AnnDataDetector (Gemma 1.32.0 API)

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

Field Summary
- Fields inherited from class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleCellDetector
  log

Constructor Summary

Constructors
Constructor Description

AnnDataDetector()

Method Summary

All Methods Instance Methods Concrete Methods
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)`

Methods inherited from class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleH5FileInSeriesSingleCellDetector
existsAndHasExpectedSize

Methods inherited from class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleFileInSeriesSingleCellDetector
downloadSingleCellData, downloadSingleCellData, downloadSingleCellData, getAdditionalSupplementaryFiles, getAdditionalSupplementaryFiles, getDest, hasSingleCellData, hasSingleCellData

Methods inherited from class ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleCellDetector
getDownloadDirectory, getSizeInBytes, openSupplementaryFileAsStream, retry, setDownloadDirectory, setFTPClientFactory, setRetryPolicy

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface ubic.gemma.core.loader.expression.geo.singleCell.SingleCellDetector
downloadSingleCellData, downloadSingleCellData, getAdditionalSupplementaryFiles, getAdditionalSupplementaryFiles, hasSingleCellData, hasSingleCellData, setDownloadDirectory, setRetryPolicy

- Constructor Detail
  - AnnDataDetector
```
public AnnDataDetector()
```
- Method Detail
  - 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
  - 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