Class SingleCellExpressionDataIntMatrix
java.lang.Object
ubic.gemma.core.datastructure.matrix.AbstractExpressionDataMatrix<Integer>
ubic.gemma.core.datastructure.matrix.AbstractSingleCellExpressionDataMatrix<Integer>
ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix
- All Implemented Interfaces:
ExpressionDataMatrix<Integer>, ExpressionDataPrimitiveIntMatrix, SingleCellExpressionDataMatrix<Integer>
public class SingleCellExpressionDataIntMatrix
extends AbstractSingleCellExpressionDataMatrix<Integer>
implements ExpressionDataPrimitiveIntMatrix
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Constructor Summary
ConstructorsConstructorDescription -
Method Summary
Modifier and TypeMethodDescriptionintcolumns()Obtain the total number of columns.protected Stringformat(int i, int j) Format a matrix entry at a particular row/column.get(int row, int column) Access a single value of the matrix by row and column.intgetAsInt(int row, int column) Retrieve the value at the given row and column without boxing.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 assayInteger[]getColumn(int column) Access a single column of the matrix.int[]getColumnAsInts(int column) Retrieve the given column without boxing.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.no.uib.cipr.matrix.sparse.CompRowMatrixObtain the sparse matrix underlying this.Obtain the quantitation type for this matrix.Integer[]getRow(int index) Access a single row of the matrix, by index.Integer[]getRow(CompositeSequence designElement) Return a row that 'came from' the given design element.int[]getRowAsInts(int index) Retrieve a row without boxing.int[]getRowAsInts(CompositeSequence designElement) Retrieve the row for the given design element without boxing.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()Methods inherited from class AbstractSingleCellExpressionDataMatrix
getColumnLabel, getRowLabelMethods inherited from class AbstractExpressionDataMatrix
format, format, formatRepresentation, toString
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Constructor Details
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SingleCellExpressionDataIntMatrix
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Method Details
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getMatrix
public no.uib.cipr.matrix.sparse.CompRowMatrix getMatrix()Obtain the sparse matrix underlying this. -
getExpressionExperiment
Description copied from interface:ExpressionDataMatrixReturn the expression experiment this matrix is holding data for, if known.- Specified by:
getExpressionExperimentin interfaceExpressionDataMatrix<Integer>
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columns
public int columns()Description copied from interface:ExpressionDataMatrixObtain the total number of columns.- Specified by:
columnsin interfaceExpressionDataMatrix<Integer>
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get
Description copied from interface:ExpressionDataMatrixAccess a single value of the matrix by row and column.- Specified by:
getin interfaceExpressionDataMatrix<Integer>
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getAsInt
public int getAsInt(int row, int column) Description copied from interface:ExpressionDataPrimitiveIntMatrixRetrieve the value at the given row and column without boxing.- Specified by:
getAsIntin interfaceExpressionDataPrimitiveIntMatrix- See Also:
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getColumn
Description copied from interface:ExpressionDataMatrixAccess a single column of the matrix.- Specified by:
getColumnin interfaceExpressionDataMatrix<Integer>- Specified by:
getColumnin interfaceSingleCellExpressionDataMatrix<Integer>- Parameters:
column- index- Returns:
- T[]
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getColumnAsInts
public int[] getColumnAsInts(int column) Description copied from interface:ExpressionDataPrimitiveIntMatrixRetrieve the given column without boxing.- Specified by:
getColumnAsIntsin interfaceExpressionDataPrimitiveIntMatrix- See Also:
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getBioAssays
Description copied from interface:SingleCellExpressionDataMatrixObtain the list of bioassays.- Specified by:
getBioAssaysin interfaceSingleCellExpressionDataMatrix<Integer>
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getBioAssayForColumn
Description copied from interface:SingleCellExpressionDataMatrixObtain a bioassay applicable to a given column.- Specified by:
getBioAssayForColumnin interfaceSingleCellExpressionDataMatrix<Integer>
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getBioMaterialForColumn
- Specified by:
getBioMaterialForColumnin interfaceSingleCellExpressionDataMatrix<Integer>
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getCellIds
Description copied from interface:SingleCellExpressionDataMatrixNote: cell IDs are only unique within a given assay- Specified by:
getCellIdsin interfaceSingleCellExpressionDataMatrix<Integer>
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getCellIdForColumn
Description copied from interface:SingleCellExpressionDataMatrixObtain the cell ID of a given column.- Specified by:
getCellIdForColumnin interfaceSingleCellExpressionDataMatrix<Integer>
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getDesignElements
Description copied from interface:ExpressionDataMatrixObtain all the design elements in this data matrix.- Specified by:
getDesignElementsin interfaceExpressionDataMatrix<Integer>
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getDesignElementForRow
Description copied from interface:ExpressionDataMatrixReturn a design element for a given index.- Specified by:
getDesignElementForRowin interfaceExpressionDataMatrix<Integer>
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getRow
Description copied from interface:ExpressionDataMatrixReturn a row that 'came from' the given design element.- Specified by:
getRowin interfaceExpressionDataMatrix<Integer>- Parameters:
designElement- de- Returns:
- the corresponding row or null if the design element is not found in the matrix
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getRowAsInts
Description copied from interface:ExpressionDataPrimitiveIntMatrixRetrieve the row for the given design element without boxing.- Specified by:
getRowAsIntsin interfaceExpressionDataPrimitiveIntMatrix- See Also:
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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<Integer>- Parameters:
index- i- Returns:
- t[]
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getRowAsInts
public int[] getRowAsInts(int index) Description copied from interface:ExpressionDataPrimitiveIntMatrixRetrieve a row without boxing.- Specified by:
getRowAsIntsin interfaceExpressionDataPrimitiveIntMatrix- See Also:
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getRowIndex
- Specified by:
getRowIndexin interfaceExpressionDataMatrix<Integer>- 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<Integer>
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getRowElements
- Specified by:
getRowElementsin interfaceExpressionDataMatrix<Integer>- Returns:
- list of elements representing the row 'labels'.
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getRowElement
- Specified by:
getRowElementin interfaceExpressionDataMatrix<Integer>
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rows
public int rows()- Specified by:
rowsin interfaceExpressionDataMatrix<Integer>- Returns:
- int
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getQuantitationType
Description copied from interface:ExpressionDataMatrixObtain the quantitation type for this matrix.- Specified by:
getQuantitationTypein interfaceExpressionDataMatrix<Integer>- Specified by:
getQuantitationTypein interfaceSingleCellExpressionDataMatrix<Integer>
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getSingleCellDimension
Description copied from interface:SingleCellExpressionDataMatrixReturn the single-cell dimension for this matrix.- Specified by:
getSingleCellDimensionin interfaceSingleCellExpressionDataMatrix<Integer>
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format
Description copied from class:AbstractExpressionDataMatrixFormat a matrix entry at a particular row/column.- Specified by:
formatin classAbstractExpressionDataMatrix<Integer>
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