Package ubic.basecode.dataStructure.matrix

Class DoubleMatrix<R,C>

java.lang.Object

ubic.basecode.dataStructure.matrix.AbstractMatrix<R,C,Double>

ubic.basecode.dataStructure.matrix.DoubleMatrix<R,C>

All Implemented Interfaces:

Serializable, Matrix2D<R,C,Double>, PrimitiveMatrix<R,C,Double>

Direct Known Subclasses:

CompressedSparseDoubleMatrix, DenseDoubleMatrix, FastRowAccessDoubleMatrix, SparseDoubleMatrix, SparseRaggedDoubleMatrix

public abstract class DoubleMatrix<R,C>
extends AbstractMatrix<R,C,Double>
implements PrimitiveMatrix<R,C,Double>

Abstract base class for 2D matrices of double values with named columns and rows.

Author:

pavlidis

See Also:

Serialized Form

Field Summary

Fields inherited from class ubic.basecode.dataStructure.matrix.AbstractMatrix

MAX_ROWS_TO_PRINT

Constructor Summary

Constructors

Constructor	Description
DoubleMatrix()

Method Summary

Modifier and Type	Method	Description
abstract double[][]	asArray()
abstract DoubleMatrix<R,C>	copy()	Create a deep copy of this
abstract double	get(int j, int i)
Double	getByKeys(R r, C c)
abstract DoubleMatrix<R,C>	getColRange(int startCol, int endCol)
abstract double[]	getColumn(int j)
double[]	getColumnByName(C s)
Double	getEntry(int row, int column)
double[][]	getRawMatrix()
abstract double[]	getRow(int i)
abstract cern.colt.list.DoubleArrayList	getRowArrayList(int i)
double[]	getRowByName(R s)
abstract DoubleMatrix<R,C>	getRowRange(int startRow, int endRow)
void	setByKeys(R r, C c, Double v)
List<R>	sortByColumnAbsoluteValues(int i, boolean descending)
abstract DoubleMatrix<R,C>	subsetColumns(List<C> columns)	Create a copy of this matrix with only the selected columns, in the selected order.
abstract DoubleMatrix<R,C>	subsetRows(List<R> rowNames)	Create a copy of this matrix with only the selected rows, in the selected order.
String	toString()
abstract DoubleMatrix<C,R>	transpose()
abstract cern.colt.matrix.DoubleMatrix1D	viewColumn(int column)
abstract cern.colt.matrix.DoubleMatrix1D	viewRow(int j)

Methods inherited from class ubic.basecode.dataStructure.matrix.AbstractMatrix

addColumnName, addRowName, asDoubles, assign, checkColRange, checkRowRange, containsColumnName, containsRowName, getColIndexByName, getColName, getColNames, getRowIndexByName, getRowName, getRowNameMapIterator, getRowNames, hasColNames, hasMissingValues, hasRow, hasRowNames, numMissing, setColumnName, setColumnNames, setRowName, setRowNames, size

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.basecode.dataStructure.matrix.Matrix2D

addColumnName, asDoubles, assign, columns, containsColumnName, containsRowName, getColIndexByName, getColName, getColNames, getRowIndexByName, getRowName, getRowNameMapIterator, getRowNames, hasColNames, hasRow, hasRowNames, isMissing, numMissing, rows, set, setColumnName, setColumnNames, setRowName, setRowNames

Methods inherited from interface ubic.basecode.dataStructure.matrix.PrimitiveMatrix

getColObj, getObject, getRowObj

Constructor Detail

DoubleMatrix

public DoubleMatrix()

Method Detail

asArray

public abstract double[][] asArray()

copy

public abstract DoubleMatrix<R,C> copy()

Create a deep copy of this

Returns:

a deep copy of this

get

public abstract double get(int j,
                           int i)

Parameters:

j -

i -

Returns:

getByKeys

public Double getByKeys(R r,
                        C c)

Specified by:

getByKeys in interface Matrix2D<R,C,Double>

getColRange

public abstract DoubleMatrix<R,C> getColRange(int startCol,
                                                    int endCol)

Parameters:

startCol - inclusive, numbered from zero

endCol - inclusive, numbered from zero

Returns:

new matrix with just the requested range of columns from this

getColumn

public abstract double[] getColumn(int j)

getColumnByName

public double[] getColumnByName(C s)

Parameters:

s - String

Returns:

double[]

getEntry

public Double getEntry(int row,
                       int column)

Specified by:

getEntry in interface Matrix2D<R,C,Double>

Returns:

getRawMatrix

public double[][] getRawMatrix()

getRow

public abstract double[] getRow(int i)

getRowArrayList

public abstract cern.colt.list.DoubleArrayList getRowArrayList(int i)

getRowByName

public double[] getRowByName(R s)

Parameters:

s - String

Returns:

double[]

getRowRange

public abstract DoubleMatrix<R,C> getRowRange(int startRow,
                                                    int endRow)

Parameters:

startRow - inclusive, numbered from zero

endRow - inclusive

Returns:

setByKeys

public void setByKeys(R r,
                      C c,
                      Double v)

Specified by:

setByKeys in interface Matrix2D<R,C,Double>

sortByColumnAbsoluteValues

public List<R> sortByColumnAbsoluteValues(int i,
                                          boolean descending)

Parameters:

i -

descending -

subsetColumns

public abstract DoubleMatrix<R,C> subsetColumns(List<C> columns)

Create a copy of this matrix with only the selected columns, in the selected order.

Parameters:

columns -

Returns:

subsetRows

public abstract DoubleMatrix<R,C> subsetRows(List<R> rowNames)

Create a copy of this matrix with only the selected rows, in the selected order.

Parameters:

rowNames -

Returns:

toString

public final String toString()

Overrides:

toString in class Object

transpose

public abstract DoubleMatrix<C,R> transpose()

viewColumn

public abstract cern.colt.matrix.DoubleMatrix1D viewColumn(int column)

viewRow

public abstract cern.colt.matrix.DoubleMatrix1D viewRow(int j)

Parameters:

j -

Returns: