Package ubic.gemma.core.loader.expression.geo.singleCell

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

Method Summary

Modifier and Type	Method	Description
Path	downloadSingleCellData(GeoSample sample)	Download single-cell data for the given GEO sample.
Path	downloadSingleCellData(GeoSeries series)	Download single-cell data for the given GEO series.
List<String>	getAdditionalSupplementaryFiles(GeoSample sample)	Obtain a list of all additional supplementary files.
List<String>	getAdditionalSupplementaryFiles(GeoSeries series)	Obtain a list of all additional supplementary files.
SingleCellDataLoader	getSingleCellDataLoader(GeoSeries series, SingleCellDataLoaderConfig config)	Obtain a single cell data loader for the given GEO series based on previously downloading data.
boolean	hasSingleCellData(GeoSample sample)	Indicate if the given GEO sample has single-cell data.
boolean	hasSingleCellData(GeoSeries series)	Indicate if the given GEO series has single-cell data.
void	setDownloadDirectory(Path dir)	Set the download directory single-cell data.
void	setRetryPolicy(SimpleRetryPolicy retryPolicy)	Set the retry policy to use when downloading single-cell data.

Method Details

setDownloadDirectory

void setDownloadDirectory(Path dir)

Set the download directory single-cell data.

setRetryPolicy

void setRetryPolicy(SimpleRetryPolicy retryPolicy)

Set the retry policy to use when downloading single-cell data.

hasSingleCellData

boolean hasSingleCellData(GeoSeries series)

Indicate if the given GEO series has single-cell data.

hasSingleCellData

boolean hasSingleCellData(GeoSample sample)

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 supported

NoSingleCellDataFoundException - if there is no single-cell data for the given series

IOException

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 supported

NoSingleCellDataFoundException - if there is no single-cell data for the given sample

IOException

getAdditionalSupplementaryFiles

List<String> getAdditionalSupplementaryFiles(GeoSeries series)

Obtain a list of all additional supplementary files.

getAdditionalSupplementaryFiles

List<String> getAdditionalSupplementaryFiles(GeoSample sample)

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 supported

NoSingleCellDataFoundException - if there is no single-cell data for the given series