Package com.compomics.util.experiment.mass_spectrometry.spectra

Class Precursor

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.mass_spectrometry.spectra.Precursor

All Implemented Interfaces:

Serializable

public class Precursor
extends ExperimentObject

This class models a precursor.

Author:

Marc Vaudel, Harald Barsnes

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
final double	intensity	The measured intensity of the precursor.
final double	mz	The measured m/z of the precursor.
final int[]	possibleCharges	The charge of the precursor.
final double	rt	The retention time when the precursor was isolated.

Fields inherited from class com.compomics.util.experiment.personalization.ExperimentObject

NO_KEY

Constructor Summary

Constructors

Constructor	Description
Precursor()	Empty default constructor.
Precursor(double rt, double mz, double intensity, int[] possibleCharges)	Constructor with retention time window.
Precursor(double rt, double mz, int[] possibleCharges)	Constructor for the precursor.
Precursor(double mz, double intensity, int[] possibleCharges, double rtMin, double rtMax)	Constructor with retention time window and no reference retention time.

Method Summary

Modifier and Type	Method	Description
double	getMass(int chargeValue)	Returns the mass of the precursor with the given charge.
String	getPossibleChargesAsString()	Returns the possible charges as a string.
double	getRtInMinutes()	Returns the retention time in minutes.
boolean	isSameAs(Precursor otherPrecursor)	Returns a boolean indicating whether the precursor is identical to the other precursor.

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams

Methods inherited from class java.lang.Object

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

Field Details

rt

public final double rt

The retention time when the precursor was isolated.

mz

public final double mz

The measured m/z of the precursor.

intensity

public final double intensity

The measured intensity of the precursor.

possibleCharges

public final int[] possibleCharges

The charge of the precursor.

Constructor Details

Precursor

public Precursor()

Empty default constructor.

Precursor

public Precursor(double rt,
 double mz,
 int[] possibleCharges)

Constructor for the precursor.

Parameters:

rt - the retention time

mz - the m/z

possibleCharges - the possible charges

Precursor

public Precursor(double rt,
 double mz,
 double intensity,
 int[] possibleCharges)

Constructor with retention time window.

Parameters:

rt - the retention time

mz - the m/z

intensity - the intensity

possibleCharges - the possible charges

Precursor

public Precursor(double mz,
 double intensity,
 int[] possibleCharges,
 double rtMin,
 double rtMax)

Constructor with retention time window and no reference retention time.

Parameters:

mz - the m/z

intensity - the intensity

possibleCharges - the possible charges

rtMin - the minimum of the RT window in seconds

rtMax - the maximum of the RT window in seconds

Method Details

getRtInMinutes

public double getRtInMinutes()

Returns the retention time in minutes.

Returns:

the retention time in minutes

getPossibleChargesAsString

public String getPossibleChargesAsString()

Returns the possible charges as a string.

Returns:

the possible charges as a string

getMass

public double getMass(int chargeValue)

Returns the mass of the precursor with the given charge.

Parameters:

chargeValue - the value of the charge

Returns:

the mass of the precursor with the given charge

isSameAs

public boolean isSameAs(Precursor otherPrecursor)

Returns a boolean indicating whether the precursor is identical to the other precursor. m/z, rt, and intensities values must have exact same double values. Charges must be identical and in the same order.

Parameters:

otherPrecursor - The other precursor.

Returns:

A boolean indicating whether the precursor is identical to the other precursor.