Class SingleCellExpressionDataVector

java.lang.Object
ubic.gemma.model.common.AbstractIdentifiable
ubic.gemma.model.expression.bioAssayData.DataVector
ubic.gemma.model.expression.bioAssayData.DesignElementDataVector
ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector
All Implemented Interfaces:
Identifiable
@Entity public class SingleCellExpressionDataVector extends DesignElementDataVector
An expression data vector that contains data at the resolution of individual cells.

This is achieved by storing cell metadata such as IDs and cell types in a SingleCellDimension that is shared among all vectors of a given ExpressionExperiment and individual non-zero cell expression in a sparse data structure similar to the rows of a CSR matrix.

Author:
poirigui

  • Constructor Details

    • SingleCellExpressionDataVector

      public SingleCellExpressionDataVector()

  • Method Details

    • equals

      public boolean equals(Object object)
      Description copied from class: AbstractIdentifiable
      Important note: Two objects with the same class and non-null ID must be considered equal. If one or both IDs are nulls, the rest of the state can be used to determine equality.
      Specified by:
      equals in class AbstractIdentifiable

    • toString

      public String toString()
      Overrides:
      toString in class AbstractIdentifiable

    • getQuantitationType

      public QuantitationType getQuantitationType()
      Description copied from class: DataVector
      Owning QuantitationType. Fetch mode varies by concrete subclass — bulk vectors keep the QT LAZY to avoid an N+1 on bulk loads, single-cell vectors fetch eagerly to match the original hbm. Declared as an abstract accessor here so each subclass can configure its own @ManyToOne fetch policy (which @MappedSuperclass + @AssociationOverride cannot do).
      Specified by:
      getQuantitationType in class DataVector

    • getSingleCellDimension

      public SingleCellDimension getSingleCellDimension()

    • getOriginalDesignElement

      @Nullable public String getOriginalDesignElement()
      Description copied from class: DesignElementDataVector
      The original design element that was used to create this vector.

      This is generally null, but if the data was imported and a mapping was done between some external data source and one of Gemma's platform, this will contain the original ID.

      Specified by:
      getOriginalDesignElement in class DesignElementDataVector

    • getDataIndices

      public int[] getDataIndices()
      Positions of the non-zero data in the DataVector.getData() vector.

      This is mapped in the database using ByteArrayType.

    • setQuantitationType

      public void setQuantitationType(QuantitationType quantitationType)
      Specified by:
      setQuantitationType in class DataVector

    • setSingleCellDimension

      public void setSingleCellDimension(SingleCellDimension singleCellDimension)

    • setOriginalDesignElement

      public void setOriginalDesignElement(@Nullable String originalDesignElement)

    • setDataIndices

      public void setDataIndices(int[] dataIndices)
      Positions of the non-zero data in the DataVector.getData() vector.

      This is mapped in the database using ByteArrayType.