umcg.genetica.math.matrix

Class DoubleMatrixDataset<T,U>

java.lang.Object

umcg.genetica.math.matrix.DoubleMatrixDatasetAC<T,U>

umcg.genetica.math.matrix.DoubleMatrixDataset<T,U>

Deprecated.

@Deprecated
public class DoubleMatrixDataset<T,U>
extends DoubleMatrixDatasetAC<T,U>

Author:

lude, juha

Nested Class Summary

Nested classes/interfaces inherited from class umcg.genetica.math.matrix.DoubleMatrixDatasetAC

DoubleMatrixDatasetAC.LoadLabels

Field Summary

Fields

Modifier and Type	Field and Description
Set<U>	colsToInclude Deprecated.
String	fileName Deprecated.
double[][]	rawData Deprecated.
Set<T>	rowsToInclude Deprecated.

Fields inherited from class umcg.genetica.math.matrix.DoubleMatrixDatasetAC

colObjects, hashCols, hashRows, nrCols, nrRows, rowObjects

Constructor Summary

Constructors

Constructor and Description
DoubleMatrixDataset() Deprecated.
DoubleMatrixDataset(double[][] data) Deprecated.
DoubleMatrixDataset(double[][] data, List<U> rowNames, List<T> columnNames) Deprecated.
DoubleMatrixDataset(int nrRows, int nrCols) Deprecated.
DoubleMatrixDataset(String fileName) Deprecated.
DoubleMatrixDataset(String fileName, DoubleMatrixDatasetAC.LoadLabels ll) Deprecated.
DoubleMatrixDataset(String fileName, Set<T> rowsToInclude) Deprecated.
DoubleMatrixDataset(String fileName, Set<T> rowsToInclude, DoubleMatrixDatasetAC.LoadLabels ll) Deprecated.
DoubleMatrixDataset(String fileName, Set<T> rowsToInclude, Set<U> colsToInclude) Deprecated.
DoubleMatrixDataset(String fileName, Set<T> rowsToInclude, Set<U> colsToInclude, DoubleMatrixDatasetAC.LoadLabels ll) Deprecated.
DoubleMatrixDataset(String fileName, Set<T> rowsToInclude, Set<U> colsToInclude, DoubleMatrixDatasetAC.LoadLabels ll, int columnOffset) Deprecated.
DoubleMatrixDataset(String fileName, Set<T> rowsToInclude, Set<U> colsToInclude, int columnOffset) Deprecated.
DoubleMatrixDataset(String fileName, String delimiter) Deprecated.

Method Summary

Modifier and Type	Method and Description
void	calculateProbeCoexpression(String outputFile) Deprecated.
double[]	get(int x) Deprecated.
double	get(int x, int y) Deprecated.
static List<Object>	getColumnObjectsOnly(String fileName) Deprecated.
double[][]	getRawData() Deprecated.
double[][]	getRawDataTransposed() Deprecated.
static List<Object>	getRowObjectsOnly(String fileName) Deprecated.
DoubleMatrixDataset<U,T>	getTransposedDataset() Deprecated.
void	loadExpressionData(String fileName, String delimiter, int columnOffset) Deprecated.
void	recalculateHashMaps() Deprecated.
void	removeColumnsWithNaNs() Deprecated.
void	save(String fileName) Deprecated.
void	setRawData(double[][] rawData) Deprecated.
void	standardNormalizeData() Deprecated.
void	transposeDataset() Deprecated.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

rawData

public double[][] rawData

Deprecated.

rowsToInclude

public Set<T> rowsToInclude

Deprecated.

colsToInclude

public Set<U> colsToInclude

Deprecated.

fileName

public String fileName

Deprecated.

Constructor Detail

DoubleMatrixDataset

public DoubleMatrixDataset()

Deprecated.

DoubleMatrixDataset

public DoubleMatrixDataset(String fileName)
                    throws IOException

Deprecated.

Throws:

IOException

DoubleMatrixDataset

public DoubleMatrixDataset(String fileName,
                           DoubleMatrixDatasetAC.LoadLabels ll)
                    throws IOException

Deprecated.

