@jbrowse/plugin-linear-comparative-view 2.8.0 → 2.9.0

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 (15) hide show
  1. package/dist/LaunchLinearSyntenyView.js +6 -2
  2. package/dist/LinearComparativeView/model.d.ts +122 -2
  3. package/dist/LinearComparativeView/model.js +2 -2
  4. package/dist/LinearReadVsRef/LinearReadVsRef.js +1 -1
  5. package/dist/LinearSyntenyView/components/ImportForm/index.js +1 -1
  6. package/dist/LinearSyntenyView/model.d.ts +364 -4
  7. package/dist/SyntenyTrack/configSchema.d.ts +5 -0
  8. package/esm/LaunchLinearSyntenyView.js +6 -2
  9. package/esm/LinearComparativeView/model.d.ts +122 -2
  10. package/esm/LinearComparativeView/model.js +2 -2
  11. package/esm/LinearReadVsRef/LinearReadVsRef.js +1 -1
  12. package/esm/LinearSyntenyView/components/ImportForm/index.js +1 -1
  13. package/esm/LinearSyntenyView/model.d.ts +364 -4
  14. package/esm/SyntenyTrack/configSchema.d.ts +5 -0
  15. package/package.json +2 -2
package/dist/LaunchLinearSyntenyView.js CHANGED
@@ -26,8 +26,12 @@ function LaunchLinearSyntenyView(pluginManager) {
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  const idsNotFound = [];
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  await Promise.all(views.map(async (data, idx) => {
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  const view = model.views[idx];
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- const { loc, tracks = [] } = data;
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- await view.navToLocString(loc);
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+ const { assembly, loc, tracks = [] } = data;
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+ const asm = await assemblyManager.waitForAssembly(assembly);
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+ if (!asm) {
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+ throw new Error(`Assembly ${data.assembly} failed to load`);
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+ }
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+ await view.navToSearchString({ input: loc, assembly: asm });
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  tracks.forEach(track => tryTrack(view, track, idsNotFound));
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  }));
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  tracks.forEach(track => tryTrack(model, track, idsNotFound));
package/dist/LinearComparativeView/model.d.ts CHANGED
@@ -123,7 +123,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
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123
  } & {
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  moveTrack(movingId: string, targetId: string): void;
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  closeView(): void;
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- toggleTrack(trackId: string): void;
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+ toggleTrack(trackId: string): boolean;
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  setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
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  toggleCenterLine(): void;
129
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  setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
@@ -173,6 +173,126 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
173
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  } & {
174
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  moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
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  navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
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+ navToSearchString({ input, assembly, }: {
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+ input: string;
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+ assembly: {
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+ configuration: any;
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+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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+ error: unknown;
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+ loaded: boolean;
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+ loadingP: Promise<void> | undefined;
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+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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+ refNameAliases: {
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+ [x: string]: string | undefined;
187
+ } | undefined;
188
+ lowerCaseRefNameAliases: {
189
+ [x: string]: string | undefined;
190
+ } | undefined;
191
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
192
+ } & {
193
+ getConf(arg: string): any;
194
+ } & {
195
+ readonly initialized: boolean; /**
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+ * #property
197
+ */
198
+ readonly name: string;
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+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
200
+ readonly aliases: string[];
201
+ readonly displayName: string | undefined;
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+ hasName(name: string): boolean;
203
+ readonly allAliases: string[];
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+ readonly allRefNames: string[] | undefined;
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+ readonly lowerCaseRefNames: string[] | undefined;
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+ readonly allRefNamesWithLowerCase: string[] | undefined;
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+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
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+ readonly refNameColors: string[];
209
+ } & {
210
+ readonly refNames: string[] | undefined;
211
+ } & {
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+ getCanonicalRefName(refName: string): string | undefined;
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+ getRefNameColor(refName: string): string | undefined;
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+ isValidRefName(refName: string): boolean;
215
+ } & {
216
+ setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
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+ setError(e: unknown): void;
218
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
219
+ setRefNameAliases(aliases: {
220
+ [x: string]: string | undefined;
221
+ }, lcAliases: {
222
+ [x: string]: string | undefined;
223
+ }): void;
224
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
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+ setLoadingP(p?: Promise<void> | undefined): void;
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+ load(): Promise<void>;
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+ loadPre(): Promise<void>;
228
+ } & {
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+ getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
