@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.
- package/dist/{deflate.8ace1ac4.mjs → deflate-f57b3163.js} +2 -2
- package/dist/hglib-1422f224.js +138925 -0
- package/dist/{index.7dac8670.mjs → index-3f1c1764.js} +67100 -52955
- package/dist/index.js +12 -0
- package/dist/{jpeg.c8011e3a.mjs → jpeg-e740c9a5.js} +1 -1
- package/dist/{lerc.ccda5eb2.mjs → lerc-01e6c4d8.js} +76 -5
- package/dist/{lzw.39876143.mjs → lzw-865bd058.js} +1 -1
- package/dist/{packbits.9e95d117.mjs → packbits-d4191efd.js} +1 -1
- package/dist/{pako.esm.4b234125.mjs → pako.esm-68f84e2a.js} +97 -15
- package/dist/{raw.0279d74b.mjs → raw-3c693341.js} +1 -1
- package/dist/{webimage.5ac7ce95.mjs → webimage-83da2258.js} +1 -1
- package/dist-tsc/Vitessce.d.ts +2 -0
- package/dist-tsc/Vitessce.d.ts.map +1 -0
- package/dist-tsc/Vitessce.js +41 -0
- package/dist-tsc/base-plugins.d.ts +854 -0
- package/dist-tsc/base-plugins.d.ts.map +1 -0
- package/dist-tsc/base-plugins.js +191 -0
- package/dist-tsc/index.d.ts +4 -0
- package/dist-tsc/index.d.ts.map +1 -0
- package/dist-tsc/index.js +3 -2
- package/dist-tsc/joint-file-types-legacy.d.ts +226 -0
- package/dist-tsc/joint-file-types-legacy.d.ts.map +1 -0
- package/dist-tsc/joint-file-types-legacy.js +266 -0
- package/dist-tsc/joint-file-types-legacy.test.d.ts +2 -0
- package/dist-tsc/joint-file-types-legacy.test.d.ts.map +1 -0
- package/dist-tsc/joint-file-types-legacy.test.js +401 -0
- package/dist-tsc/joint-file-types.d.ts +4 -0
- package/dist-tsc/joint-file-types.d.ts.map +1 -0
- package/dist-tsc/joint-file-types.js +127 -0
- package/dist-tsc/joint-file-types.test.d.ts +2 -0
- package/dist-tsc/joint-file-types.test.d.ts.map +1 -0
- package/dist-tsc/joint-file-types.test.js +128 -0
- package/dist-tsc/latest-config-schema.test.d.ts +2 -0
- package/dist-tsc/latest-config-schema.test.d.ts.map +1 -0
- package/dist-tsc/latest-config-schema.test.js +19 -0
- package/package.json +37 -21
- package/src/Vitessce.tsx +74 -0
- package/src/base-plugins.ts +362 -0
- package/src/index.ts +8 -0
- package/src/joint-file-types-legacy.test.ts +413 -0
- package/src/joint-file-types-legacy.ts +284 -0
- package/src/joint-file-types.test.ts +132 -0
- package/src/joint-file-types.ts +142 -0
- package/src/latest-config-schema.test.ts +26 -0
- package/dist/hglib.1f1ea875.mjs +0 -130303
- package/dist/index.mjs +0 -11
- package/src/index.js +0 -7
- package/src/setup.js +0 -143
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{"version":3,"file":"base-plugins.d.ts","sourceRoot":"","sources":["../src/base-plugins.ts"],"names":[],"mappings":"AASA,OAAO,EACL,cAAc,EACd,mBAAmB,EACnB,cAAc,EACd,sBAAsB,EACvB,MAAM,mBAAmB,CAAC;AAC3B,OAAO,KAAK,EACV,UAAU,EACV,UAAU,EACX,MAAM,mBAAmB,CAAC;AAC3B,OAAO,EACL,CAAC,EA4BF,MAAM,mBAAmB,CAAC;AAoG3B,eAAO,MAAM,aAAa,kBAezB,CAAC;AAEF,eAAO,MAAM,aAAa,wDA8CzB,CAAC;AAEF,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;OAc9B,CAAC;AAIF,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;OAkIjC,CAAC"}
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import { FileType, DataType, ViewType, CoordinationType, COMPONENT_COORDINATION_TYPES, } from '@vitessce/constants-internal';
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import { PluginFileType, PluginJointFileType, PluginViewType, PluginCoordinationType, } from '@vitessce/plugins';
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import { z, obsEmbeddingCsvSchema, obsSetsCsvSchema, obsLocationsCsvSchema, obsLabelsCsvSchema, featureLabelsCsvSchema, obsSetsAnndataSchema, obsEmbeddingAnndataSchema, obsLocationsAnndataSchema, obsLabelsAnndataSchema, obsFeatureMatrixAnndataSchema, obsSegmentationsAnndataSchema, featureLabelsAnndataSchema, rasterJsonSchema, anndataZarrSchema, anndataCellsZarrSchema, anndataCellSetsZarrSchema, anndataExpressionMatrixZarrSchema, cellsJsonSchema, imageOmeZarrSchema, imageOmeTiffSchema, obsSetPath, rgbArray, obsSetsSchema, imageLayerObj, cellsLayerObj, neighborhoodsLayerObj, moleculesLayerObj, } from '@vitessce/schemas';
