@jbrowse/plugin-sequence 2.4.1 → 2.5.0

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Files changed (29) hide show
  1. package/dist/BgzipFastaAdapter/configSchema.d.ts +43 -1
  2. package/dist/ChromSizesAdapter/configSchema.d.ts +12 -1
  3. package/dist/DivSequenceRenderer/components/DivSequenceRendering.d.ts +0 -1
  4. package/dist/DivSequenceRenderer/configSchema.d.ts +10 -1
  5. package/dist/IndexedFastaAdapter/configSchema.d.ts +33 -1
  6. package/dist/LinearReferenceSequenceDisplay/configSchema.d.ts +12 -1
  7. package/dist/LinearReferenceSequenceDisplay/model.d.ts +81 -31
  8. package/dist/LinearReferenceSequenceDisplay/model.js +2 -2
  9. package/dist/LinearReferenceSequenceDisplay/model.js.map +1 -1
  10. package/dist/ReferenceSequenceTrack/configSchema.d.ts +46 -1
  11. package/dist/SequenceSearchAdapter/configSchema.d.ts +38 -1
  12. package/dist/TwoBitAdapter/TwoBitAdapter.d.ts +1 -1
  13. package/dist/TwoBitAdapter/configSchema.d.ts +23 -1
  14. package/esm/BgzipFastaAdapter/configSchema.d.ts +43 -1
  15. package/esm/ChromSizesAdapter/configSchema.d.ts +12 -1
  16. package/esm/DivSequenceRenderer/components/DivSequenceRendering.d.ts +0 -1
  17. package/esm/DivSequenceRenderer/configSchema.d.ts +10 -1
  18. package/esm/IndexedFastaAdapter/configSchema.d.ts +33 -1
  19. package/esm/LinearReferenceSequenceDisplay/configSchema.d.ts +12 -1
  20. package/esm/LinearReferenceSequenceDisplay/model.d.ts +81 -31
  21. package/esm/LinearReferenceSequenceDisplay/model.js +2 -2
  22. package/esm/LinearReferenceSequenceDisplay/model.js.map +1 -1
  23. package/esm/ReferenceSequenceTrack/configSchema.d.ts +46 -1
  24. package/esm/SequenceSearchAdapter/configSchema.d.ts +38 -1
  25. package/esm/TwoBitAdapter/TwoBitAdapter.d.ts +1 -1
  26. package/esm/TwoBitAdapter/configSchema.d.ts +23 -1
  27. package/package.json +2 -2
  28. package/src/LinearReferenceSequenceDisplay/model.ts +7 -4
  29. package/src/TwoBitAdapter/TwoBitAdapter.ts +1 -1
package/dist/BgzipFastaAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,44 @@
1
- declare const BgzipFastaAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ declare const BgzipFastaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot
4
+ */
5
+ fastaLocation: {
6
+ type: string;
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+ defaultValue: {
8
+ uri: string;
9
+ locationType: string;
10
+ };
11
+ };
12
+ /**
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+ * #slot
14
+ */
15
+ faiLocation: {
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+ type: string;
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+ defaultValue: {
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+ uri: string;
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+ locationType: string;
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+ };
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+ };
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+ /**
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+ * #slot
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+ */
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+ metadataLocation: {
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+ description: string;
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+ type: string;
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+ defaultValue: {
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+ uri: string;
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+ locationType: string;
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+ };
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+ };
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+ /**
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+ * #slot
35
+ */
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+ gziLocation: {
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+ type: string;
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+ defaultValue: {
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+ uri: string;
40
+ locationType: string;
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+ };
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+ };
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2
44
  export default BgzipFastaAdapter;
package/dist/ChromSizesAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,13 @@
1
- declare const ChromSizesAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ declare const ChromSizesAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot
4
+ */
5
+ chromSizesLocation: {
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+ type: string;
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+ defaultValue: {
8
+ uri: string;
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+ locationType: string;
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+ };
11
+ };
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2
13
  export default ChromSizesAdapter;
package/dist/DivSequenceRenderer/components/DivSequenceRendering.d.ts CHANGED
@@ -1,4 +1,3 @@
1
- /// <reference types="react" />
2
1
  import { AnyConfigurationModel } from '@jbrowse/core/configuration';
3
2
  import { Feature, Region } from '@jbrowse/core/util';
4
3
  declare function Sequence(props: {
package/dist/DivSequenceRenderer/configSchema.d.ts CHANGED
@@ -1,2 +1,11 @@
1
