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

Class SpectrumUtil

java.lang.Object

com.compomics.util.experiment.mass_spectrometry.spectra.SpectrumUtil

public class SpectrumUtil
extends Object

Utilities functions to handle spectra.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor	Description
SpectrumUtil()

Method Summary

Modifier and Type	Method	Description
static double	getIntensityLimit(Spectrum spectrum, AnnotationParameters.IntensityThresholdType intensityThresholdType, double thresholdValue)	Returns the limit in intensity according to the given threshold.
static int	getNPeaksAboveThreshold(Spectrum spectrum, int startIndex, int endIndex, double intensityThreshold)	Returns the number of peaks between the start index (inclusive) and the end index (exclusive) above the intensity threshold (inclusive).
static double[][]	getPeaksAboveIntensityThreshold(Spectrum spectrum, AnnotationParameters.IntensityThresholdType intensityThresholdType, double thresholdValue)	Returns the peaks above intensity threshold as an array of double (mz, intensity).
static int[]	getWindowIndexes(Spectrum spectrum, double mzMin, double mzMax)	Returns the start (inclusive) and end (exclusive) indexes of the peaks between mzMin (inclusive) and mzMax (exclusive).

Methods inherited from class java.lang.Object

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

Constructor Details

SpectrumUtil

public SpectrumUtil()

Method Details

getIntensityLimit

public static double getIntensityLimit(Spectrum spectrum,
 AnnotationParameters.IntensityThresholdType intensityThresholdType,
 double thresholdValue)

Returns the limit in intensity according to the given threshold.

Parameters:

spectrum - The spectrum.

intensityThresholdType - The type of intensity threshold.

thresholdValue - The threshold value.

Returns:

the intensity limit

getPeaksAboveIntensityThreshold

public static double[][] getPeaksAboveIntensityThreshold(Spectrum spectrum,
 AnnotationParameters.IntensityThresholdType intensityThresholdType,
 double thresholdValue)

Returns the peaks above intensity threshold as an array of double (mz, intensity).

Parameters:

spectrum - The spectrum.

intensityThresholdType - The type of intensity threshold.

thresholdValue - The threshold value.

Returns:

The peaks above intensity threshold.

getWindowIndexes

public static int[] getWindowIndexes(Spectrum spectrum,
 double mzMin,
 double mzMax)

Returns the start (inclusive) and end (exclusive) indexes of the peaks between mzMin (inclusive) and mzMax (exclusive).

Parameters:

spectrum - The spectrum to inspect.

mzMin - The inclusive lower boundary to use.

mzMax - The exclusive upper boundary to use.

Returns:

The start and end indexes of the peaks between mzMin (inclusive) and mzMax (exclusive).

getNPeaksAboveThreshold

public static int getNPeaksAboveThreshold(Spectrum spectrum,
 int startIndex,
 int endIndex,
 double intensityThreshold)

Returns the number of peaks between the start index (inclusive) and the end index (exclusive) above the intensity threshold (inclusive).

Parameters:

spectrum - The spectrum.

startIndex - The start index (inclusive).

endIndex - The end index (exclusive).

intensityThreshold - The intensity threshold (inclusive).

Returns:

The number of peaks between the start index (inclusive) and the end index (exclusive) above the intensity threshold (inclusive).