@vitessce/all 2.0.3 → 3.0.0

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 (48) hide show
  1. package/dist/{deflate.8ace1ac4.mjs → deflate-f57b3163.js} +2 -2
  2. package/dist/hglib-1422f224.js +138925 -0
  3. package/dist/{index.7dac8670.mjs → index-3f1c1764.js} +67100 -52955
  4. package/dist/index.js +12 -0
  5. package/dist/{jpeg.c8011e3a.mjs → jpeg-e740c9a5.js} +1 -1
  6. package/dist/{lerc.ccda5eb2.mjs → lerc-01e6c4d8.js} +76 -5
  7. package/dist/{lzw.39876143.mjs → lzw-865bd058.js} +1 -1
  8. package/dist/{packbits.9e95d117.mjs → packbits-d4191efd.js} +1 -1
  9. package/dist/{pako.esm.4b234125.mjs → pako.esm-68f84e2a.js} +97 -15
  10. package/dist/{raw.0279d74b.mjs → raw-3c693341.js} +1 -1
  11. package/dist/{webimage.5ac7ce95.mjs → webimage-83da2258.js} +1 -1
  12. package/dist-tsc/Vitessce.d.ts +2 -0
  13. package/dist-tsc/Vitessce.d.ts.map +1 -0
  14. package/dist-tsc/Vitessce.js +41 -0
  15. package/dist-tsc/base-plugins.d.ts +854 -0
  16. package/dist-tsc/base-plugins.d.ts.map +1 -0
  17. package/dist-tsc/base-plugins.js +191 -0
  18. package/dist-tsc/index.d.ts +4 -0
  19. package/dist-tsc/index.d.ts.map +1 -0
  20. package/dist-tsc/index.js +3 -2
  21. package/dist-tsc/joint-file-types-legacy.d.ts +226 -0
  22. package/dist-tsc/joint-file-types-legacy.d.ts.map +1 -0
  23. package/dist-tsc/joint-file-types-legacy.js +266 -0
  24. package/dist-tsc/joint-file-types-legacy.test.d.ts +2 -0
  25. package/dist-tsc/joint-file-types-legacy.test.d.ts.map +1 -0
  26. package/dist-tsc/joint-file-types-legacy.test.js +401 -0
  27. package/dist-tsc/joint-file-types.d.ts +4 -0
  28. package/dist-tsc/joint-file-types.d.ts.map +1 -0
  29. package/dist-tsc/joint-file-types.js +127 -0
  30. package/dist-tsc/joint-file-types.test.d.ts +2 -0
  31. package/dist-tsc/joint-file-types.test.d.ts.map +1 -0
  32. package/dist-tsc/joint-file-types.test.js +128 -0
  33. package/dist-tsc/latest-config-schema.test.d.ts +2 -0
  34. package/dist-tsc/latest-config-schema.test.d.ts.map +1 -0
  35. package/dist-tsc/latest-config-schema.test.js +19 -0
  36. package/package.json +37 -21
  37. package/src/Vitessce.tsx +74 -0
  38. package/src/base-plugins.ts +362 -0
  39. package/src/index.ts +8 -0
  40. package/src/joint-file-types-legacy.test.ts +413 -0
  41. package/src/joint-file-types-legacy.ts +284 -0
  42. package/src/joint-file-types.test.ts +132 -0
  43. package/src/joint-file-types.ts +142 -0
  44. package/src/latest-config-schema.test.ts +26 -0
  45. package/dist/hglib.1f1ea875.mjs +0 -130303
  46. package/dist/index.mjs +0 -11
  47. package/src/index.js +0 -7
  48. package/src/setup.js +0 -143
package/dist/index.mjs DELETED
@@ -1,11 +0,0 @@
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- import { V } from "./index.7dac8670.mjs";
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- import { registerPluginCoordinationType, registerPluginFileType, registerPluginJointFileType, registerPluginViewType } from "@vitessce/vit-s";
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- import "react";
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- import "react-dom";
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- export {
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- V as Vitessce,
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- registerPluginCoordinationType,
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- registerPluginFileType,
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- registerPluginJointFileType,
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- registerPluginViewType
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- };
package/src/index.js DELETED
@@ -1,7 +0,0 @@
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- export { Vitessce } from './setup';
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- export {
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- registerPluginFileType,
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- registerPluginViewType,
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- registerPluginCoordinationType,
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- registerPluginJointFileType,
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- } from '@vitessce/vit-s';
package/src/setup.js DELETED
@@ -1,143 +0,0 @@
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- /* eslint-disable max-len */
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- import { useState, useLayoutEffect } from 'react';
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- import { VitS, registerPluginFileType } from '@vitessce/vit-s';
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-
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- // Register view type plugins
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- import { register as registerDescription } from '@vitessce/description';
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- import { register as registerObsSetsManager } from '@vitessce/obs-sets-manager';
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- import { register as registerScatterplotEmbedding } from '@vitessce/scatterplot-embedding';
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- import { register as registerScatterplotGating } from '@vitessce/scatterplot-gating';
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- import { register as registerSpatial } from '@vitessce/spatial';
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- import { register as registerHeatmap } from '@vitessce/heatmap';
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- import { register as registerFeatureList } from '@vitessce/feature-list';
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- import { register as registerLayerController } from '@vitessce/layer-controller';
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- import { register as registerStatus } from '@vitessce/status';
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- import { registerCellSetExpression, registerCellSetSizes, registerExpressionHistogram } from '@vitessce/statistical-plots';
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- import { registerHiglass, registerGenomicProfiles } from '@vitessce/genomic-profiles';
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-
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- // Register file type plugins
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- import {
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- // CSV
