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

Class Spectrum

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum

All Implemented Interfaces:

Serializable

public class Spectrum
extends ExperimentObject

This class models a spectrum. Note: throughout the code, it is assumed that the m/z array is sorted by ascending m/z. Only minimal sanity check is conducted.

Author:

Marc Vaudel, Harald Barsnes

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
double[]	intensity	The array of the intensities of the peaks.
double[]	mz	The array of the m/z of the peaks.
Precursor	precursor	The precursor if any.

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

NO_KEY

Constructor Summary

Constructors

Constructor	Description
Spectrum()	Empty default constructor.
Spectrum(Precursor precursor, double[] mz, double[] intensities, int spectrumLevel)	Constructor.Note: throughout the code, it is assumed that the m/z array is sorted by ascending m/z.

Method Summary

Modifier and Type	Method	Description
double	getMaxIntensity()	Returns the max intensity value.
double	getMaxMz()	Returns the max mz value.
double	getMinMz()	Returns the min mz value.
int	getNPeaks()	Returns the number of peaks.
String	getPeakListAsString()	Returns the peak list as an array list formatted as text, e.g.
Precursor	getPrecursor()	Returns the precursor.
int	getSpectrumLevel()	Returns the spectrum level.
double	getTotalIntensity()	Returns the total intensity of the spectrum.
boolean	isSameAs(Spectrum otherSpectrum)	Returns a boolean indicating whether the spectrum is identical to the other spectrum.
void	setSpectrumLevel(int spectrumLevel)	Set the spectrum level.
String	toString()

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, wait, wait, wait

Field Details

precursor

public Precursor precursor

The precursor if any.

mz

public double[] mz

The array of the m/z of the peaks. Note: throughout the code, it is assumed that the m/z array is sorted by ascending m/z. Only minimal sanity check is conducted.

intensity

public double[] intensity

The array of the intensities of the peaks.

Constructor Details

Spectrum

public Spectrum()

Empty default constructor.

Spectrum

public Spectrum(Precursor precursor,
 double[] mz,
 double[] intensities,
 int spectrumLevel)

Constructor.Note: throughout the code, it is assumed that the m/z array is sorted by ascending m/z. Only minimal sanity check is conducted.

Parameters:

precursor - the precursor

mz - the array of mz of the peaks

intensities - the array of intensities of the peaks

spectrumLevel - the spectrum level

Method Details

getPeakListAsString

public String getPeakListAsString()

Returns the peak list as an array list formatted as text, e.g. [[303.17334 3181.14],[318.14542 37971.93], ... ].

Returns:

the peak list as an array list formatted as text

getTotalIntensity

public double getTotalIntensity()

Returns the total intensity of the spectrum.

Returns:

the total intensity, 0 if no peak

getMaxIntensity

public double getMaxIntensity()

Returns the max intensity value.

Returns:

the max intensity value. 0 if no peak.

getMaxMz

public double getMaxMz()

Returns the max mz value.

Returns:

the max mz value

getMinMz

public double getMinMz()

Returns the min mz value.

Returns:

the min mz value

getPrecursor

public Precursor getPrecursor()

Returns the precursor. Null if none.

Returns:

the precursor

getNPeaks

public int getNPeaks()

Returns the number of peaks.

Returns:

the number of peaks

isSameAs

public boolean isSameAs(Spectrum otherSpectrum)

Returns a boolean indicating whether the spectrum is identical to the other spectrum. Precursors are compared using the isSameAs method. M/z and intensities must be in the same order with exact same double values.

Parameters:

otherSpectrum - The other spectrum.

Returns:

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

toString

public String toString()

Overrides:

toString in class Object

getSpectrumLevel

public int getSpectrumLevel()

Returns the spectrum level. Null if not set.

Returns:

the spectrumLevel

setSpectrumLevel

public void setSpectrumLevel(int spectrumLevel)

Set the spectrum level.

Parameters:

spectrumLevel - the spectrumLevel to set