public class PeptideSpectrumAnnotator extends SpectrumAnnotator
fragmentFactory, intensityLimit, isPpm, massShift, massShiftCTerm, massShiftNTerm, mzTolerance, 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,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
MSnSpectrum spectrum,
Peptide peptide,
double intensityLimit,
double mzTolerance,
boolean isPpm)
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,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges)
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,
AminoAcidPattern.MatchingType matchingType,
double mzTolerance)
Returns the possible neutral losses expected by default for a given
peptide.
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HashMap<Integer,ArrayList<Ion>> |
getExpectedIons(HashMap<Ion.IonType,ArrayList<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,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
MSnSpectrum spectrum,
Peptide peptide,
double intensityLimit,
double mzTolerance,
boolean isPpm)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
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ArrayList<IonMatch> |
matchPeak(Peptide peptide,
HashMap<Ion.IonType,ArrayList<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
public void setPeptide(Peptide peptide, int precursorCharge)
peptide
- the new peptideprecursorCharge
- the new precursor chargepublic ArrayList<IonMatch> matchPeak(Peptide peptide, HashMap<Ion.IonType,ArrayList<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,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, MSnSpectrum spectrum, Peptide peptide, double intensityLimit, double mzTolerance, boolean isPpm)
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 Dapublic HashMap<Integer,ArrayList<IonMatch>> getCoveredAminoAcids(HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, MSnSpectrum spectrum, Peptide peptide, double intensityLimit, double mzTolerance, boolean isPpm)
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 Dapublic HashMap<Integer,ArrayList<Ion>> getExpectedIons(HashMap<Ion.IonType,ArrayList<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,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges)
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 chargespublic static NeutralLossesMap getDefaultLosses(Peptide peptide, AminoAcidPattern.MatchingType matchingType, double mzTolerance) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException, SQLException
peptide
- the peptide of interestmatchingType
- the matching type to map ptms on the peptide sequencemzTolerance
- the ms2 m/z tolerance to useIOException
IllegalArgumentException
InterruptedException
FileNotFoundException
ClassNotFoundException
SQLException
public Peptide getCurrentlyLoadedPeptide()
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