public class PeptideSpectrumAnnotator 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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PeptideSpectrumAnnotator()
Constructor.
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Modifier and Type | Method and Description |
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Map<Integer,ArrayList<IonMatch>> |
getCoveredAminoAcids(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter)
Returns the ion matches corresponding to fragment ions indexed by amino
acid number in the sequence.
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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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Peptide |
getCurrentlyLoadedPeptide()
Returns the currently inspected peptide.
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static NeutralLossesMap |
getDefaultLosses(Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the possible neutral losses expected by default for a given
peptide.
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HashMap<Integer,ArrayList<Ion>> |
getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the expected ions in a map indexed by the possible charges.
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HashMap<Integer,ArrayList<Ion>> |
getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons)
Returns the expected ions in a map indexed by the possible charges.
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IonMatch[] |
getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the spectrum annotations of a spectrum in a list of IonMatches
using the intensity filter.
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IonMatch[] |
getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
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IonMatch[] |
getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in an array of IonMatches.
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java.util.stream.Stream<IonMatch> |
getSpectrumAnnotationStream(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the spectrum annotations of a spectrum in a list of IonMatches
using the intensity filter.
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java.util.stream.Stream<IonMatch> |
getSpectrumAnnotationStream(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
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java.util.stream.Stream<IonMatch> |
getSpectrumAnnotationStream(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a stream of IonMatches.
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ArrayList<IonMatch> |
matchPeak(Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
SpecificAnnotationParameters specificAnnotationSettings,
double peakMz,
double peakIntensity)
This method matches the potential fragment ions of a given peptide with a
given peak according to the annotation settings.
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void |
setPeptide(Peptide peptide,
int precursorCharge,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
SpecificAnnotationParameters specificAnnotationSettings)
Sets a new peptide to annotate.
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void |
setPeptide(Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons,
int precursorCharge,
SpecificAnnotationParameters specificAnnotationSettings)
Sets a new peptide to annotate.
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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 void setPeptide(Peptide peptide, int precursorCharge, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, SpecificAnnotationParameters specificAnnotationSettings)
peptide
- the new peptideprecursorCharge
- the new precursor chargemodificationParameters
- the modification parameters the
modification parameterssequenceProvider
- a protein sequence providermodificationsSequenceMatchingParameters
- the sequence matching
parameters to use for modificationsspecificAnnotationSettings
- if provided, only the ions detectable
using these settings will be selectedpublic void setPeptide(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons, int precursorCharge, SpecificAnnotationParameters specificAnnotationSettings)
peptide
- the new peptidemodificationParameters
- the modification parameters the
modification parameterssequenceProvider
- a protein sequence providermodificationsSequenceMatchingParameters
- the sequence matching
parameters to use for modificationspossibleFragmentIons
- the possible fragment ions of the peptideprecursorCharge
- the new precursor chargespecificAnnotationSettings
- if provided, only the ions detectable
using these settings will be selectedpublic ArrayList<IonMatch> matchPeak(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, SpecificAnnotationParameters specificAnnotationSettings, double peakMz, double peakIntensity)
peptide
- the peptidemodificationParameters
- the modification parameters the
modification parameterssequenceProvider
- a protein sequence providermodificationsSequenceMatchingParameters
- the sequence matching
parameters to use for modificationsspecificAnnotationSettings
- the specific annotation settingspeakMz
- the m/z of the peak to matchpeakIntensity
- the intensity of the peak to matchpublic IonMatch[] getSpectrumAnnotation(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)
annotationSettings
- the annotation settingsspecificAnnotationSettings
- the specific annotation settingsspectrumFile
