefined;
1654
+ } & {
1655
+ readonly snackbarMessageSet: Map<string, import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage>;
1656
+ } & {
1657
+ notify(message: string, level?: import("@jbrowse/core/util").NotificationLevel, action?: import("@jbrowse/core/util").SnackAction | import("@jbrowse/core/util").SnackAction[]): void;
1658
+ notifyError(errorMessage: string, error?: unknown, extra?: unknown, action?: import("@jbrowse/core/util").SnackAction): void;
1659
+ setErrorDialog(state: import("@jbrowse/core/ui/SnackbarModel").ErrorDialogState | undefined): void;
1660
+ pushSnackbarMessage(message: string, level?: import("@jbrowse/core/util").NotificationLevel, actions?: import("@jbrowse/core/util").SnackAction[]): void;
1661
+ popSnackbarMessage(): import("@jbrowse/core/ui/SnackbarModel").SnackbarMessage | undefined;
1662
+ removeSnackbarMessage(message: string): void;
1663
+ } & {
1664
+ afterAttach(): void;
1665
+ } & {
1666
+ /**
1667
+ * #getter
1668
+ * Serializable theme description (the canonical `themeOptions` contract
1669
+ * shared with the app-core/web sessions). This is what crosses the RPC
1670
+ * worker boundary — e.g. the canvas display reads
1671
+ * `getSession(self).themeOptions` in its rpcProps so worker-baked colors
1672
+ * (CDS frames, stroke fallback) honor the config `theme` slot.
1673
+ */
1674
+ readonly themeOptions: SerializableThemeArgs;
1675
+ /**
1676
+ * #getter
1677
+ * Every color JBrowse renders, resolved to plain strings and free of any UI
1678
+ * toolkit. This is what rendering reads. See the canonical
1679
+ * `ThemeManagerSessionMixin` getter of the same name.
1680
+ */
1681
+ readonly palette: import("@jbrowse/core/ui/palette").JBrowsePalette;
1682
+ /**
1683
+ * #getter
1684
+ * The palette plus the sizing tokens `makeStyles` reads. See the
1685
+ * canonical `ThemeManagerSessionMixin` getter of the same name.
1686
+ */
1687
+ readonly styleTheme: import("@jbrowse/core/ui/styleTheme").JBrowseStyleTheme;
1688
+ /**
1689
+ * #getter
1690
+ * Resolved MUI theme, mirroring the product's ThemeProvider. Lets
1691
+ * headless/RPC consumers derive theme-dependent state without a mounted
1692
+ * component. Shares its colors with `palette` by construction.
1693
+ */
1694
+ readonly theme: import("@mui/material").Theme;
1695
+ /**
1696
+ * #method
1697
+ * Raw `ThemeOptions` for the active theme, which every view's SVG export
1698
+ * threads into each display's `renderSvg` as a `configTheme` and rebuilds
1699
+ * outside React. The config slot is the whole answer here because it is
1700
+ * the whole of an embedded product's theming: no picker, no `allThemes`,
1701
+ * and it is what `setThemeMode` writes and `palette` resolves from. `name`
1702
+ * is accepted and ignored — the app session's counterpart looks a named
1703
+ * preset up in `allThemes()`.
1704
+ */
1705
+ getActiveThemeOptions(_name?: string): import("@mui/material").ThemeOptions | undefined;
1706
+ } & {
1707
+ /**
1708
+ * #action
1709
+ * Point the session at light or dark. One write, not two: the `theme`
1710
+ * slot is what `themeOptions` ships to the renderer, so the labels baked
1711
+ * in the worker follow it, and `palette` is derived from the same slot,
1712
+ * so what React draws follows it too. An embedder who sets only a
1713
+ * React-side palette leaves the baked labels behind.
1714
+ *
1715
+ * Merges rather than replaces, at both levels. `theme` is a frozen slot,
1716
+ * so a bare `setConf(session, 'theme', { palette: { mode } })` — the
1717
+ * obvious form, and what the build-your-own examples each wrote — drops
1718
+ * every other key in it. That silently discards whatever the host passed
1719
+ * as `createViewState`'s `configuration.theme` (a brand `primary`, say)
1720
+ * the first time their dark-mode toggle fires. `resolvePalette` spreads
1721
+ * `configTheme.palette` over the preset shallowly, so `mode` and
1722
+ * `primary` are siblings and both levels have to survive.
1723
+ */
1724
+ setThemeMode(mode: 'light' | 'dark'): void;
1725
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;