230
+ getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
231
+ [x: string]: string | undefined;
232
+ }>;
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+ getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
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+ [x: string]: string | undefined;
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+ }>;
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+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
237
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
238
+ }, {
239
+ error: unknown;
240
+ loaded: boolean;
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+ loadingP: Promise<void> | undefined;
242
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
243
+ refNameAliases: {
244
+ [x: string]: string | undefined;
245
+ } | undefined;
246
+ lowerCaseRefNameAliases: {
247
+ [x: string]: string | undefined;
248
+ } | undefined;
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+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
250
+ } & {
251
+ getConf(arg: string): any;
252
+ } & {
253
+ readonly initialized: boolean; /**
254
+ * #property
255
+ */
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+ readonly name: string;
257
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
258
+ readonly aliases: string[];
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+ readonly displayName: string | undefined;
260
+ hasName(name: string): boolean;
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+ readonly allAliases: string[];
262
+ readonly allRefNames: string[] | undefined;
263
+ readonly lowerCaseRefNames: string[] | undefined;
264
+ readonly allRefNamesWithLowerCase: string[] | undefined;
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+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
266
+ readonly refNameColors: string[];
267
+ } & {
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+ readonly refNames: string[] | undefined;
269
+ } & {
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+ getCanonicalRefName(refName: string): string | undefined;
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+ getRefNameColor(refName: string): string | undefined;
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+ isValidRefName(refName: string): boolean;
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+ } & {
274
+ setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
275
+ setError(e: unknown): void;
276
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
277
+ setRefNameAliases(aliases: {
278
+ [x: string]: string | undefined;
279
+ }, lcAliases: {
280
+ [x: string]: string | undefined;
281
+ }): void;
282
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
283
+ setLoadingP(p?: Promise<void> | undefined): void;
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+ load(): Promise<void>;
285
+ loadPre(): Promise<void>;
286
+ } & {
287
+ getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
288
+ getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
289
+ [x: string]: string | undefined;
290
+ }>;
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+ getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
292
+ [x: string]: string | undefined;
293
+ }>;
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+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
295
+ }): Promise<void>;
176
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  navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
177
297
  navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
178
298
  navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
@@ -277,7 +397,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
277
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  /**
278
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  * #action
279
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  */
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- toggleTrack(trackId: string): void;
400
+ toggleTrack(trackId: string): boolean;
281
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  /**
282
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  * #action
283
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  */
package/dist/LinearComparativeView/model.js CHANGED
@@ -214,12 +214,12 @@ function stateModelFactory(pluginManager) {
214
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  * #action
215
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  */
216
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  toggleTrack(trackId) {
217
- // if we have any tracks with that configuration, turn them off
218
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  const hiddenCount = this.hideTrack(trackId);
219
- // if none had that configuration, turn one on
220
218
  if (!hiddenCount) {
221
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  this.showTrack(trackId);
220
+ return true;
222
221
  }
222
+ return false;
223
223
  },
224
224
  /**
225
225
  * #action
package/dist/LinearReadVsRef/LinearReadVsRef.js CHANGED
@@ -169,7 +169,7 @@ function ReadVsRefDialog({ track, feature: preFeature, handleClose, }) {
169
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  {
170
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  start: 0,
171
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  end: totalLength,
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- seq: featSeq || '',
172
+ seq: featSeq || '', // can be empty if user clicks secondary read
173
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  refName: readName,
174
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  uniqueId: `${Math.random()}`,
175
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  },
package/dist/LinearSyntenyView/components/ImportForm/index.js CHANGED
@@ -45,7 +45,7 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
45
45
  },
46
46
  }));
47
47
  function TrackSelector({ setSessionTrackData, setShowTrackId, sessionTrackData, assembly1, assembly2, model, }) {
48
- const [choice, setChoice] = (0, react_1.useState)('none');
48
+ const [choice, setChoice] = (0, react_1.useState)('tracklist');
49
49
  (0, react_1.useEffect)(() => {
50
50
  if (choice === 'none') {
51
51
  setSessionTrackData(undefined);
package/dist/LinearSyntenyView/model.d.ts CHANGED
@@ -134,7 +134,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
134
134
  } & {
135
135
  moveTrack(movingId: string, targetId: string): void;
136
136
  closeView(): void;
137
- toggleTrack(trackId: string): void;
137
+ toggleTrack(trackId: string): boolean;
138
138
  setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
139
139
  toggleCenterLine(): void;
140
140
  setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
@@ -184,6 +184,126 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
184
184
  } & {
185
185
  moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
186
186
  navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
