Package com.compomics.util.experiment.identification.spectrum_annotation

Class SpectrumAnnotator

java.lang.Object
com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
Direct Known Subclasses:
PeptideSpectrumAnnotator, TagSpectrumAnnotator
public abstract class SpectrumAnnotator extends Object
The spectrum annotator annotates peaks in a spectrum.
Author:
Marc Vaudel, Harald Barsnes

  • Field Details

    • precursorCharge

      protected int precursorCharge
      The precursor charge as deduced by the search engine.

    • defaultPrecursorCharges

      protected HashSet<Integer> defaultPrecursorCharges
      The precursor charges to inspect by default.

    • theoreticalFragmentIons

      protected HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> theoreticalFragmentIons
      The theoretic fragment ions.

    • fragmentFactory

      protected IonFactory fragmentFactory
      The Fragment factory which will generate the fragment ions.

    • spectrumFile

      protected String spectrumFile
      The file of the currently loaded spectrum.

    • spectrumTitle

      protected String spectrumTitle
      The title of the currently loaded spectrum.

    • intensityLimit

      protected double intensityLimit
      The intensity limit to use.

    • mzTolerance

      protected double mzTolerance
      The m/z tolerance for peak matching.

    • isPpm

      protected boolean isPpm
      Boolean indicating whether the tolerance is in ppm (true) or in Dalton (false).

    • SUBTRACT_ISOTOPE

      protected static final boolean SUBTRACT_ISOTOPE
      Minimal isotopic correction when matching an ion.
      See Also:

    • MIN_ISOTOPIC_CORRRECTION

      protected static final Integer MIN_ISOTOPIC_CORRRECTION
      The minimum isotope correction. By default only the monoisotopic peak is annotated (min=0).

    • MAX_ISOTOPIC_CORRRECTION

      protected static final Integer MAX_ISOTOPIC_CORRRECTION
      The maximal isotope correction. By default only the monoisotopic peak is annotated (max=0).

    • massShift

      protected double massShift
      m/z shift applied to all theoretic peaks.

    • massShiftNTerm

      protected double massShiftNTerm
      N-terminal m/z shift applied to all forward ions.

    • massShiftCTerm

      protected double massShiftCTerm
      C-terminal m/z shift applied to all reverse ions.

    • tiesResolution

      protected SpectrumAnnotator.TiesResolution tiesResolution
      The methods to use to select the best peak when multiple are possible.

    • specificAnnotationSettings

      protected SpecificAnnotationParameters specificAnnotationSettings
      If provided, the annotator will only look for the ions included in the specific annotation settings.

    • ionMatchKeysCache

      protected IonMatchKeysCache ionMatchKeysCache
      The cache to use for the ion match keys.

  • Constructor Details

    • SpectrumAnnotator

      public SpectrumAnnotator()
      Empty default constructor

  • Method Details

    • getSpectrumAnnotation

      public static Vector<SpectrumAnnotation> getSpectrumAnnotation(IonMatch[] ionMatches)
      Translates the list of ion matches into a vector of annotations which can be read by the SpectrumPanel.
      Parameters:
      ionMatches - list of ion matches
      Returns:
      vector of default spectrum annotations

    • matchInSpectrum

      protected IonMatch matchInSpectrum(double[] spectrumMz, double[] spectrumIntensity, Ion theoreticIon, int inspectedCharge)
      Matches a theoretic ion in the spectrum. Returns an IonMatch containing the ion and the peak. Null if not found.
      Parameters:
      spectrumMz - the m/z array of the spectrum
      spectrumIntensity - the intensity array of the spectrum
      theoreticIon - the theoretic ion
      inspectedCharge - the expected charge
      Returns:
      the IonMatch between the ion and the peak

    • setBestPeak

      protected IonMatch setBestPeak(double[] spectrumMz, double[] spectrumIntensity, int[] matchedPeaksIndexes, IonMatch ionMatch)
      Returns the peak to retain of the matched peaks according to the ties resolution setting.
      Parameters:
      spectrumMz - The m/z array of the spectrum.
      spectrumIntensity - The intensity array of the spectrum.
      matchedPeaksIndexes - The indexes of the peaks matched.
      ionMatch - The ion match with the ion to be matched.
      Returns:
      The ion match with the peak information filled.

    • setSpectrum

      protected void setSpectrum(String spectrumFile, String spectrumTitle, Spectrum spectrum, double intensityLimit)
      Sets a new spectrum to annotate.
      Parameters:
      spectrumFile - the file of the spectrum to annotate.
      spectrumTitle - the title of the spectrum to annotate.
      spectrum - the spectrum to inspect
      intensityLimit - the minimal intensity to account for

    • setMassTolerance

      protected void setMassTolerance(double mzTolerance, boolean isPpm, SpectrumAnnotator.TiesResolution tiesResolution)
      Sets a new m/z tolerance for peak matching.
      Parameters:
      mzTolerance - the new m/z tolerance (in m/z, Th)
      isPpm - a boolean indicating whether the mass tolerance is in ppm or in Da
      tiesResolution - the method used to resolve ties

