public class TagSpectrumAnnotator extends SpectrumAnnotator
SpectrumAnnotator.TiesResolution
defaultPrecursorCharges, fragmentFactory, intensityLimit, ionMatchKeysCache, isPpm, massShift, massShiftCTerm, massShiftNTerm, MAX_ISOTOPIC_CORRRECTION, MIN_ISOTOPIC_CORRRECTION, mzTolerance, precursorCharge, specificAnnotationSettings, spectrumFile, spectrumTitle, SUBTRACT_ISOTOPE, theoreticalFragmentIons, tiesResolution
Constructor and Description |
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TagSpectrumAnnotator()
Empty default constructor
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Modifier and Type | Method and Description |
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IonMatch[] |
getCurrentAnnotation(String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter)
Returns the currently matched ions with the given settings.
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static NeutralLossesMap |
getDefaultLosses(Tag tag,
ModificationParameters modificationParameters,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the possible neutral losses expected by default for a given tag.
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IonMatch[] |
getSpectrumAnnotation(AnnotationParameters annotationSettings,
ModificationParameters modificationParameters,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Tag tag)
Returns the spectrum annotations of a spectrum in a list of IonMatches
using an intensity filter.
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IonMatch[] |
getSpectrumAnnotation(AnnotationParameters annotationSettings,
ModificationParameters modificationParameters,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Tag tag,
boolean useIntensityFilter)
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,
ModificationParameters modificationParameters,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
int precursorCharge)
Sets a new tag to match.
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chargeValidated, getCurrentAnnotation, getCurrentlyLoadedSpectrumFile, getCurrentlyLoadedSpectrumTitle, getDefaultLosses, getExpectedIons, getMassShift, getMassShiftCTerm, getMassShiftNTerm, getSpectrumAnnotation, isAccounted, lossesValidated, matchInSpectrum, matchPeak, matchReporterIon, setBestPeak, setMassShift, setMassShifts, setMassTolerance, setSpectrum, setTerminalMassShifts, updateMassShifts
public Tag getTag()
public void setTag(Tag newTag, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters, int precursorCharge)
newTag
- the new tagmodificationParameters
- the modification parameters the
modification parametersmodificationsSequenceMatchingParameters
- the sequence matching
parameters to use for modificationsprecursorCharge
- the new precursor chargepublic static NeutralLossesMap getDefaultLosses(Tag tag, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters)
tag
- the tag of interestmodificationParameters
- the modification parameters the
modification parametersmodificationsSequenceMatchingParameters
- the sequence matching
parameters to use for modificationspublic IonMatch[] getSpectrumAnnotation(AnnotationParameters annotationSettings, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Tag tag)
annotationSettings
- the annotation settingsmodificationParameters
- the modification parameters the
modification parametersmodificationsSequenceMatchingParameters
- the sequence matching
parameters to use for modificationsspecificAnnotationSettings
- the specific annotation settingsspectrumFile
- the file of the spectrum to annotatespectrumTitle
- the title of the spectrum to annotatespectrum
- the spectrum to matchtag
- the tag of interestpublic IonMatch[] getSpectrumAnnotation(AnnotationParameters annotationSettings, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Tag tag, boolean useIntensityFilter)
annotationSettings
- the annotation settingsmodificationParameters
- the modification parameters the
modification parametersmodificationsSequenceMatchingParameters
- the sequence matching
parameters to use for modificationsspecificAnnotationSettings
- the specific annotation settingsspectrumFile
- the file of the spectrum to annotatespectrumTitle
- the title of the spectrum to annotatespectrum
- the spectrum to annotatetag
- the tag of interestuseIntensityFilter
- boolean indicating whether intensity filters
should be usedpublic IonMatch[] getCurrentAnnotation(String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)
SpectrumAnnotator
getCurrentAnnotation
in class SpectrumAnnotator
spectrumFile
- the file of the spectrum to annotatespectrumTitle
- the title of the spectrum to annotatespectrum
- the spectrum to annotateannotationSettings
- the annotation settingsspecificAnnotationSettings
- the specific annotation settingsmodificationParameters
- the modification parameters the
modification parameterssequenceProvider
- a protein sequence providermodificationsSequenceMatchingParameters
- the sequence matching
parameters to use for modificationsuseIntensityFilter
- boolean indicating whether intensity filters
should be usedCopyright © 2021. All rights reserved.