@vitessce/all 4.0.8 → 4.0.10

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (31) hide show
  1. package/dist/{GeometryAndMeshXR-Caba1QEa.js → GeometryAndMeshXR-BovcVfOy.js} +1 -1
  2. package/dist/{ReactNeuroglancer-Cm_ERWOf.js → ReactNeuroglancer-Ch1xO_u5.js} +1 -1
  3. package/dist/{XREnterButton-C7Q7e8rD.js → XREnterButton-Dz4r7Jjx.js} +1 -1
  4. package/dist/{XRSceneComponents-Dgayh6-j.js → XRSceneComponents-CGcz34cr.js} +1 -1
  5. package/dist/{XRWrapper-BrRGN2E4.js → XRWrapper-C1AfBFtW.js} +2 -2
  6. package/dist/{deflate-D1RcEgtg.js → deflate-BKJk_mLF.js} +1 -1
  7. package/dist/{higlass-BLYM2C4s.js → higlass-BzshVp46.js} +1 -1
  8. package/dist/{index-Bub8madF.js → index-CNXTPnLt.js} +1 -1
  9. package/dist/{index-B8xbImKw.js → index-CfweEgJW.js} +5 -5
  10. package/dist/{index-CzTdHRMx.js → index-EoA5CfO8.js} +1907 -150
  11. package/dist/index.js +8 -1
  12. package/dist/{jpeg-g9i0I1mK.js → jpeg-DXSq15HV.js} +1 -1
  13. package/dist/{lerc-B4lSBwWt.js → lerc-uTsWAc7Y.js} +1 -1
  14. package/dist/{lzw-63HBqTiG.js → lzw-CIpLYaya.js} +1 -1
  15. package/dist/{packbits-i970u6wg.js → packbits-Cf0TB9M_.js} +1 -1
  16. package/dist/{raw-akfNT_LS.js → raw-CR3kVxsB.js} +1 -1
  17. package/dist/{webimage-CA4EiJGO.js → webimage-Dp3HLfwF.js} +1 -1
  18. package/dist/{xrStore--BrpHLm6.js → xrStore-B2qW6VGJ.js} +1 -1
  19. package/dist-tsc/base-plugins.d.ts +268 -1
  20. package/dist-tsc/base-plugins.d.ts.map +1 -1
  21. package/dist-tsc/base-plugins.js +13 -2
  22. package/dist-tsc/base-plugins.js.map +1 -1
  23. package/dist-tsc/index.d.ts +1 -0
  24. package/dist-tsc/index.d.ts.map +1 -1
  25. package/dist-tsc/index.js +1 -0
  26. package/dist-tsc/index.js.map +1 -1
  27. package/dist-tsc/joint-file-types-legacy.d.ts +18 -18
  28. package/dist-tsc/joint-file-types-legacy.d.ts.map +1 -1
  29. package/package.json +34 -33
  30. package/src/base-plugins.ts +14 -0
  31. package/src/index.ts +7 -0
package/dist-tsc/joint-file-types-legacy.d.ts CHANGED
@@ -6,7 +6,7 @@ type legacyFileDefSchema = z.infer<typeof latestFileDefSchema> & {
6
6
  export declare function expandMoleculesJson(fileDef: legacyFileDefSchema): {
7
7
  fileType: string;
8
8
  coordinationValues: {
9
- obsType: string;
9
+ obsType: any;
10
10
  };
11
11
  name?: string | undefined;
12
12
  url?: string | undefined;
@@ -27,9 +27,9 @@ export declare function expandMoleculesJson(fileDef: legacyFileDefSchema): {
27
27
  export declare function expandExpressionMatrixZarr(fileDef: legacyFileDefSchema): {
28
28
  fileType: string;
29
29
  coordinationValues: {
30
- obsType: string;
31
- featureType: string;
32
- featureValueType: string;
30
+ obsType: any;
31
+ featureType: any;
32
+ featureValueType: any;
33
33
  };
34
34
  name?: string | undefined;
35
35
  url?: string | undefined;
@@ -63,7 +63,7 @@ export declare function expandRasterJson(fileDef: legacyFileDefSchema): {
63
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  referrer?: string | undefined;
64
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  integrity?: string | undefined;
65
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  } | undefined;
66
- coordinationValues?: Record<string, string> | undefined;
66
+ coordinationValues?: Record<string, any> | undefined;
67
