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 Details

    • CELL_ID_COLUMN_NAME_KEYWORDS

      public static final String[] CELL_ID_COLUMN_NAME_KEYWORDS
      TODO

  • Constructor Details

    • AbstractAnnDataSingleCellDataLoaderConfigurer

      protected AbstractAnnDataSingleCellDataLoaderConfigurer(Path annDataFile)

  • Method Details

    • 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.