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// Register view type plugins
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import { DescriptionSubscriber } from '@vitessce/description';
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import { ObsSetsManagerSubscriber } from '@vitessce/obs-sets-manager';
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import { EmbeddingScatterplotSubscriber } from '@vitessce/scatterplot-embedding';
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import { GatingSubscriber } from '@vitessce/scatterplot-gating';
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import { SpatialSubscriber } from '@vitessce/spatial';
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import { HeatmapSubscriber } from '@vitessce/heatmap';
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import { FeatureListSubscriber } from '@vitessce/feature-list';
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import { LayerControllerSubscriber } from '@vitessce/layer-controller';
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import { StatusSubscriber } from '@vitessce/status';
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import { HiGlassSubscriber, GenomicProfilesSubscriber } from '@vitessce/genomic-profiles';
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import { CellSetExpressionPlotSubscriber, CellSetSizesPlotSubscriber, ExpressionHistogramSubscriber, } from '@vitessce/statistical-plots';
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// Register file type plugins
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import {
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// CSV
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CsvSource, ObsSetsCsvLoader, ObsEmbeddingCsvLoader, ObsLocationsCsvLoader, ObsLabelsCsvLoader, ObsFeatureMatrixCsvLoader, FeatureLabelsCsvLoader, } from '@vitessce/csv';
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import {
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// JSON
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JsonSource, JsonLoader, ObsSegmentationsJsonLoader, ObsSetsJsonLoader,
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// Legacy
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RasterJsonAsImageLoader, RasterJsonAsObsSegmentationsLoader, ClustersJsonAsObsFeatureMatrixLoader, GenesJsonAsObsFeatureMatrixLoader, CellsJsonAsObsLabelsLoader, CellsJsonAsObsEmbeddingLoader, CellsJsonAsObsLocationsLoader, CellsJsonAsObsSegmentationsLoader, MoleculesJsonAsObsLocationsLoader, MoleculesJsonAsObsLabelsLoader, } from '@vitessce/json';
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import {
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// AnnData
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AnnDataSource, ObsFeatureMatrixAnndataLoader, ObsEmbeddingAnndataLoader, ObsLocationsAnndataLoader, ObsSegmentationsAnndataLoader, ObsSetsAnndataLoader, ObsLabelsAnndataLoader, 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, MatrixZarrAsObsFeatureMatrixLoader, GenomicProfilesZarrLoader, } from '@vitessce/zarr';
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import { OmeTiffAsObsSegmentationsLoader, OmeTiffLoader, OmeTiffSource, } from '@vitessce/ome-tiff';
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// Joint file types
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import { expandAnndataZarr, } from './joint-file-types.js';
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import { expandAnndataCellSetsZarr, expandAnndataCellsZarr, expandAnndataExpressionMatrixZarr, expandCellSetsJson, expandCellsJson, expandClustersJson, expandExpressionMatrixZarr, expandGenesJson, expandMoleculesJson, expandRasterJson, expandRasterOmeZarr, } from './joint-file-types-legacy.js';
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// Helper function to use COMPONENT_COORDINATION_TYPES.
