Type Parameters:

T - type of scalar held in the matrix

All Known Subinterfaces:

BulkExpressionDataMatrix<T>, BulkExpressionDataPrimitiveDoubleMatrix, BulkExpressionDataPrimitiveIntMatrix, ExpressionDataPrimitiveDoubleMatrix, ExpressionDataPrimitiveIntMatrix, MultiAssayBulkExpressionDataMatrix<T>, SingleCellExpressionDataMatrix<T>

All Known Implementing Classes:

AbstractBulkExpressionDataMatrix, AbstractExpressionDataMatrix, AbstractMultiAssayExpressionDataMatrix, AbstractSingleCellExpressionDataMatrix, BulkExpressionDataDoubleMatrix, BulkExpressionDataIntMatrix, EmptyBulkExpressionDataMatrix, EmptyExpressionMatrix, EmptySingleCellExpressionDataMatrix, ExpressionDataBooleanMatrix, ExpressionDataDoubleMatrix, ExpressionDataIntegerMatrix, ExpressionDataStringMatrix, MaskedExpressionDataMatrix, SingleCellExpressionDataDoubleMatrix, SingleCellExpressionDataIntMatrix
```
public interface ExpressionDataMatrix<T>
```
Represents a matrix of data from an ExpressionExperiment.
The rows of this matrix represent design elements.

Author:

pavlidis, keshav

See Also:

BulkExpressionDataMatrix, SingleCellExpressionDataMatrix

Method Summary

All Methods Instance Methods Abstract Methods Deprecated Methods
Modifier and Type	Method	Description
`int`	`columns()`	Obtain the total number of columns.
`T`	`get(int row, int column)`	Access a single value of the matrix by row and column.
`T[]`	`getColumn(int column)`	Access a single column of the matrix.
`CompositeSequence`	`getDesignElementForRow(int index)`	Return a design element for a given index.
`List<CompositeSequence>`	`getDesignElements()`	Obtain all the design elements in this data matrix.
`ExpressionExperiment`	`getExpressionExperiment()`	Return the expression experiment this matrix is holding data for, if known.
`QuantitationType`	`getQuantitationType()`	Obtain the quantitation type for this matrix.
`T[]`	`getRow(int index)`	Access a single row of the matrix, by index.
`T[]`	`getRow(CompositeSequence designElement)`	Return a row that 'came from' the given design element.
`ExpressionDataMatrixRowElement`	`getRowElement(int row)`	Deprecated. use `getDesignElementForRow(int)` instead
`List<ExpressionDataMatrixRowElement>`	`getRowElements()`	Deprecated. use `getDesignElements()` instead
`int`	`getRowIndex(CompositeSequence designElement)`
`int[]`	`getRowIndices(CompositeSequence designElement)`	Obtain all the rows that correspond to the given design element, or `null` if the design element is not found.
`int`	`rows()`

- Method Detail
  - getExpressionExperiment
```
@Nullable
ExpressionExperiment getExpressionExperiment()
```
    Return the expression experiment this matrix is holding data for, if known.
  - getQuantitationType
```
QuantitationType getQuantitationType()
```
    Obtain the quantitation type for this matrix.
  - getDesignElements
```
List<CompositeSequence> getDesignElements()
```
    Obtain all the design elements in this data matrix.
  - getDesignElementForRow
```
CompositeSequence getDesignElementForRow(int index)
```
    Return a design element for a given index.
    
    Throws:
    
    IndexOutOfBoundsException - if the supplied index is not within zero and rows()
  - columns
```
int columns()
```
    Obtain the total number of columns.
  - getColumn
```
T[] getColumn(int column)
```
    Access a single column of the matrix.
    
    Parameters:
    
    column - index
    
    Returns:
    
    T[]
    
    Throws:
    
    IndexOutOfBoundsException - if the supplied index is not within zero and columns()
  - rows
```
int rows()
```
    Returns:
    
    int
  - getRow
```
T[] getRow(int index)
```
    Access a single row of the matrix, by index. A complete row is returned.
    
    Parameters:
    
    index - i
    
    Returns:
    
    t[]
    
    Throws:
    
    IndexOutOfBoundsException - if the supplied index is not within zero and rows()
  - getRow
```
@Nullable
T[] getRow(CompositeSequence designElement)
```
    Return a row that 'came from' the given design element.
    
    Parameters:
    
    designElement - de
    
    Returns:
    
    the corresponding row or null if the design element is not found in the matrix
  - getRowIndex
```
int getRowIndex(CompositeSequence designElement)
```
    Returns:
    
    the index for the given design element, or -1 if not found
  - getRowIndices
```
@Nullable
int[] getRowIndices(CompositeSequence designElement)
```
    Obtain all the rows that correspond to the given design element, or null if the design element is not found.
  - getRowElements
```
@Deprecated
List<ExpressionDataMatrixRowElement> getRowElements()
```
    Deprecated.
    use getDesignElements() instead
    
    Returns:
    
    list of elements representing the row 'labels'.
  - getRowElement
```
@Deprecated
ExpressionDataMatrixRowElement getRowElement(int row)
```
    Deprecated.
    use getDesignElementForRow(int) instead
    
    Throws:
    
    IndexOutOfBoundsException - if the supplied index is not within zero and rows()
  - get
```
T get(int row,
      int column)
```
    Access a single value of the matrix by row and column.
    
    Throws:
    
    IndexOutOfBoundsException - if either the row or column is outside the matrix bounds

Interface ExpressionDataMatrix<T>

Method Summary

Method Detail

getExpressionExperiment

getQuantitationType

getDesignElements

getDesignElementForRow

columns

getColumn

rows

getRow

getRow

getRowIndex

getRowIndices

getRowElements

getRowElement

get