peakml.chemistry
Class PeriodicTable.Derivative

java.lang.Object
  peakml.chemistry.PeriodicTable.Derivative

Enclosing class:

PeriodicTable

public static class PeriodicTable.Derivative
extends java.lang.Object

http://mass-spec.stanford.edu/assets/SUMS_common_ESI_ions.pdf http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator/

Field Summary

int	adductdeduct Indicates whether this is only an adduct (PeriodicTable.ADDUCT), deduct (PeriodicTable.DEDUCT), or both (PeriodicTable.ADDUCT_DEDUCT).
int	charge The charge needed for the basepeak of the adduct.
java.lang.String	formula The formula of the adduct.
double	mass The additional mass of the adduct.
int	mer The number of *-mer's needed for the basepeak.
java.lang.String	name The name of the adduct.

Constructor Summary

PeriodicTable.Derivative(int adductdeduct, int mer, int charge, java.lang.String name, java.lang.String formula, double mass)
Constructs a new adduct instance with the given information.

Method Summary

double	from(double basepeakmass) Calculates the mass of the peak of the given basepeak mass and the adduct.
double[]	fromDerivative(double derevativemass)
int	getCharge() Returns the charge needed for the basepeak of the adduct.
double	getMass() Returns the mass difference of the adduct.
double	getMass(double basepeakmass, int charge) Calculates the mass of the peak of the given basepeak mass and the adduct.
int	getMer() Returns the number of *-mer's needed for the basepeak.
java.lang.String	getName() Returns the name of the adduct.

Methods inherited from class java.lang.Object

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

Field Detail

adductdeduct

public final int adductdeduct

Indicates whether this is only an adduct (PeriodicTable.ADDUCT), deduct (PeriodicTable.DEDUCT), or both (PeriodicTable.ADDUCT_DEDUCT).

mer

public final int mer

The number of *-mer's needed for the basepeak.

charge

public final int charge

The charge needed for the basepeak of the adduct.

mass

public final double mass

The additional mass of the adduct.

name

public final java.lang.String name

The name of the adduct.

formula

public final java.lang.String formula

The formula of the adduct.

Constructor Detail

PeriodicTable.Derivative

public PeriodicTable.Derivative(int adductdeduct,
                                int mer,
                                int charge,
                                java.lang.String name,
                                java.lang.String formula,
                                double mass)

Constructs a new adduct instance with the given information.

Parameters:

adductdeduct - Indicates whether this is only an adduct (PeriodicTable.ADDUCT), deduct (PeriodicTable.DEDUCT), or both (PeriodicTable.ADDUCT_DEDUCT).

mer - The number of *-mer's needed for the basepeak.

charge - The charge needed for the basepeak of the adduct.

name - The name of the adduct.

formula - The formula of the adduct.

mass - The additional mass of the adduct.

Method Detail

getMer

public int getMer()

Returns the number of *-mer's needed for the basepeak.

Returns:

The number of *-mer's needed for the basepeak.

getCharge

public int getCharge()

Returns the charge needed for the basepeak of the adduct.

Returns:

The charge needed for the basepeak.

getName

public java.lang.String getName()

Returns the name of the adduct.

Returns:

The name of the adduct.

getMass

public double getMass()

Returns the mass difference of the adduct.

Returns:

The mass difference.

fromDerivative

public double[] fromDerivative(double derevativemass)

from

public double from(double basepeakmass)

Calculates the mass of the peak of the given basepeak mass and the adduct.

Parameters:

basepeakmass - The mass of the basepeak.

Returns:

The mass of the peak of the adduct+basepeak.

getMass

public double getMass(double basepeakmass,
                      int charge)

Calculates the mass of the peak of the given basepeak mass and the adduct.

Parameters:

basepeakmass - The mass of the basepeak.

charge - The charge of the basepeak.

Returns:

The mass of the peak of the adduct+basepeak.