187
+ navToSearchString({ input, assembly, }: {
188
+ input: string;
189
+ assembly: {
190
+ configuration: any;
191
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
192
+ error: unknown;
193
+ loaded: boolean;
194
+ loadingP: Promise<void> | undefined;
195
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
196
+ refNameAliases: {
197
+ [x: string]: string | undefined;
198
+ } | undefined;
199
+ lowerCaseRefNameAliases: {
200
+ [x: string]: string | undefined;
201
+ } | undefined;
202
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
203
+ } & {
204
+ getConf(arg: string): any;
205
+ } & {
206
+ readonly initialized: boolean;
207
+ readonly name: string;
208
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined; /**
209
+ * #property
210
+ */
211
+ readonly aliases: string[];
212
+ readonly displayName: string | undefined;
213
+ hasName(name: string): boolean;
214
+ readonly allAliases: string[];
215
+ readonly allRefNames: string[] | undefined;
216
+ readonly lowerCaseRefNames: string[] | undefined;
217
+ readonly allRefNamesWithLowerCase: string[] | undefined;
218
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
219
+ readonly refNameColors: string[];
220
+ } & {
221
+ readonly refNames: string[] | undefined;
222
+ } & {
223
+ getCanonicalRefName(refName: string): string | undefined;
224
+ getRefNameColor(refName: string): string | undefined;
225
+ isValidRefName(refName: string): boolean;
226
+ } & {
227
+ setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
228
+ setError(e: unknown): void;
229
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
230
+ setRefNameAliases(aliases: {
231
+ [x: string]: string | undefined;
232
+ }, lcAliases: {
233
+ [x: string]: string | undefined;
234
+ }): void;
235
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
236
+ setLoadingP(p?: Promise<void> | undefined): void;
237
+ load(): Promise<void>;
238
+ loadPre(): Promise<void>;
239
+ } & {
240
+ getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
241
+ getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
242
+ [x: string]: string | undefined;
243
+ }>;
244
+ getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
245
+ [x: string]: string | undefined;
246
+ }>;
247
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
248
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
249
+ }, {
250
+ error: unknown;
251
+ loaded: boolean;
252
+ loadingP: Promise<void> | undefined;
253
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
254
+ refNameAliases: {
255
+ [x: string]: string | undefined;
256
+ } | undefined;
257
+ lowerCaseRefNameAliases: {
258
+ [x: string]: string | undefined;
259
+ } | undefined;
260
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
261
+ } & {
262
+ getConf(arg: string): any;
263
+ } & {
264
+ readonly initialized: boolean;
265
+ readonly name: string;
266
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined; /**
267
+ * #property
268
+ */
269
+ readonly aliases: string[];
270
+ readonly displayName: string | undefined;
271
+ hasName(name: string): boolean;
272
+ readonly allAliases: string[];
273
+ readonly allRefNames: string[] | undefined;
274
+ readonly lowerCaseRefNames: string[] | undefined;
275
+ readonly allRefNamesWithLowerCase: string[] | undefined;
276
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
277
+ readonly refNameColors: string[];
278
+ } & {
279
+ readonly refNames: string[] | undefined;
280
+ } & {
281
+ getCanonicalRefName(refName: string): string | undefined;
282
+ getRefNameColor(refName: string): string | undefined;
283
+ isValidRefName(refName: string): boolean;
284
+ } & {
285
+ setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
286
+ setError(e: unknown): void;
287
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
288
+ setRefNameAliases(aliases: {
289
+ [x: string]: string | undefined;
290
+ }, lcAliases: {
291
+ [x: string]: string | undefined;
292
+ }): void;
293
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
294
+ setLoadingP(p?: Promise<void> | undefined): void;
295
+ load(): Promise<void>;
296
+ loadPre(): Promise<void>;
297
+ } & {
298
+ getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
299
+ getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
300
+ [x: string]: string | undefined;
301
+ }>;
302
+ getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
303
+ [x: string]: string | undefined;
304
+ }>;
305
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
306
+ }): Promise<void>;
187
307
  navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
188
308
  navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
189
309
  navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
@@ -385,7 +505,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
385
505
  } & {
386
506
  moveTrack(movingId: string, targetId: string): void;
387
507
  closeView(): void;
388
- toggleTrack(trackId: string): void;
508
+ toggleTrack(trackId: string): boolean;
389
509
  setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
390
510
  toggleCenterLine(): void;
391
511
  setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
@@ -435,6 +555,126 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
435
555
  } & {
436
556
  moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
437
557
  navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
558
+ navToSearchString({ input, assembly, }: {
559
+ input: string;
560
+ assembly: {
561
+ configuration: any;
562
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
563
+ error: unknown;
564
+ loaded: boolean;
565
+ loadingP: Promise<void> | undefined;
566
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
567
+ refNameAliases: {
568
+ [x: string]: string | undefined;
569
+ } | undefined;
570
+ lowerCaseRefNameAliases: {
571
+ [x: string]: string | undefined;
572
+ } | undefined;
573
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
574
+ } & {
575
+ getConf(arg: string): any;
576
+ } & {
577
+ readonly initialized: boolean;
578
+ readonly name: string;
579
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined; /**
580
+ * #property
581
+ */
582
+ readonly aliases: string[];
583
+ readonly displayName: string | undefined;
584
+ hasName(name: string): boolean;
585
+ readonly allAliases: string[];
586
+ readonly allRefNames: string[] | undefined;
587
+ readonly lowerCaseRefNames: string[] | undefined;
588
+ readonly allRefNamesWithLowerCase: string[] | undefined;
589
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
590
+ readonly refNameColors: string[];
591
+ } & {
592
+ readonly refNames: string[] | undefined;
593
+ } & {
594
+ getCanonicalRefName(refName: string): string | undefined;
595
+ getRefNameColor(refName: string): string | undefined;
596
+ isValidRefName(refName: string): boolean;
597
+ } & {
598
+ setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
599
+ setError(e: unknown): void;
600
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
