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 Detail

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 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 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