public class TagSpectrumAnnotator extends SpectrumAnnotator
fragmentFactory, intensityLimit, isPpm, massShift, massShiftCTerm, massShiftNTerm, mzTolerance, pickMostAccuratePeak, precursorCharge, spectrumAnnotation, subtractIsotope, theoreticalFragmentIons, unmatchedIons
Constructor and Description |
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TagSpectrumAnnotator() |
Modifier and Type | Method and Description |
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ArrayList<IonMatch> |
getCurrentAnnotation(MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
boolean pickMostAccuratePeak)
Returns the currently matched ions with the given settings.
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static NeutralLossesMap |
getDefaultLosses(Tag tag,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the possible neutral losses expected by default for a given tag.
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ArrayList<IonMatch> |
getSpectrumAnnotation(HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
MSnSpectrum spectrum,
Tag tag,
double intensityLimit,
double mzTolerance,
boolean isPpm,
boolean pickMostAccuratePeak)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
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Tag |
getTag()
Returns the tag to annotate.
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void |
setTag(Tag newTag,
int precursorCharge)
Sets a new tag to match.
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chargeValidated, getCurrentlyLoadedSpectrumKey, getDefaultLosses, getExpectedIons, getMassShift, getMassShiftCTerm, getMassShiftNTerm, getSpectrumAnnotation, isAccounted, lossesValidated, matchInSpectrum, matchPeak, matchReporterIon, setMassShift, setMassShifts, setMassTolerance, setSpectrum, setTerminalMassShifts, updateMassShifts
public Tag getTag()
public void setTag(Tag newTag, int precursorCharge)
newTag
- the new tagprecursorCharge
- the new precursor chargepublic static NeutralLossesMap getDefaultLosses(Tag tag, SequenceMatchingPreferences sequenceMatchingPreferences) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException
tag
- the tag of interestsequenceMatchingPreferences
- the sequence matching preferencesIOException
- if an IOException occursIllegalArgumentException
- if an IllegalArgumentException occursInterruptedException
- if an InterruptedException occursFileNotFoundException
- if a FileNotFoundException occursClassNotFoundException
- if a ClassNotFoundException occurspublic ArrayList<IonMatch> getSpectrumAnnotation(HashMap<Ion.IonType,HashSet<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, MSnSpectrum spectrum, Tag tag, double intensityLimit, double mzTolerance, boolean isPpm, boolean pickMostAccuratePeak)
iontypes
- The expected ions to look forneutralLosses
- Map of expected neutral losses: neutral loss >
first position in the sequence (first aa is 1). let null if neutral
losses should not be considered.charges
- List of expected chargesprecursorCharge
- the precursor chargespectrum
- The spectrum to matchtag
- The tag of interestintensityLimit
- The intensity limit to usemzTolerance
- The m/z tolerance to useisPpm
- a boolean indicating whether the mass tolerance is in ppm or
in DapickMostAccuratePeak
- if there are more than one matching peak for
a given annotation setting this value to true results in the most
accurate peak being annotated, while setting this to false annotates the
most intense peakpublic ArrayList<IonMatch> getCurrentAnnotation(MSnSpectrum spectrum, HashMap<Ion.IonType,HashSet<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, boolean pickMostAccuratePeak)
SpectrumAnnotator
getCurrentAnnotation
in class SpectrumAnnotator
spectrum
- the spectrum of interestiontypes
- The expected fragment ions to look forneutralLosses
- Map of expected neutral losses: neutral loss >
first position in the sequence (first aa is 1). let null if neutral
losses should not be considered.charges
- List of expected chargespickMostAccuratePeak
- if there are more than one matching peak for
a given annotation setting this value to true results in the most
accurate peak being annotated, while setting this to false annotates the
most intense peakCopyright © 2015. All rights reserved.