Class EmptySingleCellExpressionDataMatrix
java.lang.Object
ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix
- All Implemented Interfaces:
ExpressionDataMatrix<Object>,SingleCellExpressionDataMatrix<Object>
public class EmptySingleCellExpressionDataMatrix
extends Object
implements SingleCellExpressionDataMatrix<Object>
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Constructor Summary
ConstructorsConstructorDescriptionEmptySingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment, SingleCellDimension dimension, QuantitationType quantitationType) -
Method Summary
Modifier and TypeMethodDescriptionintcolumns()Obtain the total number of columns.get(int row, int column) Access a single value of the matrix by row and column.getBioAssayForColumn(int j) Obtain a bioassay applicable to a given column.Obtain the list of bioassays.getBioMaterialForColumn(int j) getCellIdForColumn(int j) Obtain the cell ID of a given column.Note: cell IDs are only unique within a given assayObject[]getColumn(int column) Access a single column of the matrix.getDesignElementForRow(int index) Return a design element for a given index.Obtain all the design elements in this data matrix.Return the expression experiment this matrix is holding data for, if known.Return the quantitation type for this matrix.Object[]getRow(int index) Access a single row of the matrix, by index.Object[]getRow(CompositeSequence designElement) Return a row that 'came from' the given design element.getRowElement(int row) intgetRowIndex(CompositeSequence designElement) int[]getRowIndices(CompositeSequence designElement) Obtain all the rows that correspond to the given design element, ornullif the design element is not found.Return the single-cell dimension for this matrix.introws()sliceRows(List<CompositeSequence> designElements)
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Constructor Details
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EmptySingleCellExpressionDataMatrix
public EmptySingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment, SingleCellDimension dimension, QuantitationType quantitationType)
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Method Details
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getExpressionExperiment
Description copied from interface:ExpressionDataMatrixReturn the expression experiment this matrix is holding data for, if known.- Specified by:
getExpressionExperimentin interfaceExpressionDataMatrix<Object>
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getQuantitationType
Description copied from interface:SingleCellExpressionDataMatrixReturn the quantitation type for this matrix.- Specified by:
getQuantitationTypein interfaceExpressionDataMatrix<Object>- Specified by:
getQuantitationTypein interfaceSingleCellExpressionDataMatrix<Object>
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getDesignElements
Description copied from interface:ExpressionDataMatrixObtain all the design elements in this data matrix.- Specified by:
getDesignElementsin interfaceExpressionDataMatrix<Object>
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getDesignElementForRow
Description copied from interface:ExpressionDataMatrixReturn a design element for a given index.- Specified by:
getDesignElementForRowin interfaceExpressionDataMatrix<Object>
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columns
public int columns()Description copied from interface:ExpressionDataMatrixObtain the total number of columns.- Specified by:
columnsin interfaceExpressionDataMatrix<Object>
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getSingleCellDimension
Description copied from interface:SingleCellExpressionDataMatrixReturn the single-cell dimension for this matrix.- Specified by:
getSingleCellDimensionin interfaceSingleCellExpressionDataMatrix<Object>
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getColumn
Description copied from interface:SingleCellExpressionDataMatrixAccess a single column of the matrix.Important note: Retrieving a column is a
O(n log m)operation wherenis the number of vectors andmis the number of cells. Always favour row-oriented operations when possible.- Specified by:
getColumnin interfaceExpressionDataMatrix<Object>- Specified by:
getColumnin interfaceSingleCellExpressionDataMatrix<Object>- Parameters:
column- index- Returns:
- T[]
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rows
public int rows()- Specified by:
rowsin interfaceExpressionDataMatrix<Object>- Returns:
- int
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getRow
Description copied from interface:ExpressionDataMatrixAccess a single row of the matrix, by index. A complete row is returned.- Specified by:
getRowin interfaceExpressionDataMatrix<Object>- Parameters:
index- i- Returns:
- t[]
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getRow
Description copied from interface:ExpressionDataMatrixReturn a row that 'came from' the given design element.- Specified by:
getRowin interfaceExpressionDataMatrix<Object>- Parameters:
designElement- de- Returns:
- the corresponding row or null if the design element is not found in the matrix
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getRowIndex
- Specified by:
getRowIndexin interfaceExpressionDataMatrix<Object>- Returns:
- the index for the given design element, or -1 if not found
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getRowIndices
Description copied from interface:ExpressionDataMatrixObtain all the rows that correspond to the given design element, ornullif the design element is not found.- Specified by:
getRowIndicesin interfaceExpressionDataMatrix<Object>
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sliceRows
- Specified by:
sliceRowsin interfaceExpressionDataMatrix<Object>
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getRowElements
- Specified by:
getRowElementsin interfaceExpressionDataMatrix<Object>- Returns:
- list of elements representing the row 'labels'.
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getRowElement
- Specified by:
getRowElementin interfaceExpressionDataMatrix<Object>
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get
Description copied from interface:ExpressionDataMatrixAccess a single value of the matrix by row and column.- Specified by:
getin interfaceExpressionDataMatrix<Object>
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getBioAssays
Description copied from interface:SingleCellExpressionDataMatrixObtain the list of bioassays.- Specified by:
getBioAssaysin interfaceSingleCellExpressionDataMatrix<Object>
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getBioAssayForColumn
Description copied from interface:SingleCellExpressionDataMatrixObtain a bioassay applicable to a given column.- Specified by:
getBioAssayForColumnin interfaceSingleCellExpressionDataMatrix<Object>
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getBioMaterialForColumn
- Specified by:
getBioMaterialForColumnin interfaceSingleCellExpressionDataMatrix<Object>
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getCellIds
Description copied from interface:SingleCellExpressionDataMatrixNote: cell IDs are only unique within a given assay- Specified by:
getCellIdsin interfaceSingleCellExpressionDataMatrix<Object>
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getCellIdForColumn
Description copied from interface:SingleCellExpressionDataMatrixObtain the cell ID of a given column.- Specified by:
getCellIdForColumnin interfaceSingleCellExpressionDataMatrix<Object>
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