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  type?: string;
68
68
  }[];
69
69
  export declare function expandRasterOmeZarr(fileDef: legacyFileDefSchema): {
@@ -82,13 +82,13 @@ export declare function expandRasterOmeZarr(fileDef: legacyFileDefSchema): {
82
82
  referrer?: string | undefined;
83
83
  integrity?: string | undefined;
84
84
  } | undefined;
85
- coordinationValues?: Record<string, string> | undefined;
85
+ coordinationValues?: Record<string, any> | undefined;
86
86
  type?: string;
87
87
  }[];
88
88
  export declare function expandCellSetsJson(fileDef: legacyFileDefSchema): {
89
89
  fileType: string;
90
90
  coordinationValues: {
91
- obsType: string;
91
+ obsType: any;
92
92
  };
93
93
  name?: string | undefined;
94
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  url?: string | undefined;
@@ -110,9 +110,9 @@ export declare function expandCellsJson(fileDef: legacyFileDefSchema): any[];
110
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  export declare function expandClustersJson(fileDef: legacyFileDefSchema): {
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  fileType: string;
112
112
  coordinationValues: {
113
- obsType: string;
114
- featureType: string;
115
- featureValueType: string;
113
+ obsType: any;
114
+ featureType: any;
115
+ featureValueType: any;
116
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  };
117
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  name?: string | undefined;
118
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  url?: string | undefined;
@@ -133,9 +133,9 @@ export declare function expandClustersJson(fileDef: legacyFileDefSchema): {
133
133
  export declare function expandGenesJson(fileDef: legacyFileDefSchema): {
134
134
  fileType: string;
135
135
  coordinationValues: {
136
- obsType: string;
137
- featureType: string;
138
- featureValueType: string;
136
+ obsType: any;
137
+ featureType: any;
138
+ featureValueType: any;
139
139
  };
140
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  name?: string | undefined;
141
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  url?: string | undefined;
@@ -158,7 +158,7 @@ export declare function expandAnndataCellSetsZarr(fileDef: legacyFileDefSchema):
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  fileType: string;
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  options: any;
160
160
  coordinationValues: {
161
- obsType: string;
161
+ obsType: any;
162
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  };
163
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  url: string | undefined;
164
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  requestInit: {
@@ -181,7 +181,7 @@ export declare function expandAnndataExpressionMatrixZarr(fileDef: legacyFileDef
181
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  initialFeatureFilterPath?: undefined;
182
182
  };
183
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  coordinationValues: {
184
- featureType: string;
184
+ featureType: any;
185
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  obsType?: undefined;
186
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  featureValueType?: undefined;
187
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  };
