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org.genepattern.data.expr
Class ResExpressionData

java.lang.Object
  extended byorg.genepattern.data.expr.ExpressionData
      extended byorg.genepattern.data.expr.ResExpressionData
All Implemented Interfaces:
IExpressionData, IResExpressionData
public class ResExpressionData
extends ExpressionData
implements IResExpressionData

Implementation of IResExpressionData interface

Field Summary
 
Fields inherited from interface org.genepattern.data.expr.IResExpressionData
ABSENT, MARGINAL, PRESENT
 
Constructor Summary
ResExpressionData(DoubleMatrix2D expressionData, IntMatrix2D calls, java.lang.String[] geneDescriptions, java.lang.String[] sampleDescriptions)
          Constructs a new res expression data instance
 
Method Summary
 int getCall(int row, int column)
          Gets the Affymetrix call at the given row and column.
 java.lang.String getCallAsString(int row, int column)
          Gets the Affymetrix call at the given row and column.
 IntMatrix2D getCallMatrix()
          Gets the 2-dimensional matrix that holds the absent-present calls
 ExpressionData slice(int[] rowIndices, int[] columnIndices)
          Constructs and returns a new res expression data instance that contains the indicated cells.
 
Methods inherited from class org.genepattern.data.expr.ExpressionData
get, getArray, getColumnCount, getColumnDescription, getColumnDescriptions, getColumnIndex, getColumnName, getColumnNames, getExpressionMatrix, getRow, getRowCount, getRowDescription, getRowDescriptions, getRowIndex, getRowName, getRowNames, getValue, getValueAsString, set, set, setColumnDescription, setColumnDescriptions, setColumnName, setRowDescription, setRowDescriptions, setRowName, slice
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface org.genepattern.data.expr.IExpressionData
getColumnCount, getColumnDescription, getColumnIndex, getColumnName, getRowCount, getRowDescription, getRowIndex, getRowName, getValue, getValueAsString
 

Constructor Detail

ResExpressionData

public ResExpressionData(DoubleMatrix2D expressionData,
                         IntMatrix2D calls,
                         java.lang.String[] geneDescriptions,
                         java.lang.String[] sampleDescriptions)
Constructs a new res expression data instance

Parameters:
expressionData - the expression data
calls - the calls
geneDescriptions - the row(gene) descriptions
sampleDescriptions - the sample(column) descriptions
Method Detail

slice

public ExpressionData slice(int[] rowIndices,
                            int[] columnIndices)
Constructs and returns a new res expression data instance that contains the indicated cells. Ensures that both the expression data and the calls are sliced. Indices can be in arbitrary order.

Overrides:
slice in class ExpressionData
Parameters:
rowIndices - The rows of the cells in the new res expressionData. To indicate that the new expressionData should contain all rows, set this parameter to null.
columnIndices - The columns of the cells in the new res expressionData. To indicate that the new expressionData should contain all columns, set this parameter to null.
Returns:
the sliced data

getCall

public int getCall(int row,
                   int column)
Description copied from interface: IResExpressionData
Gets the Affymetrix call at the given row and column. A value of IResExpressionData.PRESENT indicates a present call, IResExpressionData.ABSENT an absent call, and IResExpressionData.MARGINAL a marginal call.

Specified by:
getCall in interface IResExpressionData
Parameters:
row - The row index
column - The column index
Returns:
The call

getCallAsString

public java.lang.String getCallAsString(int row,
                                        int column)
Description copied from interface: IResExpressionData
Gets the Affymetrix call at the given row and column. A value of 'P' indicates a present call, 'A' an absent call, and 'M' a marginal call.

Specified by:
getCallAsString in interface IResExpressionData
Parameters:
row - The row index
column - The column index
Returns:
The call

getCallMatrix

public IntMatrix2D getCallMatrix()
Gets the 2-dimensional matrix that holds the absent-present calls

Returns:
The call matrix
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