com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators

Class PeptideSpectrumAnnotator

java.lang.Object

com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator

com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator

public class PeptideSpectrumAnnotator
extends SpectrumAnnotator

Annotates a spectrum with peptide fragments. Warning: not multi-thread safe, use different annotators for each thread.

Author:

Marc Vaudel

Field Summary

Fields inherited from class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator

fragmentFactory, intensityLimit, ionMatchKeysCache, isPpm, massShift, massShiftCTerm, massShiftNTerm, maxIsotopicCorrection, minIsotopicCorrection, mzTolerance, pickMostAccuratePeak, precursorCharge, specificAnnotationSettings, spectrumAnnotation, subtractIsotope, theoreticalFragmentIons, unmatchedIons

Constructor Summary

Constructors

Constructor and Description
PeptideSpectrumAnnotator() Constructor.

Method Summary

Modifier and Type	Method and Description
HashMap<Integer,ArrayList<IonMatch>>	getCoveredAminoAcids(AnnotationSettings annotationSettings, SpecificAnnotationSettings specificAnnotationSettings, MSnSpectrum spectrum, Peptide peptide) Returns the ion matches corresponding to fragment ions indexed by amino acid number in the sequence.
ArrayList<IonMatch>	getCurrentAnnotation(MSnSpectrum spectrum, AnnotationSettings annotationSettings, SpecificAnnotationSettings specificAnnotationSettings) Returns the currently matched ions with the given settings.
Peptide	getCurrentlyLoadedPeptide() Returns the currently inspected peptide.
static NeutralLossesMap	getDefaultLosses(Peptide peptide, SequenceMatchingPreferences sequenceMatchingSettings, SequenceMatchingPreferences ptmSequenceMatchingSettings) Returns the possible neutral losses expected by default for a given peptide.
HashMap<Integer,ArrayList<Ion>>	getExpectedIons(SpecificAnnotationSettings specificAnnotationSettings, Peptide peptide) Returns the expected ions in a map indexed by the possible charges.
HashMap<Integer,ArrayList<Ion>>	getExpectedIons(SpecificAnnotationSettings specificAnnotationSettings, Peptide peptide, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons) Returns the expected ions in a map indexed by the possible charges.
ArrayList<IonMatch>	getSpectrumAnnotation(AnnotationSettings annotationSettings, SpecificAnnotationSettings specificAnnotationSettings, MSnSpectrum spectrum, Peptide peptide) Returns the spectrum annotations of a spectrum in a list of IonMatches.
ArrayList<IonMatch>	getSpectrumAnnotation(AnnotationSettings annotationSettings, SpecificAnnotationSettings specificAnnotationSettings, MSnSpectrum spectrum, Peptide peptide, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments) Returns the spectrum annotations of a spectrum in a list of IonMatches.
ArrayList<IonMatch>	matchPeak(Peptide peptide, SpecificAnnotationSettings specificAnnotationSettings, Peak peak) This method matches the potential fragment ions of a given peptide with a given peak according to the annotation settings.
void	setPeptide(Peptide peptide, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons, int precursorCharge, SpecificAnnotationSettings specificAnnotationSettings) Sets a new peptide to match.
void	setPeptide(Peptide peptide, int precursorCharge, SpecificAnnotationSettings specificAnnotationSettings) Sets a new peptide to match.

Methods inherited from class com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator

chargeValidated, getCurrentlyLoadedSpectrumKey, getDefaultLosses, getExpectedIons, getMassShift, getMassShiftCTerm, getMassShiftNTerm, getSpectrumAnnotation, isAccounted, lossesValidated, matchInSpectrum, matchPeak, matchReporterIon, setMassShift, setMassShifts, setMassTolerance, setSpectrum, setTerminalMassShifts, updateMassShifts

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PeptideSpectrumAnnotator

public PeptideSpectrumAnnotator()

Constructor.

Method Detail

setPeptide

public void setPeptide(Peptide peptide,
                       int precursorCharge,
                       SpecificAnnotationSettings specificAnnotationSettings)

Sets a new peptide to match.

Parameters:

peptide - the new peptide

precursorCharge - the new precursor charge

specificAnnotationSettings - if provided, only the ions detectable using these settings will be selected

setPeptide

public void setPeptide(Peptide peptide,
                       HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons,
                       int precursorCharge,
                       SpecificAnnotationSettings specificAnnotationSettings)

Sets a new peptide to match.

Parameters:

peptide - the new peptide

possibleFragmentIons - the possible fragment ions of the peptide

precursorCharge - the new precursor charge

specificAnnotationSettings - if provided, only the ions detectable using these settings will be selected

matchPeak

public ArrayList<IonMatch> matchPeak(Peptide peptide,
                                     SpecificAnnotationSettings specificAnnotationSettings,
                                     Peak peak)

This method matches the potential fragment ions of a given peptide with a given peak according to the annotation settings.

