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Packages that use Peak | |
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com.compomics.util.experiment.identification | This package contains experiment classes related to identifications. |
com.compomics.util.experiment.identification.matches | This package contains experiment classes releated to matches. |
com.compomics.util.experiment.massspectrometry | This package contains experiment classes related to spectra. |
Uses of Peak in com.compomics.util.experiment.identification |
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Methods in com.compomics.util.experiment.identification with parameters of type Peak | |
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IonMatch |
PeptideAssumption.getPrecursorMatch(Peak precursorPeak)
Returns the ion match. |
ArrayList<IonMatch> |
SpectrumAnnotator.matchPeak(Peptide peptide,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
ArrayList<Integer> charges,
int precursorCharge,
NeutralLossesMap neutralLosses,
Peak peak)
This method matches the potential fragment ions of a given peptide with a given peak. |
Uses of Peak in com.compomics.util.experiment.identification.matches |
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Fields in com.compomics.util.experiment.identification.matches declared as Peak | |
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Peak |
IonMatch.peak
The matched peak. |
Constructors in com.compomics.util.experiment.identification.matches with parameters of type Peak | |
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IonMatch(Peak aPeak,
Ion anIon,
Charge aCharge)
Constructor for an ion peak. |
Uses of Peak in com.compomics.util.experiment.massspectrometry |
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Fields in com.compomics.util.experiment.massspectrometry with type parameters of type Peak | |
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protected HashMap<Double,Peak> |
Spectrum.peakList
Peak list. |
Methods in com.compomics.util.experiment.massspectrometry that return types with arguments of type Peak | |
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Collection<Peak> |
Spectrum.getPeakList()
Returns the peak list. |
HashMap<Double,Peak> |
Spectrum.getPeakMap()
Returns a peak map where peaks are indexed by their m/z. |
HashMap<Double,Peak> |
Spectrum.getRecalibratedPeakList(HashMap<Double,Double> mzCorrections)
Returns a recalibrated peak list. |
Methods in com.compomics.util.experiment.massspectrometry with parameters of type Peak | |
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void |
Spectrum.addPeak(Peak aPeak)
Adds a peak to the spectrum peak list. |
boolean |
Peak.isSameAs(Peak aPeak)
Returns true if the peak has the same mz and intensity. |
Method parameters in com.compomics.util.experiment.massspectrometry with type arguments of type Peak | |
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void |
Spectrum.setPeakList(HashMap<Double,Peak> peakList)
Sets the peak list. |
Constructor parameters in com.compomics.util.experiment.massspectrometry with type arguments of type Peak | |
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MS1Spectrum(String fileName,
String spectrumTitle,
double scanStartTime,
HashMap<Double,Peak> spectrum)
constructor for an MS1 spectrum |
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MSnSpectrum(int level,
Precursor precursor,
String spectrumTitle,
HashMap<Double,Peak> peakMap,
String fileName)
Constructor for the spectrum. |
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MSnSpectrum(int level,
Precursor precursor,
String spectrumTitle,
HashMap<Double,Peak> peakMap,
String fileName,
double scanStartTime)
Constructor for the spectrum. |
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