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

Class AbstractAnnDataSingleCellDataLoaderConfigurer

java.lang.Object

ubic.gemma.core.loader.expression.singleCell.AbstractAnnDataSingleCellDataLoaderConfigurer

All Implemented Interfaces:

DataLoaderConfigurer<AnnDataSingleCellDataLoader,SingleCellDataLoaderConfig>, SingleCellDataLoaderConfigurer<AnnDataSingleCellDataLoader>

Direct Known Subclasses:

AnnDataSingleCellDataLoaderConfigurer

public abstract class AbstractAnnDataSingleCellDataLoaderConfigurer
extends Object
implements SingleCellDataLoaderConfigurer<AnnDataSingleCellDataLoader>

Base class for AnnDataSingleCellDataLoader configurers.

This base class provides capabilities for detecting data stored in various columns.

Author:

poirigui

Field Summary

Fields

Modifier and Type	Field	Description
static String[]	CELL_ID_COLUMN_NAME_KEYWORDS	TODO

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractAnnDataSingleCellDataLoaderConfigurer(Path annDataFile)

Method Summary

Modifier and Type	Method	Description
AnnDataSingleCellDataLoader	configureLoader(SingleCellDataLoaderConfig config)	Automatically configure a loader for an AnnData file.
protected String	getUnknownCellTypeIndicator(Dataframe.Column<?,String> column)	Extract the unknown cell type indicator from a set of values.
protected boolean	isCellIdColumn(Dataframe.Column<?,String> column)	Check if the given dataframe column contains cell identifiers.
protected boolean	isCellTypeColumn(Dataframe.Column<?,String> column)	Check if a given column contains cell types.
protected boolean	isGeneColumn(Dataframe.Column<?,String> column)	Check if a given column contains gene identifiers.
protected boolean	isSampleNameColumn(Dataframe.Column<?,String> column)	Check if a given dataframe column contains sample names.
void	setPythonExecutable(Path pythonExecutable)	Set the path to a Python executable.
void	setScratchDir(Path scratchDir)	Set the path to a scratch directory to use for on-disk transformations.

Methods inherited from class java.lang.Object

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

Field Detail

CELL_ID_COLUMN_NAME_KEYWORDS

public static final String[] CELL_ID_COLUMN_NAME_KEYWORDS

TODO

Constructor Detail

AbstractAnnDataSingleCellDataLoaderConfigurer

protected AbstractAnnDataSingleCellDataLoaderConfigurer(Path annDataFile)

Method Detail

setPythonExecutable

public void setPythonExecutable(Path pythonExecutable)

Set the path to a Python executable. If null, no transformation will be performed on the AnnData file.

setScratchDir

public void setScratchDir(Path scratchDir)

Set the path to a scratch directory to use for on-disk transformations. If null, no transformation will be performed on the AnnData file.

configureLoader

public AnnDataSingleCellDataLoader configureLoader(SingleCellDataLoaderConfig config)

Automatically configure a loader for an AnnData file.

Specified by:

configureLoader in interface DataLoaderConfigurer<AnnDataSingleCellDataLoader,SingleCellDataLoaderConfig>

isCellIdColumn

protected boolean isCellIdColumn(Dataframe.Column<?,String> column)

Check if the given dataframe column contains cell identifiers.

isSampleNameColumn

protected boolean isSampleNameColumn(Dataframe.Column<?,String> column)

Check if a given dataframe column contains sample names.

isCellTypeColumn

protected boolean isCellTypeColumn(Dataframe.Column<?,String> column)

Check if a given column contains cell types.

getUnknownCellTypeIndicator

@Nullable
protected String getUnknownCellTypeIndicator(Dataframe.Column<?,String> column)

Extract the unknown cell type indicator from a set of values.

isGeneColumn

protected boolean isGeneColumn(Dataframe.Column<?,String> column)

Check if a given column contains gene identifiers.