- declare const DivSequenceRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ declare const DivSequenceRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot
4
+ */
5
+ height: {
6
+ type: string;
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+ description: string;
8
+ defaultValue: number;
9
+ };
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2
11
  export default DivSequenceRenderer;
package/dist/IndexedFastaAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,34 @@
1
- declare const IndexedFastaAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ declare const IndexedFastaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot
4
+ */
5
+ fastaLocation: {
6
+ type: string;
7
+ defaultValue: {
8
+ uri: string;
9
+ locationType: string;
10
+ };
11
+ };
12
+ /**
13
+ * #slot
14
+ */
15
+ faiLocation: {
16
+ type: string;
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+ defaultValue: {
18
+ uri: string;
19
+ locationType: string;
20
+ };
21
+ };
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+ /**
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+ * #slot
24
+ */
25
+ metadataLocation: {
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+ description: string;
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+ type: string;
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+ defaultValue: {
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+ uri: string;
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+ locationType: string;
31
+ };
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+ };
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2
34
  export default IndexedFastaAdapter;
package/dist/LinearReferenceSequenceDisplay/configSchema.d.ts CHANGED
@@ -1 +1,12 @@
1
- export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot
4
+ */
5
+ renderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
6
+ height: {
7
+ type: string;
8
+ description: string;
9
+ defaultValue: number;
10
+ };
11
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
12
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
package/dist/LinearReferenceSequenceDisplay/model.d.ts CHANGED
@@ -9,6 +9,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
9
9
  type: import("mobx-state-tree").ISimpleType<string>;
10
10
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
11
11
  } & {
12
+ /**
13
+ * #getter
14
+ */
12
15
  heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
13
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  blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
14
17
  key: import("mobx-state-tree").ISimpleType<string>;
@@ -27,6 +30,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
27
30
  isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
28
31
  }, {
29
32
  renderInProgress: AbortController | undefined;
33
+ /**
34
+ * #method
35
+ */
30
36
  filled: boolean;
31
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  reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
32
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  features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -58,9 +64,35 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
58
64
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
59
65
  userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
60
66
  userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
67
+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
68
+ maxFeatureScreenDensity: {
69
+ type: string;
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+ description: string;
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+ defaultValue: number;
72
+ };
73
+ fetchSizeLimit: {
74
+ type: string;
75
+ defaultValue: number;
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+ description: string;
77
+ };
78
+ height: {
79
+ /**
80
+ * #property
81
+ */
82
+ type: string;
83
+ defaultValue: number;
84
+ description: string;
85
+ };
86
+ mouseover: {
87
+ type: string;
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+ description: string;
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+ defaultValue: string;
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+ contextVariable: string[];
91
+ };
92
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
61
93
  } & {
62
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  type: import("mobx-state-tree").ISimpleType<"LinearReferenceSequenceDisplay">;
63
- configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
95
+ configuration: AnyConfigurationSchemaType;
64
96
  showForward: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
65
97
  showReverse: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
66
98
  showTranslation: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -71,15 +103,10 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
71
103
  readonly RenderingComponent: import("react").FC<{
72
104
  model: {
73
105
  id: string;
74
- /**
75
- * #property
76
- */
77
106
  type: string;
78
107
  rpcDriverName: string | undefined;
79
108
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
80
- rendererTypeName: string; /**
81
- * #property
82
- */
109
+ rendererTypeName: string;
83
110
  error: unknown;
84
111
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
85
112
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -99,9 +126,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
99