- the file of the spectrum to annotatespectrumTitle
- the title of the spectrum to annotatespectrum
- the spectrum to annotatepeptide
- the peptide of interestmodificationParameters
- the modification parameters the
modification parameterssequenceProvider
- a protein sequence providermodificationsSequenceMatchingParameters
- the sequence matching
parameters to use for modificationspublic java.util.stream.Stream<IonMatch> getSpectrumAnnotationStream(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)
annotationSettings
- the annotation settingsspecificAnnotationSettings
- the specific annotation settingsspectrumFile
- the file of the spectrum to annotatespectrumTitle
- the title of the spectrum to annotatespectrum
- the spectrum to annotatepeptide
- the peptide of interestmodificationParameters
- the modification parameters the
modification parameterssequenceProvider
- a protein sequence providermodificationsSequenceMatchingParameters
- the sequence matching
parameters to use for modificationspublic java.util.stream.Stream<IonMatch> getSpectrumAnnotationStream(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)
annotationSettings
- the annotation settingsspecificAnnotationSettings
- the specific annotation settingsspectrumFile
- the file of the spectrum to annotatespectrumTitle
- the title of the spectrum to annotatespectrum
- the spectrum to annotatepeptide
- the peptide of interestmodificationParameters
- 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 usedpublic IonMatch[] getSpectrumAnnotation(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)
annotationSettings
- the annotation settingsspecificAnnotationSettings
- the specific annotation settingsspectrumFile
- the file of the spectrum to annotatespectrumTitle
- the title of the spectrum to annotatespectrum
- the spectrum to annotatepeptide
- the peptide of interestmodificationParameters
- 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 usedpublic IonMatch[] getSpectrumAnnotation(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments, boolean useIntensityFilter)
annotationSettings
- the annotation settingsspecificAnnotationSettings
- the specific annotation settingsspectrumFile
- the file of the spectrum to annotatespectrumTitle
- the title of the spectrum to annotatespectrum
- the spectrum to annotatepeptide
- the peptide of interestmodificationParameters
- the modification parameters the
modification parameterssequenceProvider
- a protein sequence providermodificationsSequenceMatchingParameters
- the sequence matching
parameters to use for modificationspossiblePeptideFragments
- the possible peptide fragments for this
peptideuseIntensityFilter
- boolean indicating whether intensity filters
should be usedpublic java.util.stream.Stream<IonMatch> getSpectrumAnnotationStream(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments, boolean useIntensityFilter)
annotationSettings
- the annotation settingsspecificAnnotationSettings
- the specific annotation settingsspectrumFile
- the file of the spectrum to annotatespectrumTitle
- the title of the spectrum to annotatespectrum
- the spectrum to annotatepeptide
- the peptide of interestmodificationParameters
- the modification parameters the
modification parameterssequenceProvider
- a protein sequence providermodificationsSequenceMatchingParameters
- the sequence matching
parameters to use for modificationspossiblePeptideFragments
- the possible peptide fragments for this
peptideuseIntensityFilter
- boolean indicating whether intensity filters
should be usedpublic Map<Integer,ArrayList<IonMatch>> getCoveredAminoAcids(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)
annotationSettings
- the annotation settingsspecificAnnotationSettings
- the specific annotation settingsspectrumFile
- the file of the spectrum to annotatespectrumTitle
- the title of the spectrum to annotatespectrum
- The spectrum to matchpeptide
- The peptide of interestmodificationParameters
- 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 usedpublic HashMap<Integer,ArrayList<Ion>> getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)
specificAnnotationSettings
- the specific annotation settingspeptide
- The peptide of interestmodificationParameters
- the modification parameters the
modification parameterssequenceProvider
- a protein sequence providermodificationsSequenceMatchingParameters
- the sequence matching
parameters to use for modificationspublic HashMap<Integer,ArrayList<Ion>> getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons)
specificAnnotationSettings
- the specific annotation settingspeptide
- The peptide of interestmodificationParameters
- the modification parameters the
modification parameterssequenceProvider
- a protein sequence providermodificationsSequenceMatchingParameters
- the sequence matching
parameters to use for modificationspossibleFragmentIons
- the possible fragment ions for the given
peptidepublic 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 usedpublic static NeutralLossesMap getDefaultLosses(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)
peptide
- the peptide of interestmodificationParameters
- the modification parameters the
modification parameterssequenceProvider
- a protein sequence providermodificationsSequenceMatchingParameters
- the sequence matching
parameters to use for modificationspublic Peptide getCurrentlyLoadedPeptide()
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