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- CsvSource,
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- ObsSetsCsvLoader,
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- ObsEmbeddingCsvLoader,
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- ObsLocationsCsvLoader,
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- ObsLabelsCsvLoader,
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- ObsFeatureMatrixCsvLoader,
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- FeatureLabelsCsvLoader,
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- } from '@vitessce/csv';
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- import {
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- // JSON
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- JsonSource,
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- JsonLoader,
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- ObsSegmentationsJsonLoader,
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- ObsSetsJsonLoader,
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- // Legacy
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- RasterJsonAsImageLoader,
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- RasterJsonAsObsSegmentationsLoader,
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- ClustersJsonAsObsFeatureMatrixLoader,
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- GenesJsonAsObsFeatureMatrixLoader,
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- CellsJsonAsObsLabelsLoader,
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- CellsJsonAsObsEmbeddingLoader,
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- CellsJsonAsObsLocationsLoader,
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- CellsJsonAsObsSegmentationsLoader,
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- MoleculesJsonAsObsLocationsLoader,
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- MoleculesJsonAsObsLabelsLoader,
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- } from '@vitessce/json';
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- import {
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- // AnnData
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- AnnDataSource,
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- ObsFeatureMatrixAnndataLoader,
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- ObsEmbeddingAnndataLoader,
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- ObsLocationsAnndataLoader,
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- ObsSegmentationsAnndataLoader,
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- ObsSetsAnndataLoader,
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- ObsLabelsAnndataLoader,
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- FeatureLabelsAnndataLoader,
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- // MuData
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- MuDataSource,
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- // OME
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- OmeZarrLoader,
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- // Legacy
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- ZarrDataSource,
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- MatrixZarrAsObsFeatureMatrixLoader,
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- GenomicProfilesZarrLoader,
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- } from '@vitessce/zarr';
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- import { FileType, DataType } from '@vitessce/constants-internal';
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-
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- function setup() {
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- // View types
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- registerDescription();
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- registerObsSetsManager();
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- registerScatterplotEmbedding();
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- registerScatterplotGating();
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- registerSpatial();
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- registerHeatmap();
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- registerFeatureList();
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- registerLayerController();
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- registerStatus();
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- // Statistical plots
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- registerCellSetExpression();
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- registerCellSetSizes();
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- registerExpressionHistogram();
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- // Higlass
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- registerHiglass();
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- registerGenomicProfiles();
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-
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- // File types
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- // All CSV file types
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- registerPluginFileType(FileType.OBS_SETS_CSV, DataType.OBS_SETS, ObsSetsCsvLoader, CsvSource);
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- registerPluginFileType(FileType.OBS_EMBEDDING_CSV, DataType.OBS_EMBEDDING, ObsEmbeddingCsvLoader, CsvSource);
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- registerPluginFileType(FileType.OBS_LOCATIONS_CSV, DataType.OBS_LOCATIONS, ObsLocationsCsvLoader, CsvSource);
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- registerPluginFileType(FileType.OBS_LABELS_CSV, DataType.OBS_LABELS, ObsLabelsCsvLoader, CsvSource);
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- registerPluginFileType(FileType.OBS_FEATURE_MATRIX_CSV, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixCsvLoader, CsvSource);
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- registerPluginFileType(FileType.FEATURE_LABELS_CSV, DataType.FEATURE_LABELS, FeatureLabelsCsvLoader, CsvSource);
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- // All JSON file types
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- registerPluginFileType(FileType.OBS_SEGMENTATIONS_JSON, DataType.OBS_SEGMENTATIONS, ObsSegmentationsJsonLoader, JsonSource);