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function makeViewType(name, component) {
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return new PluginViewType(name, component, COMPONENT_COORDINATION_TYPES[name]);
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}
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function makeFileType(name, dataType, dataLoaderClass, dataSourceClass, optionsSchema) {
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return new PluginFileType(name, dataType, dataLoaderClass, dataSourceClass, optionsSchema);
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}
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export const baseViewTypes = [
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makeViewType(ViewType.DESCRIPTION, DescriptionSubscriber),
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makeViewType(ViewType.OBS_SETS, ObsSetsManagerSubscriber),
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makeViewType(ViewType.SCATTERPLOT, EmbeddingScatterplotSubscriber),
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makeViewType(ViewType.GATING, GatingSubscriber),
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makeViewType(ViewType.SPATIAL, SpatialSubscriber),
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makeViewType(ViewType.HEATMAP, HeatmapSubscriber),
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makeViewType(ViewType.FEATURE_LIST, FeatureListSubscriber),
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makeViewType(ViewType.LAYER_CONTROLLER, LayerControllerSubscriber),
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makeViewType(ViewType.STATUS, StatusSubscriber),
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makeViewType(ViewType.OBS_SET_FEATURE_VALUE_DISTRIBUTION, CellSetExpressionPlotSubscriber),
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makeViewType(ViewType.OBS_SET_SIZES, CellSetSizesPlotSubscriber),
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makeViewType(ViewType.FEATURE_VALUE_HISTOGRAM, ExpressionHistogramSubscriber),
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makeViewType('higlass', HiGlassSubscriber),
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makeViewType(ViewType.GENOMIC_PROFILES, GenomicProfilesSubscriber),
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];
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export const baseFileTypes = [
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// All CSV file types
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makeFileType(FileType.OBS_SETS_CSV, DataType.OBS_SETS, ObsSetsCsvLoader, CsvSource, obsSetsCsvSchema),
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makeFileType(FileType.OBS_EMBEDDING_CSV, DataType.OBS_EMBEDDING, ObsEmbeddingCsvLoader, CsvSource, obsEmbeddingCsvSchema),
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makeFileType(FileType.OBS_LOCATIONS_CSV, DataType.OBS_LOCATIONS, ObsLocationsCsvLoader, CsvSource, obsLocationsCsvSchema),
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makeFileType(FileType.OBS_LABELS_CSV, DataType.OBS_LABELS, ObsLabelsCsvLoader, CsvSource, obsLabelsCsvSchema),
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makeFileType(FileType.OBS_FEATURE_MATRIX_CSV, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixCsvLoader, CsvSource, z.null()),
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makeFileType(FileType.FEATURE_LABELS_CSV, DataType.FEATURE_LABELS, FeatureLabelsCsvLoader, CsvSource, featureLabelsCsvSchema),
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// All JSON file types
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makeFileType(FileType.OBS_SEGMENTATIONS_JSON, DataType.OBS_SEGMENTATIONS, ObsSegmentationsJsonLoader, JsonSource, z.null()),
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makeFileType(FileType.OBS_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource, z.null()),
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// All AnnData file types
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makeFileType(FileType.OBS_SETS_ANNDATA_ZARR, DataType.OBS_SETS, ObsSetsAnndataLoader, AnnDataSource, obsSetsAnndataSchema),
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makeFileType(FileType.OBS_EMBEDDING_ANNDATA_ZARR, DataType.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, AnnDataSource, obsEmbeddingAnndataSchema),
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makeFileType(FileType.OBS_LOCATIONS_ANNDATA_ZARR, DataType.OBS_LOCATIONS, ObsLocationsAnndataLoader, AnnDataSource, obsLocationsAnndataSchema),
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makeFileType(FileType.OBS_LABELS_ANNDATA_ZARR, DataType.OBS_LABELS, ObsLabelsAnndataLoader, AnnDataSource, obsLabelsAnndataSchema),
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makeFileType(FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixAnndataLoader, AnnDataSource, obsFeatureMatrixAnndataSchema),
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makeFileType(FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, AnnDataSource, obsSegmentationsAnndataSchema),
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makeFileType(FileType.FEATURE_LABELS_ANNDATA_ZARR, DataType.FEATURE_LABELS, FeatureLabelsAnndataLoader, AnnDataSource, featureLabelsAnndataSchema),
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// All MuData file types
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makeFileType(FileType.OBS_SETS_MUDATA_ZARR, DataType.OBS_SETS, ObsSetsAnndataLoader, MuDataSource, obsSetsAnndataSchema),
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makeFileType(FileType.OBS_EMBEDDING_MUDATA_ZARR, DataType.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, MuDataSource, obsEmbeddingAnndataSchema),
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makeFileType(FileType.OBS_LOCATIONS_MUDATA_ZARR, DataType.OBS_LOCATIONS, ObsLocationsAnndataLoader, MuDataSource, obsLocationsAnndataSchema),
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makeFileType(FileType.OBS_LABELS_MUDATA_ZARR, DataType.OBS_LABELS, ObsLabelsAnndataLoader, MuDataSource, obsLabelsAnndataSchema),