@@ -205,9 +205,9 @@ export declare function expandAnndataExpressionMatrixZarr(fileDef: legacyFileDef
205
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  initialFeatureFilterPath: any;
206
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  };
207
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  coordinationValues: {
208
- obsType: string;
209
- featureType: string;
210
- featureValueType: string;
208
+ obsType: any;
209
+ featureType: any;
210
+ featureValueType: any;
211
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  };
212
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  url: string | undefined;
213
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  requestInit: {
package/dist-tsc/joint-file-types-legacy.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"joint-file-types-legacy.d.ts","sourceRoot":"","sources":["../src/joint-file-types-legacy.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAC7B,OAAO,KAAK,EAAE,mBAAmB,EAAE,MAAM,mBAAmB,CAAC;AAG7D,KAAK,mBAAmB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,mBAAmB,CAAC,GAAG;IAC/D,IAAI,CAAC,EAAE,MAAM,CAAC;CACf,CAAC;AAEF,wBAAgB,mBAAmB,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;cAoRk23G,CAAC;eAAqC,CAAC;YAA+C,CAAC;YAAkC,CAAC;mBAAyC,CAAC;aAAmC,CAAC;gBAAsC,CAAC;gBAAsC,CAAC;iBAAuC,CAAC;;WAvRvt4G,MAAM;IAqBd;AAED,wBAAgB,0BAA0B,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;cAgQ213G,CAAC;eAAqC,CAAC;YAA+C,CAAC;YAAkC,CAAC;mBAAyC,CAAC;aAAmC,CAAC;gBAAsC,CAAC;gBAAsC,CAAC;iBAAuC,CAAC;;WAvRvt4G,MAAM;IAuCd;AAED,wBAAgB,gBAAgB,CAAC,OAAO,EAAE,mBAAmB;;;;;;cA8Oq23G,CAAC;eAAqC,CAAC;YAA+C,CAAC;YAAkC,CAAC;mBAAyC,CAAC;aAAmC,CAAC;gBAAsC,CAAC;gBAAsC,CAAC;iBAAuC,CAAC;;;WAvRvt4G,MAAM;IA0Dd;AAED,wBAAgB,mBAAmB,CAAC,OAAO,EAAE,mBAAmB;;;;;;cA2Nk23G,CAAC;eAAqC,CAAC;YAA+C,CAAC;YAAkC,CAAC;mBAAyC,CAAC;aAAmC,CAAC;gBAAsC,CAAC;gBAAsC,CAAC;iBAAuC,CAAC;;;WAvRvt4G,MAAM;IAqEd;AAED,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;cAgNm23G,CAAC;eAAqC,CAAC;YAA+C,CAAC;YAAkC,CAAC;mBAAyC,CAAC;aAAmC,CAAC;gBAAsC,CAAC;gBAAsC,CAAC;iBAAuC,CAAC;;WAvRvt4G,MAAM;IAmFd;AAED,wBAAgB,eAAe,CAAC,OAAO,EAAE,mBAAmB,SA0C3D;AAED,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;cAsJm23G,CAAC;eAAqC,CAAC;YAA+C,CAAC;YAAkC,CAAC;mBAAyC,CAAC;aAAmC,CAAC;gBAAsC,CAAC;gBAAsC,CAAC;iBAAuC,CAAC;;WAvRvt4G,MAAM;IAiJd;AAED,wBAAgB,eAAe,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;cAoIs23G,CAAC;eAAqC,CAAC;YAA+C,CAAC;YAAkC,CAAC;mBAAyC,CAAC;aAAmC,CAAC;gBAAsC,CAAC;gBAAsC,CAAC;iBAAuC,CAAC;;WAvRvt4G,MAAM;IAmKd;AAeD,wBAAgB,sBAAsB,CAAC,OAAO,EAAE,mBAAmB,SAkDlE;AAED,wBAAgB,yBAAyB,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;IAiBrE;AAED,wBAAgB,iCAAiC,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KA6B7E"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@vitessce/all",
3
- "version": "4.0.8",
3
+ "version": "4.0.10",
4
4
  "author": "HIDIVE Lab at HMS",
5
5
  "homepage": "http://vitessce.io",
6
6
  "repository": {
@@ -17,38 +17,39 @@
17
17
  ],
18
18
  "dependencies": {
19
19
  "zod": "^3.21.4",
20
- "@vitessce/styles": "4.0.8",
21
- "@vitessce/error": "4.0.8",
22
- "@vitessce/abstract": "4.0.8",
23
- "@vitessce/constants-internal": "4.0.8",
24
- "@vitessce/csv": "4.0.8",
25
- "@vitessce/description": "4.0.8",
26
- "@vitessce/feature-list": "4.0.8",
27
- "@vitessce/heatmap": "4.0.8",
28
