Class AnnDataDetector

java.lang.Object

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

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

ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleH5FileInSeriesSingleCellDetector

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

All Implemented Interfaces:

SingleCellDetector

public class AnnDataDetector
extends AbstractSingleH5FileInSeriesSingleCellDetector
implements SingleCellDetector

Detects AnnData in GEO series.

This detector has additional heuristics for detecting sample names.

Author:

poirigui

Constructor Summary

Constructors

Constructor	Description
AnnDataDetector()

Method Summary

Modifier and Type	Method	Description
protected boolean	accepts(String supplementaryFile)	Indicate if the given supplementary file is accepted.
SingleCellDataLoader	getSingleCellDataLoader(GeoSeries series, SingleCellDataLoaderConfig config)	Obtain a single cell data loader for the given GEO series based on previously downloading data.
protected boolean	isTruncated(Path dest)
void	setSingleCellDataTransformationFactory(SingleCellDataTransformationFactory singleCellDataTransformationFactory)

Methods inherited from class AbstractSingleH5FileInSeriesSingleCellDetector

existsAndHasExpectedSize

Methods inherited from class AbstractSingleFileInSeriesSingleCellDetector

downloadSingleCellData, downloadSingleCellData, downloadSingleCellData, getAdditionalSupplementaryFiles, getAdditionalSupplementaryFiles, getDest, hasSingleCellData, hasSingleCellData

Methods inherited from class AbstractSingleCellDetector

getDownloadDirectory, getProgressReporterFactory, getSizeInBytes, openSupplementaryFileAsStream, retry, setDownloadDirectory, setFTPClientFactory, setProgressReporterFactory, setRetryPolicy

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface SingleCellDetector

downloadSingleCellData, downloadSingleCellData, getAdditionalSupplementaryFiles, getAdditionalSupplementaryFiles, hasSingleCellData, hasSingleCellData, setDownloadDirectory, setProgressReporterFactory, setRetryPolicy

Constructor Details

AnnDataDetector

public AnnDataDetector()

Method Details

accepts

protected boolean accepts(String supplementaryFile)

Description copied from class: AbstractSingleFileInSeriesSingleCellDetector

Indicate if the given supplementary file is accepted.

The default implementation checks if the file ends with the extension (or the extension + .gz).

Overrides:

accepts in class AbstractSingleFileInSeriesSingleCellDetector

isTruncated

protected boolean isTruncated(Path dest)
                       throws IOException

Overrides:

isTruncated in class AbstractSingleH5FileInSeriesSingleCellDetector

Throws:

IOException

setSingleCellDataTransformationFactory

public void setSingleCellDataTransformationFactory(@Nullable
 SingleCellDataTransformationFactory singleCellDataTransformationFactory)

getSingleCellDataLoader

public SingleCellDataLoader getSingleCellDataLoader(GeoSeries series,
 SingleCellDataLoaderConfig config)
                                             throws NoSingleCellDataFoundException

Description copied from interface: SingleCellDetector

Obtain a single cell data loader for the given GEO series based on previously downloading data.

Specified by:

getSingleCellDataLoader in interface SingleCellDetector

Throws:

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