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makeFileType(FileType.OBS_FEATURE_MATRIX_MUDATA_ZARR, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixAnndataLoader, MuDataSource, obsFeatureMatrixAnndataSchema),
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makeFileType(FileType.OBS_SEGMENTATIONS_MUDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, MuDataSource, obsSegmentationsAnndataSchema),
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makeFileType(FileType.FEATURE_LABELS_MUDATA_ZARR, DataType.FEATURE_LABELS, FeatureLabelsAnndataLoader, MuDataSource, featureLabelsAnndataSchema),
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// All OME file types
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makeFileType(FileType.IMAGE_OME_ZARR, DataType.IMAGE, OmeZarrLoader, ZarrDataSource, imageOmeZarrSchema),
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makeFileType(FileType.IMAGE_OME_TIFF, DataType.IMAGE, OmeTiffLoader, OmeTiffSource, imageOmeTiffSchema),
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makeFileType(FileType.OBS_SEGMENTATIONS_OME_TIFF, DataType.OBS_SEGMENTATIONS, OmeTiffAsObsSegmentationsLoader, OmeTiffSource, imageOmeZarrSchema),
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// All legacy file types
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makeFileType(FileType.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR, DataType.OBS_FEATURE_MATRIX, MatrixZarrAsObsFeatureMatrixLoader, ZarrDataSource, z.null()),
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makeFileType(FileType.IMAGE_RASTER_JSON, DataType.IMAGE, RasterJsonAsImageLoader, JsonSource, rasterJsonSchema),
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makeFileType(FileType.OBS_SEGMENTATIONS_RASTER_JSON, DataType.OBS_SEGMENTATIONS, RasterJsonAsObsSegmentationsLoader, JsonSource, rasterJsonSchema),
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makeFileType(FileType.OBS_SETS_CELL_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource, z.null()),
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makeFileType(FileType.OBS_FEATURE_MATRIX_CLUSTERS_JSON, DataType.OBS_FEATURE_MATRIX, ClustersJsonAsObsFeatureMatrixLoader, JsonSource, z.null()),
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makeFileType(FileType.OBS_FEATURE_MATRIX_GENES_JSON, DataType.OBS_FEATURE_MATRIX, GenesJsonAsObsFeatureMatrixLoader, JsonSource, z.null()),
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makeFileType(FileType.OBS_LABELS_CELLS_JSON, DataType.OBS_LABELS, CellsJsonAsObsLabelsLoader, JsonSource, z.null()),
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makeFileType(FileType.OBS_EMBEDDING_CELLS_JSON, DataType.OBS_EMBEDDING, CellsJsonAsObsEmbeddingLoader, JsonSource, z.null()),
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makeFileType(FileType.OBS_LOCATIONS_CELLS_JSON, DataType.OBS_LOCATIONS, CellsJsonAsObsLocationsLoader, JsonSource, z.null()),
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makeFileType(FileType.OBS_SEGMENTATIONS_CELLS_JSON, DataType.OBS_SEGMENTATIONS, CellsJsonAsObsSegmentationsLoader, JsonSource, z.null()),
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makeFileType(FileType.OBS_LOCATIONS_MOLECULES_JSON, DataType.OBS_LOCATIONS, MoleculesJsonAsObsLocationsLoader, JsonSource, z.null()),
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makeFileType(FileType.OBS_LABELS_MOLECULES_JSON, DataType.OBS_LABELS, MoleculesJsonAsObsLabelsLoader, JsonSource, z.null()),
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makeFileType(FileType.NEIGHBORHOODS_JSON, DataType.NEIGHBORHOODS, JsonLoader, JsonSource, z.null()),
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makeFileType(FileType.GENOMIC_PROFILES_ZARR, DataType.GENOMIC_PROFILES, GenomicProfilesZarrLoader, ZarrDataSource, z.null()),
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];
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export const baseJointFileTypes = [
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new PluginJointFileType(FileType.ANNDATA_ZARR, expandAnndataZarr, anndataZarrSchema),
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// For legacy file types:
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new PluginJointFileType(FileType.ANNDATA_CELLS_ZARR, expandAnndataCellsZarr, anndataCellsZarrSchema),
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new PluginJointFileType(FileType.ANNDATA_CELL_SETS_ZARR, expandAnndataCellSetsZarr, anndataCellSetsZarrSchema),
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new PluginJointFileType(FileType.ANNDATA_EXPRESSION_MATRIX_ZARR, expandAnndataExpressionMatrixZarr, anndataExpressionMatrixZarrSchema),
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new PluginJointFileType(FileType.EXPRESSION_MATRIX_ZARR, expandExpressionMatrixZarr, z.null()),
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new PluginJointFileType(FileType.RASTER_JSON, expandRasterJson, rasterJsonSchema),
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new PluginJointFileType(FileType.RASTER_OME_ZARR, expandRasterOmeZarr, z.null()),
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new PluginJointFileType(FileType.CELL_SETS_JSON, expandCellSetsJson, z.null()),
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new PluginJointFileType(FileType.CLUSTERS_JSON, expandClustersJson, z.null()),
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new PluginJointFileType(FileType.GENES_JSON, expandGenesJson, z.null()),
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new PluginJointFileType(FileType.CELLS_JSON, expandCellsJson, cellsJsonSchema),
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new PluginJointFileType(FileType.MOLECULES_JSON, expandMoleculesJson, z.null()),
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];
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// TODO: should these schemas be imported from a common location in package/ rather than here in packages/main/?
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// That would allow view implementations to depend on them for type checking and their default values.