126
  rpcDriverName: string | undefined;
100
127
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
101
128
  rendererTypeName: string;
102
- error: unknown; /**
103
- * #action
104
- */
129
+ error: unknown;
105
130
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
106
131
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
107
132
  type: import("mobx-state-tree").ISimpleType<string>;
@@ -129,8 +154,8 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
129
154
  message: string;
130
155
  featureIdUnderMouse: string | undefined;
131
156
  contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
132
- estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
133
- estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
157
+ featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
158
+ featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
134
159
  } & {
135
160
  readonly height: number;
136
161
  readonly blockType: "dynamicBlocks" | "staticBlocks";
@@ -143,35 +168,32 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
143
168
  } & {
144
169
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
145
170
  readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
146
- getFeatureOverlapping(blockKey: string, x: number, y: number): any;
171
+ getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
147
172
  getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
148
173
  searchFeatureByID(id: string): [number, number, number, number] | undefined;
149
174
  readonly currentBytesRequested: number;
150
175
  readonly currentFeatureScreenDensity: number;
151
176
  readonly maxFeatureScreenDensity: any;
152
- readonly estimatedStatsReady: boolean;
177
+ readonly featureDensityStatsReady: boolean;
153
178
  readonly maxAllowableBytes: number;
154
179
  } & {
155
180
  setMessage(message: string): void;
181
+ } & {
156
182
  afterAttach(): void;
157
- estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
158
- headers?: Record<string, string> | undefined;
159
- signal?: AbortSignal | undefined;
160
- filters?: string[] | undefined;
161
- }): Promise<{}>;
162
- setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
163
- setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
164
- clearRegionStats(): void;
183
+ getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
184
+ setFeatureDensityStatsP(arg: any): void;
185
+ setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
186
+ clearFeatureDensityStats(): void;
165
187
  setHeight(displayHeight: number): number;
166
188
  resizeHeight(distance: number): number;
167
189
  setScrollTop(scrollTop: number): void;
168
- updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
190
+ setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
169
191
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
170
192
  setCurrBpPerPx(n: number): void;
171
193
  deleteBlock(key: string): void;
172
194
  selectFeature(feature: import("@jbrowse/core/util").Feature): void;
173
195
  clearFeatureSelection(): void;
174
- setFeatureIdUnderMouse(feature: string | undefined): void;
196
+ setFeatureIdUnderMouse(feature?: string | undefined): void;
175
197
  reload(): void;
176
198
  setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
177
199
  } & {
@@ -179,18 +201,13 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
179
201
  readonly regionTooLargeReason: string;
180
202
  } & {
181
203
  reload(): Promise<void>;
204
+ } & {
182
205
  afterAttach(): void;
183
206
  } & {
184
207
  regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
185
208
  regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
186
209
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
187
- contextMenuItems(): {
188
- label: string;
189
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
190
- muiName: string;
191
- };
192
- onClick: () => void;
193
- }[];
210
+ contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
194
211
  renderProps(): any;
195
212
  } & {
196
213
  renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
@@ -242,6 +259,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
242
259
  type: import("mobx-state-tree").ISimpleType<string>;
243
260
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
244
261
  } & {
262
+ /**
263
+ * #getter
264
+ */
245
265
  heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
246
266
  blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
247
267
  key: import("mobx-state-tree").ISimpleType<string>;
@@ -260,6 +280,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
260
280
  isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
261
281
  }, {
262
282
  renderInProgress: AbortController | undefined;
283
+ /**
284
+ * #method
285
+ */
263
286
  filled: boolean;
264
287
  reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
265
288
  features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -291,9 +314,36 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
291
314
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
292
315
  userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
293
316
  userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
317
+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
318
+ maxFeatureScreenDensity: {
319
+ type: string;
320
+ description: string;
321
+ defaultValue: number;
322
+ };
323
+ fetchSizeLimit: {
324