601
+ setRefNameAliases(aliases: {
602
+ [x: string]: string | undefined;
603
+ }, lcAliases: {
604
+ [x: string]: string | undefined;
605
+ }): void;
606
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
607
+ setLoadingP(p?: Promise<void> | undefined): void;
608
+ load(): Promise<void>;
609
+ loadPre(): Promise<void>;
610
+ } & {
611
+ getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
612
+ getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
613
+ [x: string]: string | undefined;
614
+ }>;
615
+ getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
616
+ [x: string]: string | undefined;
617
+ }>;
618
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
619
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
620
+ }, {
621
+ error: unknown;
622
+ loaded: boolean;
623
+ loadingP: Promise<void> | undefined;
624
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
625
+ refNameAliases: {
626
+ [x: string]: string | undefined;
627
+ } | undefined;
628
+ lowerCaseRefNameAliases: {
629
+ [x: string]: string | undefined;
630
+ } | undefined;
631
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
632
+ } & {
633
+ getConf(arg: string): any;
634
+ } & {
635
+ readonly initialized: boolean;
636
+ readonly name: string;
637
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined; /**
638
+ * #property
639
+ */
640
+ readonly aliases: string[];
641
+ readonly displayName: string | undefined;
642
+ hasName(name: string): boolean;
643
+ readonly allAliases: string[];
644
+ readonly allRefNames: string[] | undefined;
645
+ readonly lowerCaseRefNames: string[] | undefined;
646
+ readonly allRefNamesWithLowerCase: string[] | undefined;
647
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
648
+ readonly refNameColors: string[];
649
+ } & {
650
+ readonly refNames: string[] | undefined;
651
+ } & {
652
+ getCanonicalRefName(refName: string): string | undefined;
653
+ getRefNameColor(refName: string): string | undefined;
654
+ isValidRefName(refName: string): boolean;
655
+ } & {
656
+ setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
657
+ setError(e: unknown): void;
658
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
659
+ setRefNameAliases(aliases: {
660
+ [x: string]: string | undefined;
661
+ }, lcAliases: {
662
+ [x: string]: string | undefined;
663
+ }): void;
664
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
665
+ setLoadingP(p?: Promise<void> | undefined): void;
666
+ load(): Promise<void>;
667
+ loadPre(): Promise<void>;
668
+ } & {
669
+ getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
670
+ getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
671
+ [x: string]: string | undefined;
672
+ }>;
673
+ getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
674
+ [x: string]: string | undefined;
675
+ }>;
676
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
677
+ }): Promise<void>;
438
678
  navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
439
679
  navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
440
680
  navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
@@ -574,7 +814,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
574
814
  } & {
575
815
  moveTrack(movingId: string, targetId: string): void;
576
816
  closeView(): void;
577
- toggleTrack(trackId: string): void;
817
+ toggleTrack(trackId: string): boolean;
578
818
  setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
579
819
  toggleCenterLine(): void;
580
820
  setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
@@ -624,6 +864,126 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
624
864
  } & {
625
865
  moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
626
866
  navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
867
+ navToSearchString({ input, assembly, }: {
868
+ input: string;
869
+ assembly: {
870
+ configuration: any;
871
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
872
+ error: unknown;
873
+ loaded: boolean;
874
+ loadingP: Promise<void> | undefined;
875
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
876
+ refNameAliases: {
877
+ [x: string]: string | undefined;
878
+ } | undefined;
879
+ lowerCaseRefNameAliases: {
880
+ [x: string]: string | undefined;
881
+ } | undefined;
882
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
883
+ } & {
884
+ getConf(arg: string): any;
885
+ } & {
886
+ readonly initialized: boolean;
887
+ readonly name: string;
888
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined; /**
889
+ * #property
890
+ */
891
+ readonly aliases: string[];
892
+ readonly displayName: string | undefined;
893
+ hasName(name: string): boolean;
894
+ readonly allAliases: string[];
895
+ readonly allRefNames: string[] | undefined;
896
+ readonly lowerCaseRefNames: string[] | undefined;
897
+ readonly allRefNamesWithLowerCase: string[] | undefined;
898
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
899
+ readonly refNameColors: string[];
900
+ } & {
901
+ readonly refNames: string[] | undefined;
902
+ } & {
903
+ getCanonicalRefName(refName: string): string | undefined;
904
+ getRefNameColor(refName: string): string | undefined;
905
+ isValidRefName(refName: string): boolean;
906
+ } & {
907
+ setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
908
+ setError(e: unknown): void;
909
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
910
+ setRefNameAliases(aliases: {
911
+ [x: string]: string | undefined;
912
+ }, lcAliases: {
913
+ [x: string]: string | undefined;
914
+ }): void;
915
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
916
+ setLoadingP(p?: Promise<void> | undefined): void;
917
+ load(): Promise<void>;
918
+ loadPre(): Promise<void>;
919
+ } & {
920
+ getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
921
+ getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
922
+ [x: string]: string | undefined;
923
+ }>;
924
+ getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
925
+ [x: string]: string | undefined;
926
+ }>;
927
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
928
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
929
+ }, {
930
+ error: unknown;
931
+ loaded: boolean;
932
+ loadingP: Promise<void> | undefined;
933
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
934
+ refNameAliases: {
935
+ [x: string]: string | undefined;
936
+ } | undefined;
937
+ lowerCaseRefNameAliases: {
938
+ [x: string]: string | undefined;
939
+ } | undefined;
940
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
941
+ } & {
942
+ getConf(arg: string): any;
943
+ } & {
944
+ readonly initialized: boolean;
945
+ readonly name: string;
946
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined; /**
947
+ * #property
948
+ */
949
+ readonly aliases: string[];
950
+ readonly displayName: string | undefined;
951
+ hasName(name: string): boolean;
952
+ readonly allAliases: string[];
953
+ readonly allRefNames: string[] | undefined;
954
+ readonly lowerCaseRefNames: string[] | undefined;
955
+ readonly allRefNamesWithLowerCase: string[] | undefined;
956
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
957
+ readonly refNameColors: string[];
958
+ } & {
959
+ readonly refNames: string[] | undefined;
960
+ } & {
961
+ getCanonicalRefName(refName: string): string | undefined;
962
+ getRefNameColor(refName: string): string | undefined;
963
+ isValidRefName(refName: string): boolean;
964
+ } & {
965
+ setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
966
+ setError(e: unknown): void;
967
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
968
+ setRefNameAliases(aliases: {
969
+ [x: string]: string | undefined;
970
+ }, lcAliases: {
971
+ [x: string]: string | undefined;
972
+ }): void;
973
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
974
+ setLoadingP(p?: Promise<void> | undefined): void;
975
+ load(): Promise<void>;
976
+ loadPre(): Promise<void>;
977
+ } & {
978
+ getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
979
+ getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
980
+ [x: string]: string | undefined;
981
+ }>;
982
+ getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
983
+ [x: string]: string | undefined;
984
+ }>;
985
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
986
+ }): Promise<void>;
627
987
  navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
628
988
  navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
629
989
  navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
@@ -667,7 +1027,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
667
1027
  setMiddleComparativeHeight(n: number): number;
668
1028
  toggleLinkViews(): void;
669
1029
  activateTrackSelector(): import("@jbrowse/core/util").Widget | undefined;
670
- toggleTrack(trackId: string): void;
1030
+ toggleTrack(trackId: string): boolean;
671
1031
  showTrack(trackId: string, initialSnapshot?: {}): void;
672
1032
  hideTrack(trackId: string): number;
673
1033
  squareView(): void;
package/dist/SyntenyTrack/configSchema.d.ts CHANGED
@@ -58,6 +58,11 @@ declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/c
58
58
  defaultValue: number;
59
59
  description: string;
60
60
  };
61
+ maxDepth: {
62
+ type: string;
63
+ defaultValue: number;
64
+ description: string;
65
+ };
61
66
  }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
62
67
  formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
63
68
  config: {
package/esm/LaunchLinearSyntenyView.js CHANGED
@@ -24,8 +24,12 @@ export default function LaunchLinearSyntenyView(pluginManager) {
24
24
  const idsNotFound = [];
25
25
  await Promise.all(views.map(async (data, idx) => {
26
26
  const view = model.views[idx];
27
- const { loc, tracks = [] } = data;
28
- await view.navToLocString(loc);
27
+ const { assembly, loc, tracks = [] } = data;
28
+ const asm = await assemblyManager.waitForAssembly(assembly);
29
+ if (!asm) {
30
+ throw new Error(`Assembly ${data.assembly} failed to load`);
31
+ }
32
+ await view.navToSearchString({ input: loc, assembly: asm });
29
33
  tracks.forEach(track => tryTrack(view, track, idsNotFound));
30
34
  }));
31
35
  tracks.forEach(track => tryTrack(model, track, idsNotFound));
package/esm/LinearComparativeView/model.d.ts CHANGED
@@ -123,7 +123,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
123
123
  } & {
124
124
  moveTrack(movingId: string, targetId: string): void;
125
125
  closeView(): void;
126
- toggleTrack(trackId: string): void;
126
+ toggleTrack(trackId: string): boolean;
127
127
  setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
128
128
  toggleCenterLine(): void;
129
129
  setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
@@ -173,6 +173,126 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
173
173
  } & {
174
174
  moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
175
175
  navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
176
+ navToSearchString({ input, assembly, }: {
177
+ input: string;
178
+ assembly: {
179
+ configuration: any;
180
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
181
+ error: unknown;
182
+ loaded: boolean;
183
+ loadingP: Promise<void> | undefined;
184
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
185
+ refNameAliases: {
186
+ [x: string]: string | undefined;
187
+ } | undefined;
188
+ lowerCaseRefNameAliases: {
189
+ [x: string]: string | undefined;
190
+ } | undefined;
191
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
192
+ } & {
193
+ getConf(arg: string): any;
194
+ } & {
195
+ readonly initialized: boolean; /**
196
+ * #property
197
+ */
198
+ readonly name: string;
199
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
200
+ readonly aliases: string[];
201
+ readonly displayName: string | undefined;
202
+ hasName(name: string): boolean;
203
+ readonly allAliases: string[];
204
+ readonly allRefNames: string[] | undefined;
205
+ readonly lowerCaseRefNames: string[] | undefined;
206
+ readonly allRefNamesWithLowerCase: string[] | undefined;
207
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
208
+ readonly refNameColors: string[];
209
+ } & {
210
+ readonly refNames: string[] | undefined;
211
+ } & {
212
+ getCanonicalRefName(refName: string): string | undefined;
213
+ getRefNameColor(refName: string): string | undefined;
214
+ isValidRefName(refName: string): boolean;
215
+ } & {
216
+ setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
217
+ setError(e: unknown): void;
218
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
219
+ setRefNameAliases(aliases: {
220
+ [x: string]: string | undefined;
221
+ }, lcAliases: {
222
+ [x: string]: string | undefined;
223
+ }): void;
224
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
225
+ setLoadingP(p?: Promise<void> | undefined): void;
226
+ load(): Promise<void>;
227
+ loadPre(): Promise<void>;
228
+ } & {
229
+ getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
230
+ getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
231
+ [x: string]: string | undefined;
232
+ }>;
233
+ getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
234
+ [x: string]: string | undefined;
235
+ }>;
236
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
237
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
238
+ }, {
239
+ error: unknown;
240
+ loaded: boolean;
241
+ loadingP: Promise<void> | undefined;
242
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
243
+ refNameAliases: {
244
+ [x: string]: string | undefined;
245
+ } | undefined;
246
+ lowerCaseRefNameAliases: {
247
+ [x: string]: string | undefined;
248
+ } | undefined;
249
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
250
+ } & {
251
+ getConf(arg: string): any;
252
+ } & {
253
+ readonly initialized: boolean; /**
254
+ * #property
255
+ */
256
+ readonly name: string;
257
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
258
+ readonly aliases: string[];
259
+ readonly displayName: string | undefined;