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export const baseCoordinationTypes = [
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new PluginCoordinationType(CoordinationType.DATASET, null, z.string().nullable()),
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new PluginCoordinationType(CoordinationType.OBS_TYPE, 'cell', z.string()),
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new PluginCoordinationType(CoordinationType.FEATURE_TYPE, 'gene', z.string()),
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new PluginCoordinationType(CoordinationType.FEATURE_VALUE_TYPE, 'expression', z.string()),
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new PluginCoordinationType(CoordinationType.OBS_LABELS_TYPE, null, z.string().nullable()),
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new PluginCoordinationType(CoordinationType.EMBEDDING_ZOOM, null, z.number().nullable()),
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new PluginCoordinationType(CoordinationType.EMBEDDING_ROTATION, 0, z.number().nullable()),
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new PluginCoordinationType(CoordinationType.EMBEDDING_TARGET_X, null, z.number().nullable()),
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new PluginCoordinationType(CoordinationType.EMBEDDING_TARGET_Y, null, z.number().nullable()),
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new PluginCoordinationType(CoordinationType.EMBEDDING_TARGET_Z, 0, z.number().nullable()),
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new PluginCoordinationType(CoordinationType.EMBEDDING_TYPE, null, z.string().nullable()),
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new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_SET_POLYGONS_VISIBLE, false, z.boolean()),
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new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_SET_LABELS_VISIBLE, false, z.boolean()),
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new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_SET_LABEL_SIZE, 14, z.number()),
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new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_RADIUS, 1, z.number()),
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new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_OPACITY, 1, z.number()),
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new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_RADIUS_MODE, 'auto', z.enum(['manual', 'auto'])),
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new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_OPACITY_MODE, 'auto', z.enum(['manual', 'auto'])),
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new PluginCoordinationType(CoordinationType.SPATIAL_ZOOM, null, z.number().nullable()),
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new PluginCoordinationType(CoordinationType.SPATIAL_ROTATION, 0, z.number().nullable()),
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new PluginCoordinationType(CoordinationType.SPATIAL_TARGET_X, null, z.number().nullable()),
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new PluginCoordinationType(CoordinationType.SPATIAL_TARGET_Y, null, z.number().nullable()),
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new PluginCoordinationType(CoordinationType.SPATIAL_TARGET_Z, null, z.number().nullable()),
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new PluginCoordinationType(CoordinationType.SPATIAL_ROTATION_X, null, z.number().nullable()),
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new PluginCoordinationType(CoordinationType.SPATIAL_ROTATION_Y, null, z.number().nullable()),
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new PluginCoordinationType(CoordinationType.SPATIAL_ROTATION_Z, null, z.number().nullable()),
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new PluginCoordinationType(CoordinationType.SPATIAL_ROTATION_ORBIT, 0, z.number().nullable()),
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new PluginCoordinationType(CoordinationType.SPATIAL_ORBIT_AXIS, 'Y', z.string().nullable()),
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new PluginCoordinationType(CoordinationType.SPATIAL_AXIS_FIXED, false, z.boolean().nullable()),
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155
|
+