- "@vitessce/genomic-profiles": "4.0.8",
29
- "@vitessce/glb": "4.0.8",
30
- "@vitessce/json": "4.0.8",
31
- "@vitessce/layer-controller": "4.0.8",
32
- "@vitessce/layer-controller-beta": "4.0.8",
33
- "@vitessce/ome-tiff": "4.0.8",
34
- "@vitessce/link-controller": "4.0.8",
35
- "@vitessce/obs-sets-manager": "4.0.8",
36
- "@vitessce/scatterplot-embedding": "4.0.8",
37
- "@vitessce/plugins": "4.0.8",
38
- "@vitessce/scatterplot-gating": "4.0.8",
39
- "@vitessce/schemas": "4.0.8",
40
- "@vitessce/spatial": "4.0.8",
41
- "@vitessce/statistical-plots": "4.0.8",
42
- "@vitessce/spatial-beta": "4.0.8",
43
- "@vitessce/status": "4.0.8",
44
- "@vitessce/vit-s": "4.0.8",
45
- "@vitessce/zarr": "4.0.8",
46
- "@vitessce/globals": "4.0.8",
47
- "@vitessce/spatial-three": "4.0.8",
48
- "@vitessce/spatial-accelerated": "4.0.8",
49
- "@vitessce/biomarker-select": "4.0.8",
50
- "@vitessce/spatial-zarr": "4.0.8",
51
- "@vitessce/neuroglancer": "4.0.8"
20
+ "@vitessce/styles": "4.0.10",
21
+ "@vitessce/abstract": "4.0.10",
22
+ "@vitessce/constants-internal": "4.0.10",
23
+ "@vitessce/error": "4.0.10",
24
+ "@vitessce/csv": "4.0.10",
25
+ "@vitessce/annotation-controller": "4.0.10",
26
+ "@vitessce/description": "4.0.10",
27
+ "@vitessce/feature-list": "4.0.10",
28
+ "@vitessce/genomic-profiles": "4.0.10",
29
+ "@vitessce/heatmap": "4.0.10",
30
+ "@vitessce/glb": "4.0.10",
31
+ "@vitessce/layer-controller": "4.0.10",
32
+ "@vitessce/link-controller": "4.0.10",
33
+ "@vitessce/obs-sets-manager": "4.0.10",
34
+ "@vitessce/json": "4.0.10",
35
+ "@vitessce/ome-tiff": "4.0.10",
36
+ "@vitessce/layer-controller-beta": "4.0.10",
37
+ "@vitessce/plugins": "4.0.10",
38
+ "@vitessce/scatterplot-embedding": "4.0.10",
39
+ "@vitessce/scatterplot-gating": "4.0.10",
40
+ "@vitessce/schemas": "4.0.10",
41
+ "@vitessce/spatial": "4.0.10",
42
+ "@vitessce/statistical-plots": "4.0.10",
43
+ "@vitessce/spatial-beta": "4.0.10",
44
+ "@vitessce/status": "4.0.10",
45
+ "@vitessce/zarr": "4.0.10",
46
+ "@vitessce/vit-s": "4.0.10",
47
+ "@vitessce/globals": "4.0.10",
48
+ "@vitessce/spatial-zarr": "4.0.10",
49
+ "@vitessce/spatial-three": "4.0.10",
50
+ "@vitessce/neuroglancer": "4.0.10",
51
+ "@vitessce/biomarker-select": "4.0.10",
52
+ "@vitessce/spatial-accelerated": "4.0.10"
52
53
  },
53
54
  "devDependencies": {
54
55
  "@types/react": "^19.0.0",
package/src/base-plugins.ts CHANGED
@@ -76,6 +76,8 @@ import {
76
76
  meshGlbSchema,
77
77
  ngPrecomputedMeshSchema,
78
78
  ngPointAnnotationSchema,
79
+ annotationStoryObj,
80
+ annotationShapesArray,
79
81
  } from '@vitessce/schemas';
80
82
 
81
83
  // Register view type plugins
@@ -93,6 +95,7 @@ import { FeatureListSubscriber } from '@vitessce/feature-list';
93
95
  import { LayerControllerSubscriber } from '@vitessce/layer-controller';
94
96
  import { LayerControllerBetaSubscriber } from '@vitessce/layer-controller-beta';
95
97
  import { LinkControllerSubscriber } from '@vitessce/link-controller';
98
+ import { AnnotationControllerSubscriber } from '@vitessce/annotation-controller';
96
99
  import { StatusSubscriber } from '@vitessce/status';
97
100
  import { HiGlassSubscriber, GenomicProfilesSubscriber } from '@vitessce/genomic-profiles';
98
101
  import { NeuroglancerSubscriber } from '@vitessce/neuroglancer';
