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,
AnnotationPreferences annotationPreferences,
SpecificAnnotationPreferences specificAnnotationPreferences)
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(AnnotationPreferences annotationPreferences,
SpecificAnnotationPreferences specificAnnotationPreferences,
MSnSpectrum spectrum,
Tag tag)
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, InterruptedException, ClassNotFoundException
tag
- the tag of interestsequenceMatchingPreferences
- the sequence matching preferencesIOException
- exception thrown whenever an error occurred while
interacting with a file while mapping potential modification sitesInterruptedException
- exception thrown whenever a threading issue occurred while mapping potential modification sitesClassNotFoundException
- exception thrown whenever an error occurred while deserializing an object from the ProteinTreepublic ArrayList<IonMatch> getSpectrumAnnotation(AnnotationPreferences annotationPreferences, SpecificAnnotationPreferences specificAnnotationPreferences, MSnSpectrum spectrum, Tag tag)
annotationPreferences
- the annotation preferencesspecificAnnotationPreferences
- the specific annotation preferencesspectrum
- the spectrum to matchtag
- the tag of interestpublic ArrayList<IonMatch> getCurrentAnnotation(MSnSpectrum spectrum, AnnotationPreferences annotationPreferences, SpecificAnnotationPreferences specificAnnotationPreferences)
SpectrumAnnotator
getCurrentAnnotation
in class SpectrumAnnotator
spectrum
- the spectrum of interestannotationPreferences
- the annotation preferencesspecificAnnotationPreferences
- the specific annotation preferencesCopyright © 2015. All rights reserved.