new PluginCoordinationType(CoordinationType.SPATIAL_IMAGE_LAYER, null, imageLayerObj.nullable()),
|
156
|
+
new PluginCoordinationType(CoordinationType.SPATIAL_SEGMENTATION_LAYER, null, z.union([
|
157
|
+
cellsLayerObj, imageLayerObj,
|
158
|
+
]).nullable()),
|
159
|
+
new PluginCoordinationType(CoordinationType.SPATIAL_NEIGHBORHOOD_LAYER, null, neighborhoodsLayerObj.nullable()),
|
160
|
+
new PluginCoordinationType(CoordinationType.SPATIAL_POINT_LAYER, null, moleculesLayerObj.nullable()),
|
161
|
+
new PluginCoordinationType(CoordinationType.HEATMAP_ZOOM_X, 0, z.number()),
|
162
|
+
new PluginCoordinationType(CoordinationType.HEATMAP_ZOOM_Y, 0, z.number()),
|
163
|
+
new PluginCoordinationType(CoordinationType.HEATMAP_TARGET_X, 0, z.number()),
|
164
|
+
new PluginCoordinationType(CoordinationType.HEATMAP_TARGET_Y, 0, z.number()),
|
165
|
+
new PluginCoordinationType(CoordinationType.OBS_FILTER, null, z.array(z.string()).nullable()),
|
166
|
+
new PluginCoordinationType(CoordinationType.OBS_HIGHLIGHT, null, z.string().nullable()),
|
167
|
+
new PluginCoordinationType(CoordinationType.OBS_SET_SELECTION, null, z.array(obsSetPath).nullable()),
|
168
|
+
new PluginCoordinationType(CoordinationType.OBS_SET_EXPANSION, null, z.array(obsSetPath).nullable()),
|
169
|
+
new PluginCoordinationType(CoordinationType.OBS_SET_HIGHLIGHT, null, obsSetPath.nullable()),
|
170
|
+
new PluginCoordinationType(CoordinationType.OBS_SET_COLOR, null, z.array(z.object({
|
171
|
+
path: obsSetPath,
|
172
|
+
color: rgbArray,
|
173
|
+
})).nullable()),
|
174
|
+
new PluginCoordinationType(CoordinationType.OBS_COLOR_ENCODING, 'cellSetSelection', z.enum(['geneSelection', 'cellSetSelection'])),
|
175
|
+
new PluginCoordinationType(CoordinationType.FEATURE_FILTER, null, z.array(z.string()).nullable()),
|
176
|
+
new PluginCoordinationType(CoordinationType.FEATURE_HIGHLIGHT, null, z.string().nullable()),
|
177
|
+
new PluginCoordinationType(CoordinationType.FEATURE_SELECTION, null, z.array(z.string()).nullable()),
|
178
|
+
new PluginCoordinationType(CoordinationType.FEATURE_VALUE_TRANSFORM, null, z.enum(['log1p', 'arcsinh']).nullable()),
|
179
|
+
new PluginCoordinationType(CoordinationType.FEATURE_VALUE_TRANSFORM_COEFFICIENT, 1, z.number()),
|
180
|
+
new PluginCoordinationType(CoordinationType.TOOLTIPS_VISIBLE, true, z.boolean()),
|
181
|
+
new PluginCoordinationType(CoordinationType.FEATURE_VALUE_COLORMAP, 'plasma', z.string().nullable()),
|
182
|
+
new PluginCoordinationType(CoordinationType.FEATURE_VALUE_COLORMAP_RANGE, [0.0, 1.0], z.array(z.number()).length(2)),
|
183
|
+
new PluginCoordinationType(CoordinationType.GATING_FEATURE_SELECTION_X, null, z.string().nullable()),
|
184
|
+
new PluginCoordinationType(CoordinationType.GATING_FEATURE_SELECTION_Y, null, z.string().nullable()),
|
185
|
+
new PluginCoordinationType(CoordinationType.GENOMIC_ZOOM_X, 0, z.number()),
|
186
|
+
new PluginCoordinationType(CoordinationType.GENOMIC_ZOOM_Y, 0, z.number()),
|
187
|
+
new PluginCoordinationType(CoordinationType.GENOMIC_TARGET_X, 1549999999.5, z.number()),
|
188
|
+
new PluginCoordinationType(CoordinationType.GENOMIC_TARGET_Y, 1549999999.5, z.number()),
|
189
|
+
new PluginCoordinationType(CoordinationType.ADDITIONAL_OBS_SETS, null, obsSetsSchema.nullable()),
|
190
|
+
new PluginCoordinationType(CoordinationType.MOLECULE_HIGHLIGHT, null, z.string().nullable()),
|
191
|
+
];
|
@@ -0,0 +1 @@
|
|
1
|
+
{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AACzC,OAAO,EACL,cAAc,EACd,cAAc,EACd,sBAAsB,EACtB,mBAAmB,GACpB,MAAM,mBAAmB,CAAC;AAC3B,OAAO,EAAE,CAAC,EAAE,MAAM,mBAAmB,CAAC"}
|
package/dist-tsc/index.js
CHANGED
@@ -1,2 +1,3 @@
|
|
1
|
-
export { Vitessce } from './
|
2
|
-
export {
|
1
|
+
export { Vitessce } from './Vitessce.js';
|
2
|
+
export { PluginFileType, PluginViewType, PluginCoordinationType, PluginJointFileType, } from '@vitessce/plugins';
|
3
|
+
export { z } from '@vitessce/schemas';
|
@@ -0,0 +1,226 @@
|
|
1
|
+
import type { z } from 'zod';
|
2
|
+
import type { latestFileDefSchema } from '@vitessce/schemas';
|
3
|
+
declare type legacyFileDefSchema = z.infer<typeof latestFileDefSchema> & {
|
4
|
+
type?: string;
|
5
|
+
};
|
6
|
+
export declare function expandMoleculesJson(fileDef: legacyFileDefSchema): {
|
7
|
+
fileType: string;
|
8
|
+
coordinationValues: {
|
9
|
+
obsType: string;
|
10
|
+
};
|
11
|
+