Throws:

IOException

DoubleMatrixDataset

public DoubleMatrixDataset(String fileName,
                           Set<T> rowsToInclude)
                    throws IOException

Deprecated.

Throws:

IOException

DoubleMatrixDataset

public DoubleMatrixDataset(String fileName,
                           Set<T> rowsToInclude,
                           DoubleMatrixDatasetAC.LoadLabels ll)
                    throws IOException

Deprecated.

Throws:

IOException

DoubleMatrixDataset

public DoubleMatrixDataset(String fileName,
                           Set<T> rowsToInclude,
                           Set<U> colsToInclude)
                    throws IOException

Deprecated.

Throws:

IOException

DoubleMatrixDataset

public DoubleMatrixDataset(String fileName,
                           Set<T> rowsToInclude,
                           Set<U> colsToInclude,
                           int columnOffset)
                    throws IOException

Deprecated.

Throws:

IOException

DoubleMatrixDataset

public DoubleMatrixDataset(String fileName,
                           Set<T> rowsToInclude,
                           Set<U> colsToInclude,
                           DoubleMatrixDatasetAC.LoadLabels ll)
                    throws IOException

Deprecated.

Throws:

IOException

DoubleMatrixDataset

public DoubleMatrixDataset(String fileName,
                           Set<T> rowsToInclude,
                           Set<U> colsToInclude,
                           DoubleMatrixDatasetAC.LoadLabels ll,
                           int columnOffset)
                    throws IOException

Deprecated.

Throws:

IOException

DoubleMatrixDataset

public DoubleMatrixDataset(String fileName,
                           String delimiter)
                    throws IOException

Deprecated.

Throws:

IOException

DoubleMatrixDataset

public DoubleMatrixDataset(double[][] data)

Deprecated.

DoubleMatrixDataset

public DoubleMatrixDataset(double[][] data,
                           List<U> rowNames,
                           List<T> columnNames)

Deprecated.

DoubleMatrixDataset

public DoubleMatrixDataset(int nrRows,
                           int nrCols)

Deprecated.

Method Detail

loadExpressionData

public void loadExpressionData(String fileName,
                               String delimiter,
                               int columnOffset)
                        throws IOException

Deprecated.

Throws:

IOException

getRowObjectsOnly

public static List<Object> getRowObjectsOnly(String fileName)
                                      throws FileNotFoundException,
                                             IOException,
                                             ClassNotFoundException

Deprecated.

Throws:

FileNotFoundException

IOException

ClassNotFoundException

getColumnObjectsOnly

public static List<Object> getColumnObjectsOnly(String fileName)
                                         throws FileNotFoundException,
                                                IOException,
                                                ClassNotFoundException

Deprecated.

Throws:

FileNotFoundException

IOException

ClassNotFoundException

recalculateHashMaps

public void recalculateHashMaps()

Deprecated.

Specified by:

recalculateHashMaps in class DoubleMatrixDatasetAC<T,U>

transposeDataset

public void transposeDataset()

Deprecated.

getRawDataTransposed

public double[][] getRawDataTransposed()

Deprecated.

calculateProbeCoexpression

public void calculateProbeCoexpression(String outputFile)
                                throws IOException

Deprecated.

Throws:

IOException

standardNormalizeData

public void standardNormalizeData()

Deprecated.

save

public void save(String fileName)
          throws IOException

Deprecated.

Throws:

IOException

get

public double[] get(int x)

Deprecated.

Specified by:

get in class DoubleMatrixDatasetAC<T,U>

get

public double get(int x,
                  int y)

Deprecated.

Specified by:

get in class DoubleMatrixDatasetAC<T,U>

getTransposedDataset

public DoubleMatrixDataset<U,T> getTransposedDataset()

Deprecated.

Returns:

transposed dataset with references to the SAME row and column objects and maps, no cloning

removeColumnsWithNaNs

public void removeColumnsWithNaNs()

Deprecated.

getRawData

public double[][] getRawData()

Deprecated.

setRawData

public void setRawData(double[][] rawData)

Deprecated.