Interface SingleCellDetector
- All Known Subinterfaces:
ArchiveBasedSingleCellDetector,SeriesAwareSingleCellDetector
- All Known Implementing Classes:
AbstractSingleCellDetector,AbstractSingleFileInSeriesSingleCellDetector,AbstractSingleH5FileInSeriesSingleCellDetector,AnnDataDetector,GeoSingleCellDetector,LoomSingleCellDetector,MexDetector,SeuratDiskDetector
public interface SingleCellDetector
Interface for single-cell data detectors from GEO.
- Author:
- poirigui
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Method Summary
Modifier and TypeMethodDescriptiondownloadSingleCellData(GeoSample sample) Download single-cell data for the given GEO sample.downloadSingleCellData(GeoSeries series) Download single-cell data for the given GEO series.Obtain a list of all additional supplementary files.Obtain a list of all additional supplementary files.getSingleCellDataLoader(GeoSeries series, SingleCellDataLoaderConfig config) Obtain a single cell data loader for the given GEO series based on previously downloading data.booleanhasSingleCellData(GeoSample sample) Indicate if the given GEO sample has single-cell data.booleanhasSingleCellData(GeoSeries series) Indicate if the given GEO series has single-cell data.voidsetDownloadDirectory(Path dir) Set the download directory single-cell data.voidsetRetryPolicy(SimpleRetryPolicy retryPolicy) Set the retry policy to use when downloading single-cell data.
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Method Details
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setDownloadDirectory
Set the download directory single-cell data. -
setRetryPolicy
Set the retry policy to use when downloading single-cell data. -
hasSingleCellData
Indicate if the given GEO series has single-cell data. -
hasSingleCellData
Indicate if the given GEO sample has single-cell data. -
downloadSingleCellData
Path downloadSingleCellData(GeoSeries series) throws UnsupportedOperationException, NoSingleCellDataFoundException, IOException Download single-cell data for the given GEO series.- Returns:
- a directory or file containing the downloaded series data
- Throws:
UnsupportedOperationException- if downloading single-cell data for a given series is not supportedNoSingleCellDataFoundException- if there is no single-cell data for the given seriesIOException
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downloadSingleCellData
Path downloadSingleCellData(GeoSample sample) throws UnsupportedOperationException, NoSingleCellDataFoundException, IOException Download single-cell data for the given GEO sample.- Returns:
- a directory or file containing the downloaded sample data
- Throws:
UnsupportedOperationException- if downloading single-cell data for a given sample is not supportedNoSingleCellDataFoundException- if there is no single-cell data for the given sampleIOException
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getAdditionalSupplementaryFiles
Obtain a list of all additional supplementary files. -
getAdditionalSupplementaryFiles
Obtain a list of all additional supplementary files. -
getSingleCellDataLoader
SingleCellDataLoader getSingleCellDataLoader(GeoSeries series, SingleCellDataLoaderConfig config) throws UnsupportedOperationException, NoSingleCellDataFoundException Obtain a single cell data loader for the given GEO series based on previously downloading data.- Throws:
UnsupportedOperationException- if loading single-cell data is not supportedNoSingleCellDataFoundException- if there is no single-cell data for the given series
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