Parameters:

peptide - the peptide

specificAnnotationSettings - the specific annotation settings

peak - the peak to match

Returns:

a list of potential ion matches

getSpectrumAnnotation

public ArrayList<IonMatch> getSpectrumAnnotation(AnnotationSettings annotationSettings,
                                                 SpecificAnnotationSettings specificAnnotationSettings,
                                                 MSnSpectrum spectrum,
                                                 Peptide peptide)

Returns the spectrum annotations of a spectrum in a list of IonMatches. Note that, except for +1 precursors, fragments ions will be expected to have a charge strictly smaller than the precursor ion charge.

Parameters:

annotationSettings - the annotation settings

specificAnnotationSettings - the specific annotation settings

spectrum - the spectrum to match

peptide - the peptide of interest

Returns:

an ArrayList of IonMatch containing the ion matches with the given settings

getSpectrumAnnotation

public ArrayList<IonMatch> getSpectrumAnnotation(AnnotationSettings annotationSettings,
                                                 SpecificAnnotationSettings specificAnnotationSettings,
                                                 MSnSpectrum spectrum,
                                                 Peptide peptide,
                                                 HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments)

Returns the spectrum annotations of a spectrum in a list of IonMatches. Note that, except for +1 precursors, fragments ions will be expected to have a charge strictly smaller than the precursor ion charge.

Parameters:

annotationSettings - the annotation settings

specificAnnotationSettings - the specific annotation settings

spectrum - the spectrum to match

peptide - the peptide of interest

possiblePeptideFragments - the possible peptide fragments for this peptide

Returns:

an ArrayList of IonMatch containing the ion matches with the given settings

getCoveredAminoAcids

public HashMap<Integer,ArrayList<IonMatch>> getCoveredAminoAcids(AnnotationSettings annotationSettings,
                                                                 SpecificAnnotationSettings specificAnnotationSettings,
                                                                 MSnSpectrum spectrum,
                                                                 Peptide peptide)

Returns the ion matches corresponding to fragment ions indexed by amino acid number in the sequence. 1 is first amino acid.

Parameters:

annotationSettings - the annotation settings

specificAnnotationSettings - the specific annotation settings

spectrum - The spectrum to match

peptide - The peptide of interest

Returns:

the ion matches corresponding to fragment ions indexed by amino acid number in the sequence

getExpectedIons

public HashMap<Integer,ArrayList<Ion>> getExpectedIons(SpecificAnnotationSettings specificAnnotationSettings,
                                                       Peptide peptide)

Returns the expected ions in a map indexed by the possible charges. Note that, except for +1 precursors, fragments ions will be expected to have a charge strictly smaller than the precursor ion charge.

Parameters:

specificAnnotationSettings - the specific annotation settings

peptide - The peptide of interest

Returns:

an ArrayList of IonMatch containing the ion matches with the given settings

getExpectedIons

public HashMap<Integer,ArrayList<Ion>> getExpectedIons(SpecificAnnotationSettings specificAnnotationSettings,
                                                       Peptide peptide,
                                                       HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons)

Returns the expected ions in a map indexed by the possible charges. Note that, except for +1 precursors, fragments ions will be expected to have a charge strictly smaller than the precursor ion charge.

Parameters:

specificAnnotationSettings - the specific annotation settings

peptide - The peptide of interest

possibleFragmentIons - the possible fragment ions for the given peptide

Returns:

an ArrayList of IonMatch containing the ion matches with the given settings

getCurrentAnnotation

public ArrayList<IonMatch> getCurrentAnnotation(MSnSpectrum spectrum,
                                                AnnotationSettings annotationSettings,
                                                SpecificAnnotationSettings specificAnnotationSettings)

Description copied from class: SpectrumAnnotator

Returns the currently matched ions with the given settings.

Specified by:

getCurrentAnnotation in class SpectrumAnnotator

Parameters:

spectrum - the spectrum of interest

annotationSettings - the annotation settings

specificAnnotationSettings - the specific annotation settings

Returns:

the currently matched ions with the given settings

getDefaultLosses

public static NeutralLossesMap getDefaultLosses(Peptide peptide,
                                                SequenceMatchingPreferences sequenceMatchingSettings,
                                                SequenceMatchingPreferences ptmSequenceMatchingSettings)
                                         throws IOException,
                                                InterruptedException,
                                                ClassNotFoundException,
                                                SQLException

Returns the possible neutral losses expected by default for a given peptide. /!\ this method will work only if the PTM found in the peptide are in the PTMFactory.

Parameters:

peptide - the peptide of interest

sequenceMatchingSettings - the sequence matching settings for peptide to protein mapping

ptmSequenceMatchingSettings - the sequence matching settings for PTM to peptide mapping

Returns:

the expected possible neutral losses

Throws:

IOException - exception thrown whenever an error occurred while interacting with a file while mapping potential modification sites

InterruptedException - exception thrown whenever a threading issue occurred while mapping potential modification sites

ClassNotFoundException - exception thrown whenever an error occurred while deserializing an object from the ProteinTree

SQLException - exception thrown whenever an error occurred while interacting with the ProteinTree

getCurrentlyLoadedPeptide

public Peptide getCurrentlyLoadedPeptide()

Returns the currently inspected peptide.

Returns:

the currently inspected peptide