@@ -131,6 +134,7 @@ import {
131
134
  JsonLoader,
132
135
  ObsSegmentationsJsonLoader,
133
136
  ObsSetsJsonLoader,
137
+ AnnotationStoryJsonLoader,
134
138
  // Legacy
135
139
  RasterJsonAsImageLoader,
136
140
  RasterJsonAsObsSegmentationsLoader,
@@ -291,6 +295,7 @@ export const baseViewTypes = [
291
295
  makeViewType(ViewType.SAMPLE_SET_PAIR_MANAGER, SampleSetPairManagerSubscriber),
292
296
  makeViewType(ViewType.OBS_SET_COMPOSITION_BAR_PLOT, CellSetCompositionBarPlotSubscriber),
293
297
  makeViewType(ViewType.FEATURE_SET_ENRICHMENT_BAR_PLOT, FeatureSetEnrichmentBarPlotSubscriber),
298
+ makeViewType(ViewType.ANNOTATION_CONTROLLER, AnnotationControllerSubscriber),
294
299
  ];
295
300
 
296
301
  export const baseFileTypes = [
@@ -308,6 +313,7 @@ export const baseFileTypes = [
308
313
  // All JSON file types
309
314
  makeFileType(FileType.OBS_SEGMENTATIONS_JSON, DataType.OBS_SEGMENTATIONS, ObsSegmentationsJsonLoader, JsonSource, z.null()),
310
315
  makeFileType(FileType.OBS_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource, z.null()),
316
+ makeFileType(FileType.ANNOTATION_STORY_JSON, DataType.ANNOTATION_STORY, AnnotationStoryJsonLoader, JsonSource, z.null()),
311
317
  // All AnnData file types
312
318
  ...makeZarrFileTypes(FileType.OBS_SETS_ANNDATA_ZARR, DataType.OBS_SETS, ObsSetsAnndataLoader, AnnDataSource, obsSetsAnndataSchema),
313
319
  ...makeZarrFileTypes(FileType.OBS_EMBEDDING_ANNDATA_ZARR, DataType.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, AnnDataSource, obsEmbeddingAnndataSchema),
@@ -656,6 +662,14 @@ export const baseCoordinationTypes = [
656
662
  new PluginCoordinationType(CoordinationType.FEATURE_LABEL_SIGNIFICANCE_THRESHOLD, 0.01, z.number().nullable()),
657
663
  new PluginCoordinationType(CoordinationType.FEATURE_POINT_FOLD_CHANGE_THRESHOLD, 1.0, z.number().nullable()),
658
664
  new PluginCoordinationType(CoordinationType.FEATURE_LABEL_FOLD_CHANGE_THRESHOLD, 5.0, z.number().nullable()),
665
+ // Annotation frames
666
+ new PluginCoordinationType(CoordinationType.ANNOTATION_STORY, null, annotationStoryObj.nullable()),
667
+ new PluginCoordinationType(CoordinationType.ANNOTATION_SHAPES, null, annotationShapesArray.nullable()),
668
+ new PluginCoordinationType(CoordinationType.ANNOTATION_FRAME_INDEX, null, z.number().nullable()),
669
+ new PluginCoordinationType(CoordinationType.ANNOTATION_OVERLAY_VISIBLE, true, z.boolean()),
670
+ new PluginCoordinationType(CoordinationType.ANNOTATION_TRANSITION_DURATION, 0, z.number()), // TODO: make this non-zero by default?
671
+ new PluginCoordinationType(CoordinationType.ANNOTATION_SEMANTIC_ZOOM, true, z.boolean()),
672
+ new PluginCoordinationType(CoordinationType.ANNOTATION_EDITABLE, false, z.boolean()),
659
673
  ];
660
674
 
661
675
  export const baseAsyncFunctions = [
package/src/index.ts CHANGED
@@ -7,6 +7,13 @@ export {
7
7
  PluginAsyncFunction,
8
8
  } from '@vitessce/plugins';
9
9
  export { z } from '@vitessce/schemas';
10
+ export {
11
+ hasAnnotationControllerView,
12
+ addAnnotationControllerView,
13
+ isAnyAnnotationEditing,
14
+ enableAnnotationEditing,
15
+ disableAnnotationEditing,
16
+ } from '@vitessce/annotation-controller';
10
17
  export {
11
18
  useCoordination,
12
19
  useGridItemSize,