Package eu.isas.reporter.calculation

Class CorrectionMatrix

java.lang.Object

eu.isas.reporter.calculation.CorrectionMatrix

public class CorrectionMatrix
extends Object

A correction matrix contains the deisotoping coefficients as well as the labels to be corrected.

Author:

Marc Vaudel, Harald Barsnes

Constructor Summary

Constructors

Constructor	Description
CorrectionMatrix(double[][] correctionMatrix, HashMap<Integer,String> reagentNames, double refMass)	Constructor.

Method Summary

Modifier and Type	Method	Description
int	getDimension()	Returns the dimension of the correction matrix.
double	getReagentMass(int isotope)	Returns the mass affected by the given column of the matrix.
HashMap<Integer,String>	getReagentsNames()	Returns the names of the reagents involved in the deisotoping by this matrix indexed by their isotopic number.
double	getValueAt(int i, int j)	Returns the value of the matrix at row i and column j.

Methods inherited from class java.lang.Object

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

Constructor Details

CorrectionMatrix

public CorrectionMatrix(double[][] correctionMatrix,
 HashMap<Integer,String> reagentNames,
 double refMass)

Constructor.

Parameters:

correctionMatrix - the correction matrix

reagentNames - he name of the reagents affected by this matrix

refMass - the mass affected by the first column of the matrix

Method Details

getReagentMass

public double getReagentMass(int isotope)

Returns the mass affected by the given column of the matrix.

Parameters:

isotope - the column of the matrix

Returns:

the mass affected by the given column of the matrix

getReagentsNames

public HashMap<Integer,String> getReagentsNames()

Returns the names of the reagents involved in the deisotoping by this matrix indexed by their isotopic number.

Returns:

the names of the reagents involved in the deisotoping by this matrix

getDimension

public int getDimension()

Returns the dimension of the correction matrix.

Returns:

the dimension of the correction matrix

getValueAt

public double getValueAt(int i,
 int j)

Returns the value of the matrix at row i and column j.

Parameters:

i - the row number

j - the column number

Returns:

the value of the matrix at row i and column j