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(HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
MSnSpectrum spectrum,
Peptide peptide,
double intensityLimit,
double mzTolerance,
boolean isPpm,
boolean pickMostAccuratePeak)
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,
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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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(HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
Peptide peptide)
Returns the expected ions in a map indexed by the possible charges.
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ArrayList<IonMatch> |
getSpectrumAnnotation(HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
MSnSpectrum spectrum,
Peptide peptide,
double intensityLimit,
double mzTolerance,
boolean isPpm,
boolean pickMostAccuratePeak)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
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ArrayList<IonMatch> |
matchPeak(Peptide peptide,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
ArrayList<Integer> charges,
int precursorCharge,
NeutralLossesMap neutralLosses,
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, HashMap<Ion.IonType,HashSet<Integer>> iontypes, ArrayList<Integer> charges, int precursorCharge, NeutralLossesMap neutralLosses, Peak peak)
peptide
- The peptideiontypes
- The fragment ions selectedcharges
- The charges of the fragment to search forprecursorCharge
- The precursor charge as deduced by the search
engineneutralLosses
- Map of expected neutral losses: neutral loss >
maximal position in the sequence (first aa is 1). let null if neutral
losses should not be considered.peak
- The peak to matchpublic ArrayList<IonMatch> getSpectrumAnnotation(HashMap<Ion.IonType,HashSet<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, MSnSpectrum spectrum, Peptide peptide, 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 matchpeptide
- The peptide 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 HashMap<Integer,ArrayList<IonMatch>> getCoveredAminoAcids(HashMap<Ion.IonType,HashSet<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, MSnSpectrum spectrum, Peptide peptide, 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 matchpeptide
- The peptide 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 HashMap<Integer,ArrayList<Ion>> getExpectedIons(HashMap<Ion.IonType,HashSet<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, Peptide peptide)
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 chargespeptide
- The peptide of interestprecursorCharge
- The precursor chargepublic 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 peakpublic static NeutralLossesMap getDefaultLosses(Peptide peptide, SequenceMatchingPreferences sequenceMatchingPreferences) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException, SQLException
peptide
- the peptide of interestsequenceMatchingPreferences
- the sequence matching preferencesIOException
IllegalArgumentException
InterruptedException
FileNotFoundException
ClassNotFoundException
SQLException
public Peptide getCurrentlyLoadedPeptide()
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