Package | Description |
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com.compomics.util.experiment.identification |
This package contains experiment classes related to identifications.
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com.compomics.util.experiment.identification.matches |
This package contains experiment classes releated to matches.
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com.compomics.util.experiment.massspectrometry |
This package contains experiment classes related to spectra.
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Modifier and Type | Method and Description |
---|---|
IonMatch |
PeptideAssumption.getPrecursorMatch(Peak precursorPeak)
Returns the ion match.
|
java.util.ArrayList<IonMatch> |
SpectrumAnnotator.matchPeak(Peptide peptide,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
NeutralLossesMap neutralLosses,
Peak peak)
This method matches the potential fragment ions of a given peptide with a
given peak.
|
Modifier and Type | Field and Description |
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Peak |
IonMatch.peak
The matched peak.
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Constructor and Description |
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IonMatch(Peak aPeak,
Ion anIon,
Charge aCharge)
Constructor for an ion peak.
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Modifier and Type | Field and Description |
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protected java.util.HashMap<java.lang.Double,Peak> |
Spectrum.peakList
Peak list.
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Modifier and Type | Method and Description |
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java.util.HashMap<java.lang.Double,Peak> |
Spectrum.getDesignaledPeakList(java.util.ArrayList<IonMatch> matches)
Returns the peak list of this spectrum without matched peaks.
|
java.util.Collection<Peak> |
Spectrum.getPeakList()
Returns the peak list.
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java.util.HashMap<java.lang.Double,Peak> |
Spectrum.getPeakMap()
Returns a peak map where peaks are indexed by their m/z.
|
java.util.HashMap<java.lang.Double,Peak> |
Spectrum.getRecalibratedPeakList(java.util.HashMap<java.lang.Double,java.lang.Double> mzCorrections)
Returns a recalibrated peak list.
|
java.util.HashMap<java.lang.Double,Peak> |
Spectrum.getSubSpectrum(double mzMin,
double mzMax)
Returns the part of the spectrum contained between mzMin (inclusive) and
mzMax (exclusive) as a peak list
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Modifier and Type | Method and Description |
---|---|
void |
Spectrum.addPeak(Peak aPeak)
Adds a peak to the spectrum peak list.
|
int |
Peak.compareTo(Peak p)
Compare two peaks in regards to their intensity.
|
boolean |
Peak.isSameAs(Peak aPeak)
Returns true if the peak has the same mz and intensity.
|
Modifier and Type | Method and Description |
---|---|
void |
Spectrum.setPeakList(java.util.HashMap<java.lang.Double,Peak> peakList)
Sets the peak list.
|
void |
Spectrum.setPeaks(java.util.ArrayList<Peak> peaks)
Set the peaks.
|
Constructor and Description |
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MS1Spectrum(java.lang.String fileName,
java.lang.String spectrumTitle,
double scanStartTime,
java.util.HashMap<java.lang.Double,Peak> spectrum)
constructor for an MS1 spectrum
|
MSnSpectrum(int level,
Precursor precursor,
java.lang.String spectrumTitle,
java.util.HashMap<java.lang.Double,Peak> peakMap,
java.lang.String fileName)
Constructor for the spectrum.
|
MSnSpectrum(int level,
Precursor precursor,
java.lang.String spectrumTitle,
java.util.HashMap<java.lang.Double,Peak> peakMap,
java.lang.String fileName,
double scanStartTime)
Constructor for the spectrum.
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