public class PeptideSpectrumAnnotator extends SpectrumAnnotator
fragmentFactory, intensityLimit, isPpm, massShift, massShiftCTerm, massShiftNTerm, mzTolerance, pickMostAccuratePeak, precursorCharge, spectrumAnnotation, subtractIsotope, theoreticalFragmentIons, unmatchedIons
Constructor and Description |
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PeptideSpectrumAnnotator()
Constructor.
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Modifier and Type | Method and Description |
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HashMap<Integer,ArrayList<IonMatch>> |
getCoveredAminoAcids(AnnotationPreferences annotationPreferences,
SpecificAnnotationPreferences specificAnnotationPreferences,
MSnSpectrum spectrum,
Peptide peptide)
Returns the ion matches corresponding to fragment ions indexed by amino
acid number in the sequence.
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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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Peptide |
getCurrentlyLoadedPeptide()
Returns the currently inspected peptide.
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static NeutralLossesMap |
getDefaultLosses(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the possible neutral losses expected by default for a given
peptide.
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HashMap<Integer,ArrayList<Ion>> |
getExpectedIons(SpecificAnnotationPreferences specificAnnotationPreferences,
Peptide peptide)
Returns the expected ions in a map indexed by the possible charges.
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ArrayList<IonMatch> |
getSpectrumAnnotation(AnnotationPreferences annotationPreferences,
SpecificAnnotationPreferences specificAnnotationPreferences,
MSnSpectrum spectrum,
Peptide peptide)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
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ArrayList<IonMatch> |
matchPeak(Peptide peptide,
SpecificAnnotationPreferences specificAnnotationPreferences,
Peak peak)
This method matches the potential fragment ions of a given peptide with a
given peak.
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void |
setPeptide(Peptide peptide,
int precursorCharge)
Sets a new peptide 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 void setPeptide(Peptide peptide, int precursorCharge)
peptide
- the new peptideprecursorCharge
- the new precursor chargepublic ArrayList<IonMatch> matchPeak(Peptide peptide, SpecificAnnotationPreferences specificAnnotationPreferences, Peak peak)
peptide
- the peptidespecificAnnotationPreferences
- the specific annotation preferencespeak
- the peak to matchpublic ArrayList<IonMatch> getSpectrumAnnotation(AnnotationPreferences annotationPreferences, SpecificAnnotationPreferences specificAnnotationPreferences, MSnSpectrum spectrum, Peptide peptide)
annotationPreferences
- the annotation preferencesspecificAnnotationPreferences
- the specific annotation preferencesspectrum
- the spectrum to matchpeptide
- the peptide of interestpublic HashMap<Integer,ArrayList<IonMatch>> getCoveredAminoAcids(AnnotationPreferences annotationPreferences, SpecificAnnotationPreferences specificAnnotationPreferences, MSnSpectrum spectrum, Peptide peptide)
annotationPreferences
- the annotation preferencesspecificAnnotationPreferences
- the specific annotation preferencesspectrum
- The spectrum to matchpeptide
- The peptide of interestpublic HashMap<Integer,ArrayList<Ion>> getExpectedIons(SpecificAnnotationPreferences specificAnnotationPreferences, Peptide peptide)
specificAnnotationPreferences
- the specific annotation preferencespeptide
- The peptide 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 preferencespublic static NeutralLossesMap getDefaultLosses(Peptide peptide, SequenceMatchingPreferences sequenceMatchingPreferences) throws IOException, InterruptedException, ClassNotFoundException, SQLException
peptide
- the peptide 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 ProteinTreeSQLException
- exception thrown whenever an error occurred while
interacting with the ProteinTreepublic Peptide getCurrentlyLoadedPeptide()
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