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- registerPluginFileType(FileType.OBS_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource);
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- // All AnnData file types
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- registerPluginFileType(FileType.OBS_SETS_ANNDATA_ZARR, DataType.OBS_SETS, ObsSetsAnndataLoader, AnnDataSource);
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- registerPluginFileType(FileType.OBS_EMBEDDING_ANNDATA_ZARR, DataType.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, AnnDataSource);
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- registerPluginFileType(FileType.OBS_LOCATIONS_ANNDATA_ZARR, DataType.OBS_LOCATIONS, ObsLocationsAnndataLoader, AnnDataSource);
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- registerPluginFileType(FileType.OBS_LABELS_ANNDATA_ZARR, DataType.OBS_LABELS, ObsLabelsAnndataLoader, AnnDataSource);
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- registerPluginFileType(FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixAnndataLoader, AnnDataSource);
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- registerPluginFileType(FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, AnnDataSource);
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- registerPluginFileType(FileType.FEATURE_LABELS_ANNDATA_ZARR, DataType.FEATURE_LABELS, FeatureLabelsAnndataLoader, AnnDataSource);
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- // All MuData file types
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- registerPluginFileType(FileType.OBS_SETS_MUDATA_ZARR, DataType.OBS_SETS, ObsSetsAnndataLoader, MuDataSource);
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- registerPluginFileType(FileType.OBS_EMBEDDING_MUDATA_ZARR, DataType.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, MuDataSource);
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- registerPluginFileType(FileType.OBS_LOCATIONS_MUDATA_ZARR, DataType.OBS_LOCATIONS, ObsLocationsAnndataLoader, MuDataSource);
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- registerPluginFileType(FileType.OBS_LABELS_MUDATA_ZARR, DataType.OBS_LABELS, ObsLabelsAnndataLoader, MuDataSource);
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- registerPluginFileType(FileType.OBS_FEATURE_MATRIX_MUDATA_ZARR, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixAnndataLoader, MuDataSource);
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- registerPluginFileType(FileType.OBS_SEGMENTATIONS_MUDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, MuDataSource);
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- registerPluginFileType(FileType.FEATURE_LABELS_MUDATA_ZARR, DataType.FEATURE_LABELS, FeatureLabelsAnndataLoader, MuDataSource);
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- // All OME file types
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- registerPluginFileType(FileType.IMAGE_OME_ZARR, DataType.IMAGE, OmeZarrLoader, ZarrDataSource);
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-
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- // All legacy file types
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- registerPluginFileType(FileType.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR, DataType.OBS_FEATURE_MATRIX, MatrixZarrAsObsFeatureMatrixLoader, ZarrDataSource);
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- registerPluginFileType(FileType.IMAGE_RASTER_JSON, DataType.IMAGE, RasterJsonAsImageLoader, JsonSource);
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- registerPluginFileType(FileType.OBS_SEGMENTATIONS_RASTER_JSON, DataType.OBS_SEGMENTATIONS, RasterJsonAsObsSegmentationsLoader, JsonSource);
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- registerPluginFileType(FileType.OBS_SETS_CELL_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource);
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- registerPluginFileType(FileType.OBS_FEATURE_MATRIX_CLUSTERS_JSON, DataType.OBS_FEATURE_MATRIX, ClustersJsonAsObsFeatureMatrixLoader, JsonSource);
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- registerPluginFileType(FileType.OBS_FEATURE_MATRIX_GENES_JSON, DataType.OBS_FEATURE_MATRIX, GenesJsonAsObsFeatureMatrixLoader, JsonSource);
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- registerPluginFileType(FileType.OBS_LABELS_CELLS_JSON, DataType.OBS_LABELS, CellsJsonAsObsLabelsLoader, JsonSource);
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- registerPluginFileType(FileType.OBS_EMBEDDING_CELLS_JSON, DataType.OBS_EMBEDDING, CellsJsonAsObsEmbeddingLoader, JsonSource);
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- registerPluginFileType(FileType.OBS_LOCATIONS_CELLS_JSON, DataType.OBS_LOCATIONS, CellsJsonAsObsLocationsLoader, JsonSource);
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- registerPluginFileType(FileType.OBS_SEGMENTATIONS_CELLS_JSON, DataType.OBS_SEGMENTATIONS, CellsJsonAsObsSegmentationsLoader, JsonSource);
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- registerPluginFileType(FileType.OBS_LOCATIONS_MOLECULES_JSON, DataType.OBS_LOCATIONS, MoleculesJsonAsObsLocationsLoader, JsonSource);
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- registerPluginFileType(FileType.OBS_LABELS_MOLECULES_JSON, DataType.OBS_LABELS, MoleculesJsonAsObsLabelsLoader, JsonSource);
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- registerPluginFileType(FileType.NEIGHBORHOODS_JSON, DataType.NEIGHBORHOODS, JsonLoader, JsonSource);
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- registerPluginFileType(FileType.GENOMIC_PROFILES_ZARR, DataType.GENOMIC_PROFILES, GenomicProfilesZarrLoader, ZarrDataSource);
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- }
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-
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- export function Vitessce(props) {
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- const [ready, setReady] = useState(false);
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- useLayoutEffect(() => {
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- setup();
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- setReady(true);
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- }, []);
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- return (ready ? (
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- <VitS {...props} />
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- ) : null);
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- }