Package | Description |
---|---|
com.compomics.util.experiment.identification |
Experiment classes related to identifications.
|
com.compomics.util.experiment.identification.matches |
Experiment classes related to matches.
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com.compomics.util.experiment.identification.spectrum_annotation |
Classes used for ms2 spectrum annotation.
|
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators |
Spectrum annotation.
|
com.compomics.util.experiment.massspectrometry |
Experiment classes related to spectra.
|
Modifier and Type | Method and Description |
---|---|
IonMatch |
SpectrumIdentificationAssumption.getPrecursorMatch(Peak precursorPeak)
Returns the ion match.
|
Modifier and Type | Field and Description |
---|---|
Peak |
IonMatch.peak
The matched peak.
|
Constructor and Description |
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IonMatch(Peak aPeak,
Ion anIon,
Charge aCharge)
Constructor for an ion peak.
|
Modifier and Type | Method and Description |
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protected ArrayList<IonMatch> |
SpectrumAnnotator.matchPeak(SpecificAnnotationSettings specificAnnotationSettings,
Peak peak)
This method matches the potential fragment ions of a given peptide with a
given peak.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.matchPeak(Peptide peptide,
SpecificAnnotationSettings specificAnnotationSettings,
Peak peak)
This method matches the potential fragment ions of a given peptide with a
given peak according to the annotation settings.
|
Modifier and Type | Field and Description |
---|---|
static Comparator<Peak> |
Peak.AscendingIntensityComparator
This comparator compares two Peak instances on ascending intensity.
|
static Comparator<Peak> |
Peak.AscendingMzComparator
This comparator compares two Peak instances on ascending m/z value.
|
static Comparator<Peak> |
Peak.DescendingIntensityComparator
This comparator compares two Peak instances on descending intensity.
|
protected HashMap<Double,ArrayList<Peak>> |
Spectrum.intensityPeakMap
Intensity indexed Peak map.
|
protected HashMap<Double,Peak> |
Spectrum.peakList
mz indexed Peak list.
|
Modifier and Type | Method and Description |
---|---|
HashMap<Double,Peak> |
Spectrum.getDesignaledPeakList(ArrayList<IonMatch> matches)
Returns the peak list of this spectrum without matched peaks.
|
HashMap<Double,ArrayList<Peak>> |
Spectrum.getIntensityMap()
Returns the peak list in a map where peaks are indexed by their
intensity.
|
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.
|
HashMap<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
|
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(HashMap<Double,Peak> peakList)
Sets the peak list.
|
void |
Spectrum.setPeaks(ArrayList<Peak> peaks)
Set the peaks.
|
Constructor and Description |
---|
MS1Spectrum(String fileName,
String spectrumTitle,
double scanStartTime,
HashMap<Double,Peak> spectrum)
Constructor for an MS1 spectrum.
|
MSnSpectrum(int level,
Precursor precursor,
String spectrumTitle,
HashMap<Double,Peak> peakMap,
String fileName)
Constructor for the spectrum.
|
MSnSpectrum(int level,
Precursor precursor,
String spectrumTitle,
HashMap<Double,Peak> peakMap,
String fileName,
double scanStartTime)
Constructor for the spectrum.
|
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