Package ubic.gemma.core.loader.expression

Class DataLoaderConfig.DataLoaderConfigBuilder<C extends DataLoaderConfig,B extends DataLoaderConfig.DataLoaderConfigBuilder<C,B>>

java.lang.Object
ubic.gemma.core.loader.expression.DataLoaderConfig.DataLoaderConfigBuilder<C,B>
Direct Known Subclasses:
SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder
Enclosing class:
DataLoaderConfig
public abstract static class DataLoaderConfig.DataLoaderConfigBuilder<C extends DataLoaderConfig,B extends DataLoaderConfig.DataLoaderConfigBuilder<C,B>> extends Object

  • Constructor Details

    • DataLoaderConfigBuilder

      public DataLoaderConfigBuilder()

  • Method Details

    • dataPath

      public B dataPath(@Nullable Path dataPath)
      Load data from that specific path instead of looking up standard locations.
      Returns:
      this.

    • quantitationTypeName

      public B quantitationTypeName(@Nullable String quantitationTypeName)
      Name of the QT to use if more than one is present in the data as per DataLoader.getQuantitationTypes().

      This may be set to null, in which case the loader must only detect a single QT.

      Returns:
      this.

    • replaceExistingQuantitationType

      public B replaceExistingQuantitationType(boolean replaceExistingQuantitationType)
      Replace the vectors of an existing QT.

      Requires quantitationTypeName to be set.

      Returns:
      this.

    • quantitationTypeNewName

      public B quantitationTypeNewName(@Nullable String quantitationTypeNewName)
      Override the name of the resulting QT.
      Returns:
      this.

    • quantitationTypeNewType

      public B quantitationTypeNewType(@Nullable StandardQuantitationType quantitationTypeNewType)
      Override the type of the resulting QT.
      Returns:
      this.

    • quantitationTypeNewScaleType

      public B quantitationTypeNewScaleType(@Nullable ScaleType quantitationTypeNewScaleType)
      Override the scale type of the resulting QT.
      Returns:
      this.

    • markQuantitationTypeAsRecomputedFromRawData

      public B markQuantitationTypeAsRecomputedFromRawData(boolean markQuantitationTypeAsRecomputedFromRawData)
      Mark the quantitation type as recomputed from raw data.
      Returns:
      this.
      See Also:

    • markQuantitationTypeAsPreferred

      public B markQuantitationTypeAsPreferred(boolean markQuantitationTypeAsPreferred)
      Mark the QT as preferred.

      All other QTs of the same kind will be set to non-preferred as a result.

      Returns:
      this.
      See Also:

    • renamingFile

      public B renamingFile(@Nullable Path renamingFile)
      A file containing a mapping of sample names to bioassay names.
      Returns:
      this.
      See Also:

    • self

      protected abstract B self()

    • build

      public abstract C build()

    • toString

      public String toString()
      Overrides:
      toString in class Object