com.compomics.util.math.matrix

Class DoubleMatrix

java.lang.Object

com.compomics.util.math.matrix.DoubleMatrix

public class DoubleMatrix
extends java.lang.Object

Implementation of a matrix for double objects. Warning: all indexes start from 0.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
DoubleMatrix()
DoubleMatrix(DoubleMatrix matrix)
DoubleMatrix(int nColumns)

Method Summary

Methods

Modifier and Type	Method and Description
void	addColumn(java.util.ArrayList<java.lang.Double> column)
void	addLine(java.util.ArrayList<java.lang.Double> line)
void	appendColumns(DoubleMatrix columns)
void	appendLines(DoubleMatrix lines)
void	columnPermutation(int column1, int column2)
boolean	equals(DoubleMatrix anotherMatrix)
java.util.ArrayList<java.lang.Double>	getColumn(int columnIndex)
java.util.ArrayList<java.util.ArrayList<java.lang.Double>>	getColumns()
double	getDeterminant()
static DoubleMatrix	getIdentityMatrix(int n)
java.util.ArrayList<java.lang.Double>	getLine(int lineIndex)
java.util.ArrayList<java.util.ArrayList<java.lang.Double>>	getLines()
int	getNColumns()
int	getNLines()
double	getNonDiagonalScore() Returns a score based on the non-diagonal values.
DoubleMatrix	getSubMatrix(int lineStart, int lineStop, int columnStart, int columnStop)
double	getTrace()
java.lang.Double	getValueAt(int lineIndex, int columnIndex) Returns the value of the matrix at given indexes.
boolean	isSquare()
void	linePermutation(int line1, int line2)
void	setColumn(int columnIndex, java.util.ArrayList<java.lang.Double> column)
void	setLine(int lineIndex, java.util.ArrayList<java.lang.Double> line)
void	setValueAt(int lineIndex, int columnIndex, java.lang.Double value)
static DoubleMatrix	transpose(DoubleMatrix matrix)

Methods inherited from class java.lang.Object

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

Constructor Detail

DoubleMatrix

public DoubleMatrix()

DoubleMatrix

public DoubleMatrix(int nColumns)

DoubleMatrix

public DoubleMatrix(DoubleMatrix matrix)

Method Detail

addColumn

public void addColumn(java.util.ArrayList<java.lang.Double> column)

addLine

public void addLine(java.util.ArrayList<java.lang.Double> line)

setLine

public void setLine(int lineIndex,
           java.util.ArrayList<java.lang.Double> line)

setColumn

public void setColumn(int columnIndex,
             java.util.ArrayList<java.lang.Double> column)

getNColumns

public int getNColumns()

getNLines

public int getNLines()

isSquare

public boolean isSquare()

getColumn

public java.util.ArrayList<java.lang.Double> getColumn(int columnIndex)

getColumns

public java.util.ArrayList<java.util.ArrayList<java.lang.Double>> getColumns()

getLines

public java.util.ArrayList<java.util.ArrayList<java.lang.Double>> getLines()

getLine

public java.util.ArrayList<java.lang.Double> getLine(int lineIndex)

getValueAt

public java.lang.Double getValueAt(int lineIndex,
                          int columnIndex)

Returns the value of the matrix at given indexes. 0 is the first index.

Parameters:

lineIndex -

columnIndex -

Returns:

the value of the matrix at given indexes, 0 is the first index

setValueAt

public void setValueAt(int lineIndex,
              int columnIndex,
              java.lang.Double value)

transpose

public static DoubleMatrix transpose(DoubleMatrix matrix)

equals

public boolean equals(DoubleMatrix anotherMatrix)

getIdentityMatrix

public static DoubleMatrix getIdentityMatrix(int n)

getTrace

public double getTrace()

getSubMatrix

public DoubleMatrix getSubMatrix(int lineStart,
                        int lineStop,
                        int columnStart,
                        int columnStop)

appendColumns

public void appendColumns(DoubleMatrix columns)

appendLines

public void appendLines(DoubleMatrix lines)

getDeterminant

public double getDeterminant()

getNonDiagonalScore

public double getNonDiagonalScore()

Returns a score based on the non-diagonal values. Score is 0 for identity, 1 for the (1) matrix.

Returns:

a score based on the non-diagonal values

linePermutation

public void linePermutation(int line1,
                   int line2)

columnPermutation

public void columnPermutation(int column1,
                     int column2)