260
+ hasName(name: string): boolean;
261
+ readonly allAliases: string[];
262
+ readonly allRefNames: string[] | undefined;
263
+ readonly lowerCaseRefNames: string[] | undefined;
264
+ readonly allRefNamesWithLowerCase: string[] | undefined;
265
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
266
+ readonly refNameColors: string[];
267
+ } & {
268
+ readonly refNames: string[] | undefined;
269
+ } & {
270
+ getCanonicalRefName(refName: string): string | undefined;
271
+ getRefNameColor(refName: string): string | undefined;
272
+ isValidRefName(refName: string): boolean;
273
+ } & {
274
+ setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
275
+ setError(e: unknown): void;
276
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
277
+ setRefNameAliases(aliases: {
278
+ [x: string]: string | undefined;
279
+ }, lcAliases: {
280
+ [x: string]: string | undefined;
281
+ }): void;
282
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
283
+ setLoadingP(p?: Promise<void> | undefined): void;
284
+ load(): Promise<void>;
285
+ loadPre(): Promise<void>;
286
+ } & {
287
+ getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
288
+ getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
289
+ [x: string]: string | undefined;
290
+ }>;
291
+ getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
292
+ [x: string]: string | undefined;
293
+ }>;
294
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
295
+ }): Promise<void>;
176
296
  navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
177
297
  navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
178
298
  navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
@@ -277,7 +397,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
277
397
  /**
278
398
  * #action
279
399
  */
280
- toggleTrack(trackId: string): void;
400
+ toggleTrack(trackId: string): boolean;
281
401
  /**
282
402
  * #action
283
403
  */
package/esm/LinearComparativeView/model.js CHANGED
@@ -186,12 +186,12 @@ function stateModelFactory(pluginManager) {
186
186
  * #action
187
187
  */
188
188
  toggleTrack(trackId) {
189
- // if we have any tracks with that configuration, turn them off
190
189
  const hiddenCount = this.hideTrack(trackId);
191
- // if none had that configuration, turn one on
192
190
  if (!hiddenCount) {
193
191
  this.showTrack(trackId);
192
+ return true;
194
193
  }
194
+ return false;
195
195
  },
196
196
  /**
197
197
  * #action
package/esm/LinearReadVsRef/LinearReadVsRef.js CHANGED
@@ -144,7 +144,7 @@ export default function ReadVsRefDialog({ track, feature: preFeature, handleClos
144
144
  {
145
145
  start: 0,
146
146
  end: totalLength,
147
- seq: featSeq || '',
147
+ seq: featSeq || '', // can be empty if user clicks secondary read
148
148
  refName: readName,
149
149
  uniqueId: `${Math.random()}`,
150
150
  },
package/esm/LinearSyntenyView/components/ImportForm/index.js CHANGED
@@ -17,7 +17,7 @@ const useStyles = makeStyles()(theme => ({
17
17
  },
18
18
  }));
19
19
  function TrackSelector({ setSessionTrackData, setShowTrackId, sessionTrackData, assembly1, assembly2, model, }) {
20
- const [choice, setChoice] = useState('none');
20
+ const [choice, setChoice] = useState('tracklist');
21
21
  useEffect(() => {
22
22
  if (choice === 'none') {
23
23
  setSessionTrackData(undefined);
package/esm/LinearSyntenyView/model.d.ts CHANGED
@@ -134,7 +134,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
134
134
  } & {
135
135
  moveTrack(movingId: string, targetId: string): void;
136
136
  closeView(): void;
137
- toggleTrack(trackId: string): void;
137
+ toggleTrack(trackId: string): boolean;
138
138
  setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
139
139
  toggleCenterLine(): void;
140
140
  setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
@@ -184,6 +184,126 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
184
184
  } & {
185
185
  moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
186
186
  navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
187
+ navToSearchString({ input, assembly, }: {
188
+ input: string;
189
+ assembly: {
190
+ configuration: any;
191
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
192
+ error: unknown;
193
+ loaded: boolean;
194
+ loadingP: Promise<void> | undefined;
195
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
196
+ refNameAliases: {
197
+ [x: string]: string | undefined;
198
+ } | undefined;
199
+ lowerCaseRefNameAliases: {
200
+ [x: string]: string | undefined;
201
+ } | undefined;
202
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
203
+ } & {
204
+ getConf(arg: string): any;
205
+ } & {
206
+ readonly initialized: boolean;
207
+ readonly name: string;
208
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined; /**
209
+ * #property
210
+ */
211
+ readonly aliases: string[];
212
+ readonly displayName: string | undefined;
213
+ hasName(name: string): boolean;
214
+ readonly allAliases: string[];
215
+ readonly allRefNames: string[] | undefined;
216
+ readonly lowerCaseRefNames: string[] | undefined;
217
+ readonly allRefNamesWithLowerCase: string[] | undefined;
218
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
219
+ readonly refNameColors: string[];
220
+ } & {
221
+ readonly refNames: string[] | undefined;
222
+ } & {
223
+ getCanonicalRefName(refName: string): string | undefined;
224
+ getRefNameColor(refName: string): string | undefined;
225
+ isValidRefName(refName: string): boolean;
226
+ } & {
227
+ setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
228
+ setError(e: unknown): void;
229
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
230
+ setRefNameAliases(aliases: {
231
+ [x: string]: string | undefined;
232
+ }, lcAliases: {
233
+ [x: string]: string | undefined;
234
+ }): void;
235
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
236
+ setLoadingP(p?: Promise<void> | undefined): void;
237
+ load(): Promise<void>;
238
+ loadPre(): Promise<void>;
239
+ } & {
240
+ getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
241
+ getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
242
+ [x: string]: string | undefined;
243
+ }>;
244
+ getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
245
+ [x: string]: string | undefined;
246
+ }>;
247
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
248
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
249
+ }, {
250
+ error: unknown;
251
+ loaded: boolean;
252
+ loadingP: Promise<void> | undefined;
253
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
254
+ refNameAliases: {
255
+ [x: string]: string | undefined;
256
+ } | undefined;
257
+ lowerCaseRefNameAliases: {
258
+ [x: string]: string | undefined;
259
+ } | undefined;
260
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
261
+ } & {
262
+ getConf(arg: string): any;
263
+ } & {
264
+ readonly initialized: boolean;
265
+ readonly name: string;
266
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined; /**
267