+ type: string;
325
+ defaultValue: number;
326
+ description: string;
327
+ };
328
+ height: {
329
+ /**
330
+ * #property
331
+ */
332
+ type: string;
333
+ defaultValue: number;
334
+ description: string;
335
+ };
336
+ mouseover: {
337
+ type: string;
338
+ description: string;
339
+ defaultValue: string;
340
+ contextVariable: string[];
341
+ };
342
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
294
343
  }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
295
344
  type: string;
296
345
  id: string;
346
+ configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
297
347
  rpcDriverName: string | undefined;
298
348
  heightPreConfig: number | undefined;
299
349
  userBpPerPxLimit: number | undefined;
package/dist/LinearReferenceSequenceDisplay/model.js CHANGED
@@ -41,11 +41,11 @@ function modelFactory(configSchema) {
41
41
  * #method
42
42
  */
43
43
  renderProps() {
44
- const { showForward, showReverse, showTranslation } = self;
44
+ const { showForward, rpcDriverName, showReverse, showTranslation } = self;
45
45
  return {
46
46
  ...superRenderProps(),
47
- rpcDriverName: self.rpcDriverName,
48
47
  config: self.configuration.renderer,
48
+ rpcDriverName,
49
49
  showForward,
50
50
  showReverse,
51
51
  showTranslation,
package/dist/LinearReferenceSequenceDisplay/model.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/model.ts"],"names":[],"mappings":";;;AAAA,qDAAoD;AACpD,kFAG2C;AAC3C,+DAGoC;AACpC,6CAAsD;AACtD,+BAA8B;AAI9B;;;GAGG;AACH,SAAgB,YAAY,CAAC,YAAwC;IACnE,OAAO,uBAAK;SACT,OAAO,CACN,gCAAgC,EAChC,6CAAiB,EACjB,uBAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,gCAAgC,CAAC;QACrD;;WAEG;QACH,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;QACnD;;WAEG;QACH,WAAW,EAAE,IAAI;QACjB;;WAEG;QACH,WAAW,EAAE,IAAI;QACjB;;WAEG;QACH,eAAe,EAAE,IAAI;KACtB,CAAC,CACH;SACA,KAAK,CAAC,IAAI,CAAC,EAAE;QACZ,MAAM,EAAE,WAAW,EAAE,gBAAgB,EAAE,GAAG,IAAI,CAAA;QAC9C,OAAO;YACL;;eAEG;YACH,WAAW;gBACT,MAAM,EAAE,WAAW,EAAE,aAAa,EAAE,WAAW,EAAE,eAAe,EAAE,GAChE,IAAI,CAAA;gBACN,OAAO;oBACL,GAAG,gBAAgB,EAAE;oBACrB,MAAM,EAAE,IAAI,CAAC,aAAa,CAAC,QAAQ;oBACnC,aAAa;oBACb,WAAW;oBACX,WAAW;oBACX,eAAe;iBAChB,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CAAC;SACD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,sBAAsB,EAAC,YAAY;YACjC,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAQ,CAAA;YAC3C,OAAO,CAAA,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,OAAO,KAAI,CAAC,CAAC,CAAC,CAAC,yBAAyB,CAAC,CAAC,CAAC,SAAS,CAAA;QACnE,CAAC;QACD;;WAEG;QACH,IAAI,gBAAgB;YAClB,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAC,IAAI,CAAA;QACzC,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,iBAAiB;YACf,IAAI,CAAC,WAAW,GAAG,CAAC,IAAI,CAAC,WAAW,CAAA;QACtC,CAAC;QACD;;WAEG;QACH,iBAAiB;YACf,IAAI,CAAC,WAAW,GAAG,CAAC,IAAI,CAAC,WAAW,CAAA;QACtC,CAAC;QACD;;WAEG;QACH,qBAAqB;YACnB,IAAI,CAAC,eAAe,GAAG,CAAC,IAAI,CAAC,eAAe,CAAA;QAC9C,CAAC;QACD,WAAW;YACT,IAAA,6BAAW,EACT,IAAI,EACJ,IAAA,cAAO,EAAC,GAAG,EAAE;gBACX,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAQ,CAAA;gBAC3C,IAAI,CAAA,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,OAAO,KAAI,CAAC,EAAE;oBACtB,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC,CAAA;iBACnB;qBAAM;oBACL,MAAM,EAAE,eAAe,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAA;oBAC1D,MAAM,EAAE,GAAG,WAAW,IAAI,eAAe,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;oBAClD,MAAM,EAAE,GAAG,WAAW,IAAI,eAAe,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;oBAClD,MAAM,CAAC,GAAG,EAAE,GAAG,EAAE,CAAA;oBACjB,MAAM,CAAC,GAAG,WAAW,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;oBAC9B,MAAM,CAAC,GAAG,WAAW,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;oBAC9B,IAAI,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAA;iBAC1B;YACH,CAAC,CAAC,CACH,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,cAAc;YACZ,OAAO;gBACL;oBACE,KAAK,EAAE,cAAc;oBACrB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,IAAI,CAAC,WAAW;oBACzB,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,iBAAiB,EAAE;iBACxC;gBACD;oBACE,KAAK,EAAE,cAAc;oBACrB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,IAAI,CAAC,WAAW;oBACzB,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,iBAAiB,EAAE;iBACxC;gBACD;oBACE,KAAK,EAAE,kBAAkB;oBACzB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,IAAI,CAAC,eAAe;oBAC7B,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,qBAAqB,EAAE;iBAC5C;aACF,CAAA;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC;AAjID,oCAiIC"}
package/dist/ReferenceSequenceTrack/configSchema.d.ts CHANGED
@@ -1,2 +1,47 @@
1
1
  import PluginManager from '@jbrowse/core/PluginManager';
2
- export declare function createReferenceSeqTrackConfig(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
+ export declare function createReferenceSeqTrackConfig(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
3
+ /**
4
+ * #slot
5
+ * configuration for track adapter
6
+ */
7
+ adapter: import("mobx-state-tree").IAnyModelType;
8
+ /**
9
+ * #slot
10
+ * configuration for the displays e.g. LinearReferenceSequenceDisplay
11
+ */
12
+ displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
13
+ /**
14
+ * #slot
15
+ */
16
+ name: {
17
+ type: string;
18
+ description: string;
19
+ defaultValue: string;
20
+ };
21
+ /**
22
+ * #slot
23
+ */
24
+ metadata: {
25
+ type: string;
26
+ description: string;
27
+ defaultValue: {};
28
+ };
29
+ formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
30
+ /**
31
+ * #slot formatAbout.config
32
+ */
33
+ config: {
34
+ type: string;
35
+ description: string;
36
+ defaultValue: {};
37
+ contextVariable: string[];
38
+ };
39
+ /**
40
+ * #slot formatAbout.hideUris
41
+ */
42
+ hideUris: {
43
+ type: string;
44
+ defaultValue: boolean;
45
+ };
46
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
47
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>;
package/dist/SequenceSearchAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,39 @@
1
- declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot
4
+ */
5
+ search: {
6
+ type: string;
7
+ defaultValue: string;
8
+ description: string;
9
+ };
10
+ /**
11
+ * #slot
12
+ */
13
+ sequenceAdapter: {
14
+ type: string;
15
+ defaultValue: null;
16
+ };
17
+ /**
18
+ * #slot
19
+ */
20
+ searchForward: {
21
+ type: string;
22
+ defaultValue: boolean;
23
+ };
24
+ /**
25
+ * #slot
26
+ */
27
+ searchReverse: {
28
+ type: string;
29
+ defaultValue: boolean;
30
+ };
31
+ /**
32
+ * #slot
33
+ */
34
+ caseInsensitive: {
35
+ type: string;
36
+ defaultValue: boolean;
37
+ };
38
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2
39
  export default configSchema;
package/dist/TwoBitAdapter/TwoBitAdapter.d.ts CHANGED
@@ -1,7 +1,7 @@
1
1
  import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
2
2
  import { NoAssemblyRegion } from '@jbrowse/core/util/types';
3
3
  import { Feature } from '@jbrowse/core/util/simpleFeature';
4
- import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
4
+ import { AnyConfigurationModel } from '@jbrowse/core/configuration';
5
5
  import PluginManager from '@jbrowse/core/PluginManager';
6
6
  import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
7
7
  export default class TwoBitAdapter extends BaseSequenceAdapter {
package/dist/TwoBitAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,24 @@
1
- declare const TwoBitAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ declare const TwoBitAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot
4
+ */
5
+ twoBitLocation: {
6
+ type: string;
7
+ defaultValue: {
8
+ uri: string;
9
+ locationType: string;
10
+ };
11
+ };
12
+ /**
13
+ * #slot
14
+ */
15
+ chromSizesLocation: {
16
+ type: string;
17
+ defaultValue: {
18
+ uri: string;
19
+ locationType: string;
20
+ };
21
+ description: string;
22
+ };
23
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2
24
  export default TwoBitAdapter;
package/esm/BgzipFastaAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,44 @@
1
- declare const BgzipFastaAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ declare const BgzipFastaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot
4
+ */
5
+ fastaLocation: {
6
+ type: string;
7
+ defaultValue: {
8
+ uri: string;
9
+ locationType: string;
10
+ };
11
+ };
12
+ /**
13
+ * #slot
14
+ */
15
+ faiLocation: {
16
+ type: string;
17
+ defaultValue: {
18
+ uri: string;
19
+ locationType: string;
20
+ };
21
+ };
22
+ /**
23
+ * #slot
24
+ */
25
+ metadataLocation: {
26
+ description: string;
27
+ type: string;
28
+ defaultValue: {
29
+ uri: string;
30
+ locationType: string;
31
+ };
32
+ };
33
+ /**
34
+ * #slot
35
+ */
36
+ gziLocation: {
37
+ type: string;
38
+ defaultValue: {
39
+ uri: string;
40
+ locationType: string;
41
+ };
42
+ };
43
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2
44
  export default BgzipFastaAdapter;
package/esm/ChromSizesAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,13 @@
1
- declare const ChromSizesAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ declare const ChromSizesAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot
4
+ */
5
+ chromSizesLocation: {
6
+ type: string;
7
+ defaultValue: {
8
+ uri: string;
9
+ locationType: string;
10
+ };
11
+ };
12
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2
13
  export default ChromSizesAdapter;
package/esm/DivSequenceRenderer/components/DivSequenceRendering.d.ts CHANGED
@@ -1,4 +1,3 @@
1
- /// <reference types="react" />
2
1
  import { AnyConfigurationModel } from '@jbrowse/core/configuration';
3
2
  import { Feature, Region } from '@jbrowse/core/util';
4
3
  declare function Sequence(props: {
package/esm/DivSequenceRenderer/configSchema.d.ts CHANGED
@@ -1,2 +1,11 @@
1
- declare const DivSequenceRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ declare const DivSequenceRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot
4
+ */
5
+ height: {
6
+ type: string;
7
+ description: string;
8
+ defaultValue: number;
9
+ };
10
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2
11
  export default DivSequenceRenderer;
package/esm/IndexedFastaAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,34 @@
1
- declare const IndexedFastaAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ declare const IndexedFastaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot
4
+ */
5
+ fastaLocation: {
6
+ type: string;
7
+ defaultValue: {
8
+ uri: string;
9
+ locationType: string;
10
+ };
11
+ };
12
+ /**
13
+ * #slot
14
+ */
15
+ faiLocation: {
16
+ type: string;
17
+ defaultValue: {
18
+ uri: string;
19
+ locationType: string;
20
+ };
21
+ };
22
+ /**
23
+ * #slot
24
+ */
25
+ metadataLocation: {
26
+ description: string;
27
+ type: string;
28
+ defaultValue: {
29
+ uri: string;
30
+ locationType: string;
31
+ };
32
+ };
33