name?: string | undefined;
|
12
|
+
url?: string | undefined;
|
13
|
+
options?: any;
|
14
|
+
requestInit?: {
|
15
|
+
method?: string | undefined;
|
16
|
+
headers?: Record<string, any> | undefined;
|
17
|
+
body?: string | undefined;
|
18
|
+
mode?: string | undefined;
|
19
|
+
credentials?: string | undefined;
|
20
|
+
cache?: string | undefined;
|
21
|
+
redirect?: string | undefined;
|
22
|
+
referrer?: string | undefined;
|
23
|
+
integrity?: string | undefined;
|
24
|
+
} | undefined;
|
25
|
+
type?: string | undefined;
|
26
|
+
}[];
|
27
|
+
export declare function expandExpressionMatrixZarr(fileDef: legacyFileDefSchema): {
|
28
|
+
fileType: string;
|
29
|
+
coordinationValues: {
|
30
|
+
obsType: string;
|
31
|
+
featureType: string;
|
32
|
+
featureValueType: string;
|
33
|
+
};
|
34
|
+
name?: string | undefined;
|
35
|
+
url?: string | undefined;
|
36
|
+
options?: any;
|
37
|
+
requestInit?: {
|
38
|
+
method?: string | undefined;
|
39
|
+
headers?: Record<string, any> | undefined;
|
40
|
+
body?: string | undefined;
|
41
|
+
mode?: string | undefined;
|
42
|
+
credentials?: string | undefined;
|
43
|
+
cache?: string | undefined;
|
44
|
+
redirect?: string | undefined;
|
45
|
+
referrer?: string | undefined;
|
46
|
+
integrity?: string | undefined;
|
47
|
+
} | undefined;
|
48
|
+
type?: string | undefined;
|
49
|
+
}[];
|
50
|
+
export declare function expandRasterJson(fileDef: legacyFileDefSchema): {
|
51
|
+
fileType: string;
|
52
|
+
name?: string | undefined;
|
53
|
+
url?: string | undefined;
|
54
|
+
options?: any;
|
55
|
+
requestInit?: {
|
56
|
+
method?: string | undefined;
|
57
|
+
headers?: Record<string, any> | undefined;
|
58
|
+
body?: string | undefined;
|
59
|
+
mode?: string | undefined;
|
60
|
+
credentials?: string | undefined;
|
61
|
+
cache?: string | undefined;
|
62
|
+
redirect?: string | undefined;
|
63
|
+
referrer?: string | undefined;
|
64
|
+
integrity?: string | undefined;
|
65
|
+
} | undefined;
|
66
|
+
coordinationValues?: Record<string, string> | undefined;
|
67
|
+
type?: string | undefined;
|
68
|
+
}[];
|
69
|
+
export declare function expandRasterOmeZarr(fileDef: legacyFileDefSchema): {
|
70
|
+
fileType: string;
|
71
|
+
name?: string | undefined;
|
72
|
+
url?: string | undefined;
|
73
|
+
options?: any;
|
74
|
+
requestInit?: {
|
75
|
+
method?: string | undefined;
|
76
|
+
headers?: Record<string, any> | undefined;
|
77
|
+
body?: string | undefined;
|
78
|
+
mode?: string | undefined;
|
79
|
+
credentials?: string | undefined;
|
80
|
+
cache?: string | undefined;
|
81
|
+
redirect?: string | undefined;
|
82
|
+
referrer?: string | undefined;
|
83
|
+
integrity?: string | undefined;
|
84
|
+
} | undefined;
|
85
|
+
coordinationValues?: Record<string, string> | undefined;
|
86
|
+
type?: string | undefined;
|
87
|
+
}[];
|
88
|
+
export declare function expandCellSetsJson(fileDef: legacyFileDefSchema): {
|
89
|
+
fileType: string;
|
90
|
+
coordinationValues: {
|
91
|
+
obsType: string;
|
92
|
+
};
|
93
|
+
name?: string | undefined;
|
94
|
+
url?: string | undefined;
|
95
|
+
options?: any;
|
96
|
+
requestInit?: {
|
97
|
+
method?: string | undefined;
|
98
|
+
headers?: Record<string, any> | undefined;
|
99
|
+
body?: string | undefined;
|
100
|
+
mode?: string | undefined;
|
101
|
+
credentials?: string | undefined;
|
102
|
+
cache?: string | undefined;
|
103
|
+
redirect?: string | undefined;
|
104
|
+
referrer?: string | undefined;
|
105
|
+
integrity?: string | undefined;
|
106
|
+
} | undefined;
|
107
|
+
type?: string | undefined;
|
108
|
+
}[];
|
109
|
+
export declare function expandCellsJson(fileDef: legacyFileDefSchema): any[];
|
110
|
+
export declare function expandClustersJson(fileDef: legacyFileDefSchema): {
|
111
|
+
fileType: string;
|
112
|
+
coordinationValues: {
|
113
|
+
obsType: string;
|
114
|
+
featureType: string;
|
115
|
+
featureValueType: string;
|
116
|
+
};
|
117
|
+
name?: string | undefined;
|
118
|
+
url?: string | undefined;
|
119
|
+
options?: any;
|
120
|
+
requestInit?: {
|
121
|
+
method?: string | undefined;
|
122
|
+
headers?: Record<string, any> | undefined;
|
123
|
+
body?: string | undefined;
|
124
|
+
mode?: string | undefined;
|
125
|
+
credentials?: string | undefined;
|
126
|
+
cache?: string | undefined;
|
127
|
+
redirect?: string | undefined;
|
128
|
+
referrer?: string | undefined;