+ * #property
268
+ */
269
+ readonly aliases: string[];
270
+ readonly displayName: string | undefined;
271
+ hasName(name: string): boolean;
272
+ readonly allAliases: string[];
273
+ readonly allRefNames: string[] | undefined;
274
+ readonly lowerCaseRefNames: string[] | undefined;
275
+ readonly allRefNamesWithLowerCase: string[] | undefined;
276
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
277
+ readonly refNameColors: string[];
278
+ } & {
279
+ readonly refNames: string[] | undefined;
280
+ } & {
281
+ getCanonicalRefName(refName: string): string | undefined;
282
+ getRefNameColor(refName: string): string | undefined;
283
+ isValidRefName(refName: string): boolean;
284
+ } & {
285
+ setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
286
+ setError(e: unknown): void;
287
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
288
+ setRefNameAliases(aliases: {
289
+ [x: string]: string | undefined;
290
+ }, lcAliases: {
291
+ [x: string]: string | undefined;
292
+ }): void;
293
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
294
+ setLoadingP(p?: Promise<void> | undefined): void;
295
+ load(): Promise<void>;
296
+ loadPre(): Promise<void>;
297
+ } & {
298
+ getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
299
+ getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
300
+ [x: string]: string | undefined;
301
+ }>;
302
+ getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
303
+ [x: string]: string | undefined;
304
+ }>;
305
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
306
+ }): Promise<void>;
187
307
  navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
188
308
  navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
189
309
  navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
@@ -385,7 +505,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
385
505
  } & {
386
506
  moveTrack(movingId: string, targetId: string): void;
387
507
  closeView(): void;
388
- toggleTrack(trackId: string): void;
508
+ toggleTrack(trackId: string): boolean;
389
509
  setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
390
510
  toggleCenterLine(): void;
391
511
  setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
@@ -435,6 +555,126 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
435
555
  } & {
436
556
  moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
437
557
  navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
558
+ navToSearchString({ input, assembly, }: {
559
+ input: string;
560
+ assembly: {
561
+ configuration: any;
562
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
563
+ error: unknown;
564
+ loaded: boolean;
565
+ loadingP: Promise<void> | undefined;
566
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
567
+ refNameAliases: {
568
+ [x: string]: string | undefined;
569
+ } | undefined;
570
+ lowerCaseRefNameAliases: {
571
+ [x: string]: string | undefined;
572
+ } | undefined;
573
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
574
+ } & {
575
+ getConf(arg: string): any;
576
+ } & {
577
+ readonly initialized: boolean;
578
+ readonly name: string;
579
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined; /**
580
+ * #property
581
+ */
582
+ readonly aliases: string[];
583
+ readonly displayName: string | undefined;
584
+ hasName(name: string): boolean;
585
+ readonly allAliases: string[];
586
+ readonly allRefNames: string[] | undefined;
587
+ readonly lowerCaseRefNames: string[] | undefined;
588
+ readonly allRefNamesWithLowerCase: string[] | undefined;
589
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
590
+ readonly refNameColors: string[];
591
+ } & {
592
+ readonly refNames: string[] | undefined;
593
+ } & {
594
+ getCanonicalRefName(refName: string): string | undefined;
595
+ getRefNameColor(refName: string): string | undefined;
596
+ isValidRefName(refName: string): boolean;
597
+ } & {
598
+ setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
599
+ setError(e: unknown): void;
600
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
601
+ setRefNameAliases(aliases: {
602
+ [x: string]: string | undefined;
603
+ }, lcAliases: {
604
+ [x: string]: string | undefined;
605
+ }): void;
606
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
607
+ setLoadingP(p?: Promise<void> | undefined): void;
608
+ load(): Promise<void>;
609
+ loadPre(): Promise<void>;
610
+ } & {
611
+ getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
612
+ getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
613
+ [x: string]: string | undefined;
614
+ }>;
615
+ getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
616
+ [x: string]: string | undefined;
617
+ }>;
618
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
619
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
620
+ }, {
621
+ error: unknown;
622
+ loaded: boolean;
623
+ loadingP: Promise<void> | undefined;
624
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
625
+ refNameAliases: {
626
+ [x: string]: string | undefined;
627
+ } | undefined;
628
+ lowerCaseRefNameAliases: {
629
+ [x: string]: string | undefined;
630
+ } | undefined;
631
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
632
+ } & {
633
+ getConf(arg: string): any;
634
+ } & {
635
+ readonly initialized: boolean;
636
+ readonly name: string;
637
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined; /**
638
+ * #property
639
+ */
640
+ readonly aliases: string[];
641
+ readonly displayName: string | undefined;
642
+ hasName(name: string): boolean;
643
+ readonly allAliases: string[];
644
+ readonly allRefNames: string[] | undefined;
645
+ readonly lowerCaseRefNames: string[] | undefined;
646
+ readonly allRefNamesWithLowerCase: string[] | undefined;
647
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
648
+ readonly refNameColors: string[];
649
+ } & {
650
+ readonly refNames: string[] | undefined;
651
+ } & {
652
+ getCanonicalRefName(refName: string): string | undefined;
653
+ getRefNameColor(refName: string): string | undefined;
654
+ isValidRefName(refName: string): boolean;
655
+ } & {
656
+ setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
657
+ setError(e: unknown): void;
658
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
659
+ setRefNameAliases(aliases: {
660
+ [x: string]: string | undefined;
661
+ }, lcAliases: {
662
+ [x: string]: string | undefined;
663
+ }): void;
664
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
665
+ setLoadingP(p?: Promise<void> | undefined): void;
666
+ load(): Promise<void>;
667
+ loadPre(): Promise<void>;
668
+ } & {
669
+ getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
670
+ getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
671
+ [x: string]: string | undefined;
672
+ }>;
673
+ getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
674
+ [x: string]: string | undefined;
675
+ }>;
676
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
677
+ }): Promise<void>;
438
678
  navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
439
679
  navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
440
680
  navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
@@ -574,7 +814,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
574
814
  } & {
575
815
  moveTrack(movingId: string, targetId: string): void;
576
816
  closeView(): void;
577
- toggleTrack(trackId: string): void;
817
+ toggleTrack(trackId: string): boolean;
578
818
  setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
579
819
  toggleCenterLine(): void;
580
820
  setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
@@ -624,6 +864,126 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
624
864
  } & {
625
865
  moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
626
866
  navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
867
+ navToSearchString({ input, assembly, }: {
868
+ input: string;
869
+ assembly: {
870
+ configuration: any;
871
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
872
+ error: unknown;
873
+ loaded: boolean;
874
+ loadingP: Promise<void> | undefined;
875
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
876
+ refNameAliases: {
877
+ [x: string]: string | undefined;
878
+ } | undefined;
879
+ lowerCaseRefNameAliases: {
880
+ [x: string]: string | undefined;
881
+ } | undefined;
882
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
883
+ } & {
884
+ getConf(arg: string): any;
885
+ } & {
886
+ readonly initialized: boolean;
887
+ readonly name: string;
888
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined; /**
889
+ * #property
890
+ */
891
+ readonly aliases: string[];
892
+ readonly displayName: string | undefined;
893
+ hasName(name: string): boolean;
894
+ readonly allAliases: string[];
895
+ readonly allRefNames: string[] | undefined;
896
+ readonly lowerCaseRefNames: string[] | undefined;
897
+ readonly allRefNamesWithLowerCase: string[] | undefined;
898
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
899
+ readonly refNameColors: string[];
900
+ } & {
901
+ readonly refNames: string[] | undefined;
902
+ } & {
903
+ getCanonicalRefName(refName: string): string | undefined;
904
+ getRefNameColor(refName: string): string | undefined;
905
+ isValidRefName(refName: string): boolean;
906
+ } & {
907
+ setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
908
+ setError(e: unknown): void;
909
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
910
+ setRefNameAliases(aliases: {
911
+ [x: string]: string | undefined;
912
+ }, lcAliases: {
913
+ [x: string]: string | undefined;
914
+ }): void;
915
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
916
+ setLoadingP(p?: Promise<void> | undefined): void;
917
+ load(): Promise<void>;
918
+ loadPre(): Promise<void>;
919
+ } & {
920
+ getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
921
+ getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
922
+ [x: string]: string | undefined;
923
+ }>;
924
+ getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
925
+ [x: string]: string | undefined;
926
+ }>;
927
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
928
+ configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
929
+ }, {
930
+ error: unknown;
931
+ loaded: boolean;
932
+ loadingP: Promise<void> | undefined;
933
+ volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
934
+ refNameAliases: {
935
+ [x: string]: string | undefined;
936
+ } | undefined;
937
+ lowerCaseRefNameAliases: {
938
+ [x: string]: string | undefined;
939
+ } | undefined;
940
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined;
941
+ } & {
942
+ getConf(arg: string): any;
943
+ } & {
944
+ readonly initialized: boolean;
945
+ readonly name: string;
946
+ readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined; /**
947
+ * #property
948
+ */
949
+ readonly aliases: string[];
950
+ readonly displayName: string | undefined;
951
+ hasName(name: string): boolean;
952
+ readonly allAliases: string[];
953
+ readonly allRefNames: string[] | undefined;
954
+ readonly lowerCaseRefNames: string[] | undefined;
955
+ readonly allRefNamesWithLowerCase: string[] | undefined;
956
+ readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
957
+ readonly refNameColors: string[];
958
+ } & {
959
+ readonly refNames: string[] | undefined;
960
+ } & {
961
+ getCanonicalRefName(refName: string): string | undefined;
962
+ getRefNameColor(refName: string): string | undefined;
963
+ isValidRefName(refName: string): boolean;
964
+ } & {
965
+ setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
966
+ setError(e: unknown): void;
967
+ setRegions(regions: import("@jbrowse/core/util").Region[]): void;
968
+ setRefNameAliases(aliases: {
969
+ [x: string]: string | undefined;
970
+ }, lcAliases: {
971
+ [x: string]: string | undefined;
972
+ }): void;
973
+ setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
974
+ setLoadingP(p?: Promise<void> | undefined): void;
975
+ load(): Promise<void>;
976
+ loadPre(): Promise<void>;
977
+ } & {
978
+ getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
979
+ getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
980
+ [x: string]: string | undefined;
981
+ }>;
982
+ getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
983
+ [x: string]: string | undefined;
984
+ }>;
985
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
986
+ }): Promise<void>;
627
987
  navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
628
988
  navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
629
989
  navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
@@ -667,7 +1027,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
667
1027
  setMiddleComparativeHeight(n: number): number;
668
1028
  toggleLinkViews(): void;
669
1029
  activateTrackSelector(): import("@jbrowse/core/util").Widget | undefined;
670
- toggleTrack(trackId: string): void;
1030
+ toggleTrack(trackId: string): boolean;
671
1031
  showTrack(trackId: string, initialSnapshot?: {}): void;
672
1032
  hideTrack(trackId: string): number;
673
1033
  squareView(): void;
package/esm/SyntenyTrack/configSchema.d.ts CHANGED
@@ -58,6 +58,11 @@ declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/c
58
58
  defaultValue: number;
59
59
  description: string;
60
60
  };
61
+ maxDepth: {
62
+ type: string;
63
+ defaultValue: number;
64
+ description: string;
65
+ };
61
66
  }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
62
67
  formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
63
68
  config: {
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-linear-comparative-view",
3
- "version": "2.8.0",
3
+ "version": "2.9.0",
4
4
  "description": "JBrowse 2 linear comparative view",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -62,5 +62,5 @@
62
62
  "publishConfig": {
63
63
  "access": "public"
64
64
  },
65
- "gitHead": "ee8c2bdc8bd4f1a70b1eefda984f04a2830d9ca0"
65
+ "gitHead": "a50b6f67cf8c8f3c65a7b8cd858de2fcca1f2909"
66
66
  }