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2
34
  export default IndexedFastaAdapter;
package/esm/LinearReferenceSequenceDisplay/configSchema.d.ts CHANGED
@@ -1 +1,12 @@
1
- export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot
4
+ */
5
+ renderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
6
+ height: {
7
+ type: string;
8
+ description: string;
9
+ defaultValue: number;
10
+ };
11
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
12
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
package/esm/LinearReferenceSequenceDisplay/model.d.ts CHANGED
@@ -9,6 +9,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
9
9
  type: import("mobx-state-tree").ISimpleType<string>;
10
10
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
11
11
  } & {
12
+ /**
13
+ * #getter
14
+ */
12
15
  heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
13
16
  blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
14
17
  key: import("mobx-state-tree").ISimpleType<string>;
@@ -27,6 +30,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
27
30
  isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
28
31
  }, {
29
32
  renderInProgress: AbortController | undefined;
33
+ /**
34
+ * #method
35
+ */
30
36
  filled: boolean;
31
37
  reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
32
38
  features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -58,9 +64,35 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
58
64
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
59
65
  userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
60
66
  userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
67
+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
68
+ maxFeatureScreenDensity: {
69
+ type: string;
70
+ description: string;
71
+ defaultValue: number;
72
+ };
73
+ fetchSizeLimit: {
74
+ type: string;
75
+ defaultValue: number;
76
+ description: string;
77
+ };
78
+ height: {
79
+ /**
80
+ * #property
81
+ */
82
+ type: string;
83
+ defaultValue: number;
84
+ description: string;
85
+ };
86
+ mouseover: {
87
+ type: string;
88
+ description: string;
89
+ defaultValue: string;
90
+ contextVariable: string[];
91
+ };
92
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
61
93
  } & {
62
94
  type: import("mobx-state-tree").ISimpleType<"LinearReferenceSequenceDisplay">;
63
- configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
95
+ configuration: AnyConfigurationSchemaType;
64
96
  showForward: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
65
97
  showReverse: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
66
98
  showTranslation: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -71,15 +103,10 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
71
103
  readonly RenderingComponent: import("react").FC<{
72
104
  model: {
73
105
  id: string;
74
- /**
75
- * #property
76
- */
77
106
  type: string;
78
107
  rpcDriverName: string | undefined;
79
108
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
80
- rendererTypeName: string; /**
81
- * #property
82
- */
109
+ rendererTypeName: string;
83
110
  error: unknown;
84
111
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
85
112
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -99,9 +126,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
99
126
  rpcDriverName: string | undefined;
100
127
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
101
128
  rendererTypeName: string;
102
- error: unknown; /**
103
- * #action
104
- */
129
+ error: unknown;
105
130
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
106
131
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
107
132
  type: import("mobx-state-tree").ISimpleType<string>;
@@ -129,8 +154,8 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
129
154
  message: string;
130
155
  featureIdUnderMouse: string | undefined;
131
156
  contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
132
- estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
133
- estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
157
+ featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
158
+ featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
134
159
  } & {
135
160
  readonly height: number;
136
161
  readonly blockType: "dynamicBlocks" | "staticBlocks";
@@ -143,35 +168,32 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
143
168
  } & {
144
169
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
145
170
  readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
146
- getFeatureOverlapping(blockKey: string, x: number, y: number): any;
171
+ getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
147
172
  getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
148
173
  searchFeatureByID(id: string): [number, number, number, number] | undefined;
149
174
  readonly currentBytesRequested: number;
150
175
  readonly currentFeatureScreenDensity: number;
151
176
  readonly maxFeatureScreenDensity: any;
152
- readonly estimatedStatsReady: boolean;
177
+ readonly featureDensityStatsReady: boolean;
153
178
  readonly maxAllowableBytes: number;
154
179
  } & {
155
180
  setMessage(message: string): void;
181
+ } & {
156
182
  afterAttach(): void;
157
- estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
158
- headers?: Record<string, string> | undefined;
159
- signal?: AbortSignal | undefined;
160