|
129
|
+
integrity?: string | undefined;
|
130
|
+
} | undefined;
|
131
|
+
type?: string | undefined;
|
132
|
+
}[];
|
133
|
+
export declare function expandGenesJson(fileDef: legacyFileDefSchema): {
|
134
|
+
fileType: string;
|
135
|
+
coordinationValues: {
|
136
|
+
obsType: string;
|
137
|
+
featureType: string;
|
138
|
+
featureValueType: string;
|
139
|
+
};
|
140
|
+
name?: string | undefined;
|
141
|
+
url?: string | undefined;
|
142
|
+
options?: any;
|
143
|
+
requestInit?: {
|
144
|
+
method?: string | undefined;
|
145
|
+
headers?: Record<string, any> | undefined;
|
146
|
+
body?: string | undefined;
|
147
|
+
mode?: string | undefined;
|
148
|
+
credentials?: string | undefined;
|
149
|
+
cache?: string | undefined;
|
150
|
+
redirect?: string | undefined;
|
151
|
+
referrer?: string | undefined;
|
152
|
+
integrity?: string | undefined;
|
153
|
+
} | undefined;
|
154
|
+
type?: string | undefined;
|
155
|
+
}[];
|
156
|
+
export declare function expandAnndataCellsZarr(fileDef: legacyFileDefSchema): any[];
|
157
|
+
export declare function expandAnndataCellSetsZarr(fileDef: legacyFileDefSchema): {
|
158
|
+
fileType: string;
|
159
|
+
options: any;
|
160
|
+
coordinationValues: {
|
161
|
+
obsType: string;
|
162
|
+
};
|
163
|
+
url: string | undefined;
|
164
|
+
requestInit: {
|
165
|
+
method?: string | undefined;
|
166
|
+
headers?: Record<string, any> | undefined;
|
167
|
+
body?: string | undefined;
|
168
|
+
mode?: string | undefined;
|
169
|
+
credentials?: string | undefined;
|
170
|
+
cache?: string | undefined;
|
171
|
+
redirect?: string | undefined;
|
172
|
+
referrer?: string | undefined;
|
173
|
+
integrity?: string | undefined;
|
174
|
+
} | undefined;
|
175
|
+
}[];
|
176
|
+
export declare function expandAnndataExpressionMatrixZarr(fileDef: legacyFileDefSchema): ({
|
177
|
+
fileType: string;
|
178
|
+
options: {
|
179
|
+
path: any;
|
180
|
+
featureFilterPath?: undefined;
|
181
|
+
initialFeatureFilterPath?: undefined;
|
182
|
+
};
|
183
|
+
coordinationValues: {
|
184
|
+
featureType: string;
|
185
|
+
obsType?: undefined;
|
186
|
+
featureValueType?: undefined;
|
187
|
+
};
|
188
|
+
url: string | undefined;
|
189
|
+
requestInit: {
|
190
|
+
method?: string | undefined;
|
191
|
+
headers?: Record<string, any> | undefined;
|
192
|
+
body?: string | undefined;
|
193
|
+
mode?: string | undefined;
|
194
|
+
credentials?: string | undefined;
|
195
|
+
cache?: string | undefined;
|
196
|
+
redirect?: string | undefined;
|
197
|
+
referrer?: string | undefined;
|
198
|
+
integrity?: string | undefined;
|
199
|
+
} | undefined;
|
200
|
+
} | {
|
201
|
+
fileType: string;
|
202
|
+
options: {
|
203
|
+
path: any;
|
204
|
+
featureFilterPath: any;
|
205
|
+
initialFeatureFilterPath: any;
|
206
|
+
};
|
207
|
+
coordinationValues: {
|
208
|
+
obsType: string;
|
209
|
+
featureType: string;
|
210
|
+
featureValueType: string;
|
211
|
+
};
|
212
|
+
url: string | undefined;
|
213
|
+
requestInit: {
|
214
|
+
method?: string | undefined;
|
215
|
+
headers?: Record<string, any> | undefined;
|
216
|
+
body?: string | undefined;
|
217
|
+
mode?: string | undefined;
|
218
|
+
credentials?: string | undefined;
|
219
|
+
cache?: string | undefined;
|
220
|
+
redirect?: string | undefined;
|
221
|
+
referrer?: string | undefined;
|
222
|
+
integrity?: string | undefined;
|
223
|
+
} | undefined;
|
224
|
+
})[];
|
225
|
+
export {};
|
226
|
+
//# sourceMappingURL=joint-file-types-legacy.d.ts.map
|
@@ -0,0 +1 @@
|
|
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,aAAK,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;;;;;;;;;;;;;;;;;;;;IAkB/D;AAED,wBAAgB,0BAA0B,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;;;;;IAgBtE;AAED,wBAAgB,gBAAgB,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;IAiB5D;AAED,wBAAgB,mBAAmB,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;IAS/D;AAED,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;;;IAY9D;AAED,wBAAgB,eAAe,CAAC,OAAO,EAAE,mBAAmB,SA0C3D;AAED,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;;;;;IAgB9D;AAED,wBAAgB,eAAe,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;;;;;IAgB3D;AAeD,wBAAgB,sBAAsB,CAAC,OAAO,EAAE,mBAAmB,SAkDlE;AAED,wBAAgB,yBAAyB,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;IAiBrE;AAED,wBAAgB,iCAAiC,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KA6B7E"}
|