umcg.genetica.math.matrix2

Class DoubleMatrixDataset<R extends Comparable,C extends Comparable>

java.lang.Object

umcg.genetica.math.matrix2.DoubleMatrixDataset<R,C>

Type Parameters:

R -

C -

public class DoubleMatrixDataset<R extends Comparable,C extends Comparable>
extends Object

Author:

MarcJan, Juha, Harm-Jan, Patrick

Field Summary

Fields

Modifier and Type	Field and Description
protected LinkedHashMap<C,Integer>	hashCols
protected LinkedHashMap<R,Integer>	hashRows
protected cern.colt.matrix.tdouble.DoubleMatrix2D	matrix

Constructor Summary

Constructors

Constructor and Description
DoubleMatrixDataset()
DoubleMatrixDataset(Collection<R> rowNames, Collection<C> colNames)
DoubleMatrixDataset(cern.colt.matrix.tdouble.DoubleMatrix2D matrix, LinkedHashMap<R,Integer> hashRows, LinkedHashMap<C,Integer> hashCols)
DoubleMatrixDataset(int rows, int columns)
DoubleMatrixDataset(LinkedHashMap<R,Integer> hashRows, LinkedHashMap<C,Integer> hashCols)

Method Summary

Modifier and Type	Method and Description
int	columns()
boolean	containsCol(C colId)
boolean	containsRow(R rowId)
ArrayList<C>	getColObjects()
double	getElement(int row, int column) Get specific element.
double	getElement(R rowName, C columnName) Get specific element.
LinkedHashMap<C,Integer>	getHashCols()
LinkedHashMap<R,Integer>	getHashRows()
cern.colt.matrix.tdouble.DoubleMatrix2D	getMatrix()
cern.colt.matrix.tdouble.DoubleMatrix1D	getRow(R rowName)
ArrayList<R>	getRowObjects()
static DoubleMatrixDataset<String,String>	loadDoubleData(String fileName)
static DoubleMatrixDataset<String,String>	loadDoubleTextData(String expressionDataPath, char c)
static DoubleMatrixDataset<String,String>	loadDoubleTextData(String fileName, String delimiter)
static DoubleMatrixDataset<String,String>	loadSubsetOfTextDoubleData(String fileName, String delimiter, HashSet<String> desiredRows, HashSet<String> desiredCols)
void	OrderOnColumnnames() Order columns
void	OrderOnRownames() Order rows
void	reorderCols(LinkedHashMap<C,Integer> mappingIndex)
void	reorderRows(LinkedHashMap<R,Integer> mappingIndex)
int	rows()
void	save(File file)
void	save(String fileName)
void	saveDice(String fileName)
void	setColObjects(List<C> arrayList)
void	setElement(R rowName, C columnName, double value) Set a element of the dataset.
void	setHashCols(LinkedHashMap<C,Integer> hashCols)
void	setHashRows(LinkedHashMap<R,Integer> hashRows)
void	setMatrix(double[][] matrix)
void	setMatrix(cern.colt.matrix.tdouble.DoubleMatrix2D matrix)
void	setRowObjects(List<R> arrayList)
DoubleMatrixDataset<C,R>	viewDice()

Methods inherited from class java.lang.Object

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

Field Detail

matrix

protected cern.colt.matrix.tdouble.DoubleMatrix2D matrix

hashRows

protected LinkedHashMap<R extends Comparable,Integer> hashRows

hashCols

protected LinkedHashMap<C extends Comparable,Integer> hashCols

Constructor Detail

DoubleMatrixDataset

public DoubleMatrixDataset()

DoubleMatrixDataset

public DoubleMatrixDataset(int rows,
                           int columns)

DoubleMatrixDataset

public DoubleMatrixDataset(LinkedHashMap<R,Integer> hashRows,
                           LinkedHashMap<C,Integer> hashCols)

DoubleMatrixDataset

public DoubleMatrixDataset(cern.colt.matrix.tdouble.DoubleMatrix2D matrix,
                           LinkedHashMap<R,Integer> hashRows,
                           LinkedHashMap<C,Integer> hashCols)

DoubleMatrixDataset

public DoubleMatrixDataset(Collection<R> rowNames,
                           Collection<C> colNames)

Method Detail

loadDoubleTextData

public static DoubleMatrixDataset<String,String> loadDoubleTextData(String expressionDataPath,
                                                                    char c)

loadDoubleData

public static DoubleMatrixDataset<String,String> loadDoubleData(String fileName)
                                                         throws IOException

Throws:

IOException

loadDoubleTextData

public static DoubleMatrixDataset<String,String> loadDoubleTextData(String fileName,
                                                                    String delimiter)
                                                             throws IOException

Throws:

IOException

loadSubsetOfTextDoubleData

public static DoubleMatrixDataset<String,String> loadSubsetOfTextDoubleData(String fileName,
                                                                            String delimiter,
                                                                            HashSet<String> desiredRows,
                                                                            HashSet<String> desiredCols)
                                                                     throws IOException

Throws:

IOException

save

public void save(File file)
          throws IOException

Throws:

IOException

save

public void save(String fileName)
          throws IOException

Throws:

IOException

saveDice

public void saveDice(String fileName)
              throws IOException

Throws:

IOException

rows

public int rows()

columns

public int columns()

getHashRows

public LinkedHashMap<R,Integer> getHashRows()

setHashRows

public void setHashRows(LinkedHashMap<R,Integer> hashRows)

getHashCols

public LinkedHashMap<C,Integer> getHashCols()

setHashCols

public void setHashCols(LinkedHashMap<C,Integer> hashCols)

getRowObjects

public ArrayList<R> getRowObjects()

setRowObjects

public void setRowObjects(List<R> arrayList)
                   throws Exception

Throws:

Exception

getColObjects

public ArrayList<C> getColObjects()

setColObjects

public void setColObjects(List<C> arrayList)
                   throws Exception

Throws:

Exception

getMatrix

public cern.colt.matrix.tdouble.DoubleMatrix2D getMatrix()

setMatrix

public void setMatrix(cern.colt.matrix.tdouble.DoubleMatrix2D matrix)

setMatrix

public void setMatrix(double[][] matrix)

OrderOnColumnnames

public void OrderOnColumnnames()

Order columns

OrderOnRownames

public void OrderOnRownames()

Order rows

reorderRows

public void reorderRows(LinkedHashMap<R,Integer> mappingIndex)

reorderCols

public void reorderCols(LinkedHashMap<C,Integer> mappingIndex)

viewDice

public DoubleMatrixDataset<C,R> viewDice()

setElement

public void setElement(R rowName,
                       C columnName,
                       double value)

Set a element of the dataset.

Parameters:

rowName -

columnName -

value -

getElement

public double getElement(R rowName,
                         C columnName)

Get specific element.

Parameters:

rowName -

columnName -

Returns:

getRow

public cern.colt.matrix.tdouble.DoubleMatrix1D getRow(R rowName)

getElement

public double getElement(int row,
                         int column)

Get specific element.

Parameters:

row -

column -

Returns:

containsRow

public boolean containsRow(R rowId)

containsCol

public boolean containsCol(C colId)