- filters?: string[] | undefined;
161
- }): Promise<{}>;
162
- setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
163
- setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
164
- clearRegionStats(): void;
183
+ getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
184
+ setFeatureDensityStatsP(arg: any): void;
185
+ setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
186
+ clearFeatureDensityStats(): void;
165
187
  setHeight(displayHeight: number): number;
166
188
  resizeHeight(distance: number): number;
167
189
  setScrollTop(scrollTop: number): void;
168
- updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
190
+ setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
169
191
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
170
192
  setCurrBpPerPx(n: number): void;
171
193
  deleteBlock(key: string): void;
172
194
  selectFeature(feature: import("@jbrowse/core/util").Feature): void;
173
195
  clearFeatureSelection(): void;
174
- setFeatureIdUnderMouse(feature: string | undefined): void;
196
+ setFeatureIdUnderMouse(feature?: string | undefined): void;
175
197
  reload(): void;
176
198
  setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
177
199
  } & {
@@ -179,18 +201,13 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
179
201
  readonly regionTooLargeReason: string;
180
202
  } & {
181
203
  reload(): Promise<void>;
204
+ } & {
182
205
  afterAttach(): void;
183
206
  } & {
184
207
  regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
185
208
  regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
186
209
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
187
- contextMenuItems(): {
188
- label: string;
189
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
190
- muiName: string;
191
- };
192
- onClick: () => void;
193
- }[];
210
+ contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
194
211
  renderProps(): any;
195
212
  } & {
196
213
  renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
@@ -242,6 +259,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
242
259
  type: import("mobx-state-tree").ISimpleType<string>;
243
260
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
244
261
  } & {
262
+ /**
263
+ * #getter
264
+ */
245
265
  heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
246
266
  blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
247
267
  key: import("mobx-state-tree").ISimpleType<string>;
@@ -260,6 +280,9 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
260
280
  isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
261
281
  }, {
262
282
  renderInProgress: AbortController | undefined;
283
+ /**
284
+ * #method
285
+ */
263
286
  filled: boolean;
264
287
  reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
265
288
  features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -291,9 +314,36 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
291
314
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
292
315
  userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
293
316
  userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
317
+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
318
+ maxFeatureScreenDensity: {
319
+ type: string;
320
+ description: string;
321
+ defaultValue: number;
322
+ };
323
+ fetchSizeLimit: {
324
+ type: string;
325
+ defaultValue: number;
326
+ description: string;
327
+ };
328
+ height: {
329
+ /**
330
+ * #property
331
+ */
332
+ type: string;
333
+ defaultValue: number;
334
+ description: string;
335
+ };
336
+ mouseover: {
337
+ type: string;
338
+ description: string;
339
+ defaultValue: string;
340
+ contextVariable: string[];
341
+ };
342
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
294
343
  }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
295
344
  type: string;
296
345
  id: string;
346
+ configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
297
347
  rpcDriverName: string | undefined;
298
348
  heightPreConfig: number | undefined;
299
349
  userBpPerPxLimit: number | undefined;
package/esm/LinearReferenceSequenceDisplay/model.js CHANGED
@@ -38,11 +38,11 @@ export function modelFactory(configSchema) {
38
38
  * #method
39
39
  */
40
40
  renderProps() {
41
- const { showForward, showReverse, showTranslation } = self;
41
+ const { showForward, rpcDriverName, showReverse, showTranslation } = self;
42
42
  return {
43
43
  ...superRenderProps(),
44
- rpcDriverName: self.rpcDriverName,
45
44
  config: self.configuration.renderer,
45
+ rpcDriverName,
46
46
  showForward,
47
47
  showReverse,
48
48
  showTranslation,
package/esm/LinearReferenceSequenceDisplay/model.js.map CHANGED
@@ -1 +1 @@
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package/esm/ReferenceSequenceTrack/configSchema.d.ts CHANGED
@@ -1,2 +1,47 @@
1
1
  import PluginManager from '@jbrowse/core/PluginManager';
2
- export declare function createReferenceSeqTrackConfig(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
+ export declare function createReferenceSeqTrackConfig(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
3
+ /**
4
+ * #slot
5
+ * configuration for track adapter
6
+ */
7
+ adapter: import("mobx-state-tree").IAnyModelType;
8
+ /**
9
+ * #slot
10
+ * configuration for the displays e.g. LinearReferenceSequenceDisplay
11
+ */
12
+ displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
13
+ /**
14
