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
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Constructor Summary
Constructors Constructor Description SpectrumUtil()
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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).
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Constructor Details
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SpectrumUtil
public SpectrumUtil()
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Method Details
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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
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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.
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getWindowIndexes
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).
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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).
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