+ * #slot
15
+ */
16
+ name: {
17
+ type: string;
18
+ description: string;
19
+ defaultValue: string;
20
+ };
21
+ /**
22
+ * #slot
23
+ */
24
+ metadata: {
25
+ type: string;
26
+ description: string;
27
+ defaultValue: {};
28
+ };
29
+ formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
30
+ /**
31
+ * #slot formatAbout.config
32
+ */
33
+ config: {
34
+ type: string;
35
+ description: string;
36
+ defaultValue: {};
37
+ contextVariable: string[];
38
+ };
39
+ /**
40
+ * #slot formatAbout.hideUris
41
+ */
42
+ hideUris: {
43
+ type: string;
44
+ defaultValue: boolean;
45
+ };
46
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
47
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>;
package/esm/SequenceSearchAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,39 @@
1
- declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot
4
+ */
5
+ search: {
6
+ type: string;
7
+ defaultValue: string;
8
+ description: string;
9
+ };
10
+ /**
11
+ * #slot
12
+ */
13
+ sequenceAdapter: {
14
+ type: string;
15
+ defaultValue: null;
16
+ };
17
+ /**
18
+ * #slot
19
+ */
20
+ searchForward: {
21
+ type: string;
22
+ defaultValue: boolean;
23
+ };
24
+ /**
25
+ * #slot
26
+ */
27
+ searchReverse: {
28
+ type: string;
29
+ defaultValue: boolean;
30
+ };
31
+ /**
32
+ * #slot
33
+ */
34
+ caseInsensitive: {
35
+ type: string;
36
+ defaultValue: boolean;
37
+ };
38
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2
39
  export default configSchema;
package/esm/TwoBitAdapter/TwoBitAdapter.d.ts CHANGED
@@ -1,7 +1,7 @@
1
1
  import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
2
2
  import { NoAssemblyRegion } from '@jbrowse/core/util/types';
3
3
  import { Feature } from '@jbrowse/core/util/simpleFeature';
4
- import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
4
+ import { AnyConfigurationModel } from '@jbrowse/core/configuration';
5
5
  import PluginManager from '@jbrowse/core/PluginManager';
6
6
  import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
7
7
  export default class TwoBitAdapter extends BaseSequenceAdapter {
package/esm/TwoBitAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,24 @@
1
- declare const TwoBitAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ declare const TwoBitAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot
4
+ */
5
+ twoBitLocation: {
6
+ type: string;
7
+ defaultValue: {
8
+ uri: string;
9
+ locationType: string;
10
+ };
11
+ };
12
+ /**
13
+ * #slot
14
+ */
15
+ chromSizesLocation: {
16
+ type: string;
17
+ defaultValue: {
18
+ uri: string;
19
+ locationType: string;
20
+ };
21
+ description: string;
22
+ };
23
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2
24
  export default TwoBitAdapter;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-sequence",
3
- "version": "2.4.1",
3
+ "version": "2.5.0",
4
4
  "description": "JBrowse 2 sequence adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -58,5 +58,5 @@
58
58
  "distModule": "esm/index.js",
59
59
  "srcModule": "src/index.ts",
60
60
  "module": "esm/index.js",
61
- "gitHead": "747c50c4edc0184827efa4f8dfc576ca9a72caeb"
61
+ "gitHead": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
62
62
  }
package/src/LinearReferenceSequenceDisplay/model.ts CHANGED
@@ -10,6 +10,8 @@ import {
10
10
  import { getContainingView } from '@jbrowse/core/util'
11
11
  import { autorun } from 'mobx'
12
12
 
13
+ type LGV = LinearGenomeViewModel
14
+
13
15
  /**
14
16
  * #stateModel LinearReferenceSequenceDisplay
15
17
  * base model `BaseLinearDisplay`
@@ -49,11 +51,12 @@ export function modelFactory(configSchema: AnyConfigurationSchemaType) {
49
51
  * #method
50
52
  */
51
53
  renderProps() {
52
- const { showForward, showReverse, showTranslation } = self
54
+ const { showForward, rpcDriverName, showReverse, showTranslation } =
55
+ self
53
56
  return {
54
57
  ...superRenderProps(),
55
- rpcDriverName: self.rpcDriverName,
56
58
  config: self.configuration.renderer,
59
+ rpcDriverName,
57
60
  showForward,
58
61
  showReverse,
59
62
  showTranslation,
@@ -66,7 +69,7 @@ export function modelFactory(configSchema: AnyConfigurationSchemaType) {
66
69
  * #method
67
70
  */
68
71
  regionCannotBeRendered(/* region */) {
69
- const view = getContainingView(self) as LinearGenomeViewModel
72
+ const view = getContainingView(self) as LGV
70
73
  return view?.bpPerPx >= 1 ? 'Zoom in to see sequence' : undefined
71
74
  },
72
75
  /**
@@ -99,7 +102,7 @@ export function modelFactory(configSchema: AnyConfigurationSchemaType) {
99
102
  addDisposer(
100
103
  self,
101
104
  autorun(() => {
102
- const view = getContainingView(self) as LinearGenomeViewModel
105
+ const view = getContainingView(self) as LGV
103
106
  if (view?.bpPerPx >= 1) {
104
107
  self.setHeight(50)
105
108
  } else {
package/src/TwoBitAdapter/TwoBitAdapter.ts CHANGED
@@ -5,7 +5,7 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs'
5
5
  import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
6
6
  import { TwoBitFile } from '@gmod/twobit'
7
7
  import { readConfObject } from '@jbrowse/core/configuration'
8
- import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'
8
+ import { AnyConfigurationModel } from '@jbrowse/core/configuration'
9
9
  import PluginManager from '@jbrowse/core/PluginManager'
10
10
  import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
11
11