    • isAccounted

      public boolean isAccounted(NeutralLossesMap neutralLosses, NeutralLoss neutralLoss, Ion ion)
      Returns a boolean indicating whether the neutral loss should be accounted for.
      Parameters:
      neutralLosses - map of expected neutral losses
      neutralLoss - the neutral loss of interest
      ion - the fragment ion of interest
      Returns:
      boolean indicating whether the neutral loss should be considered

    • lossesValidated

      public boolean lossesValidated(NeutralLossesMap neutralLosses, Ion theoreticIon)
      Returns a boolean indicating whether the neutral losses of the given fragment ion fit the requirement of the given neutral losses map.
      Parameters:
      neutralLosses - map of expected neutral losses: neutral loss
      theoreticIon - the ion of interest
      Returns:
      a boolean indicating whether the neutral losses of the given fragment ion are fit the requirement of the given neutral losses map

    • chargeValidated

      public boolean chargeValidated(Ion theoreticIon, int charge, int precursorCharge)
      Returns a boolean indicating whether the given charge can be found on the given fragment ion.
      Parameters:
      theoreticIon - the ion of interest
      charge - the candidate charge
      precursorCharge - the precursor charge
      Returns:
      a boolean indicating whether the given charge can be found on the given fragment ion

    • getCurrentAnnotation

      public IonMatch[] getCurrentAnnotation(String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)
      Returns the currently matched ions with the given settings using the intensity filter.
      Parameters:
      spectrumFile - the file of the spectrum to annotate
      spectrumTitle - the title of the spectrum to annotate
      spectrum - the spectrum of interest
      annotationSettings - the annotation settings
      specificAnnotationSettings - the specific annotation settings
      modificationParameters - the modification parameters the modification parameters
      sequenceProvider - a protein sequence provider
      modificationsSequenceMatchingParameters - the sequence matching parameters to use for modifications
      Returns:
      the currently matched ions with the given settings

    • getCurrentAnnotation

      public abstract 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.
      Parameters:
      spectrumFile - the file of the spectrum to annotate
      spectrumTitle - the title of the spectrum to annotate
      spectrum - the spectrum to annotate
      annotationSettings - the annotation settings
      specificAnnotationSettings - the specific annotation settings
      modificationParameters - the modification parameters the modification parameters
      sequenceProvider - a protein sequence provider
      modificationsSequenceMatchingParameters - the sequence matching parameters to use for modifications
      useIntensityFilter - boolean indicating whether intensity filters should be used
      Returns:
      the currently matched ions with the given settings

    • getCurrentlyLoadedSpectrumFile

      public String getCurrentlyLoadedSpectrumFile()
      Returns the file of the spectrum currently inspected.
      Returns:
      the file of the spectrum currently inspected

    • getCurrentlyLoadedSpectrumTitle

      public String getCurrentlyLoadedSpectrumTitle()
      Returns the title of the spectrum currently inspected.
      Returns:
      the title of the spectrum currently inspected

    • getMassShift

      public double getMassShift()
      Returns the m/z shift applied to the fragment ions.
      Returns:
      the m/z shift applied to the fragment ions

    • getMassShiftNTerm

      public double getMassShiftNTerm()
      Returns the N-terminal m/z shift applied to all forward ions.
      Returns:
      the N-terminal m/z shift applied to all forward ions

    • getMassShiftCTerm

      public double getMassShiftCTerm()
      Returns the C-terminal m/z shift applied to all reverse ions.
      Returns:
      the C-terminal m/z shift applied to all reverse ions

    • setMassShift

      public void setMassShift(double massShift)
      Sets an m/z shift on all ions. The previous mass main shift will be removed.
      Parameters:
      massShift - the m/z shift to apply

    • setMassShifts

      public void setMassShifts(double massShift, double massShiftNTerm, double massShiftCTerm)
      Sets the m/z shifts. The previous mass shifts will be removed.
      Parameters:
      massShift - the m/z shift to apply
      massShiftNTerm - the n-terminal mass shift to apply to all forward ions
      massShiftCTerm - the c-terminal mass shift to apply to all reverse ions

    • setTerminalMassShifts

      public void setTerminalMassShifts(double massShiftNTerm, double massShiftCTerm)
      Sets the terminal m/z shifts.
      Parameters:
      massShiftNTerm - the n-terminal mass shift to apply to all forward ions
      massShiftCTerm - the c-terminal mass shift to apply to all reverse ions

    • updateMassShifts

      protected void updateMassShifts()
      Updates the mass shifts.

    • getDefaultLosses

      public static NeutralLossesMap getDefaultLosses(SpectrumIdentificationAssumption spectrumIdentificationAssumption, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)
      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:
      spectrumIdentificationAssumption - the spectrumIdentificationAssumption of interest
      modificationParameters - the modification parameters the modification parameters
      sequenceProvider - a protein sequence provider
      modificationsSequenceMatchingParameters - the sequence matching parameters to use for modifications
      Returns:
      the expected possible neutral losses

    • matchPeak

      protected ArrayList<IonMatch> matchPeak(SpecificAnnotationParameters specificAnnotationSettings, double peakMz, double peakIntensity)
      This method matches the potential fragment ions of a given peptide with a given peak. Note: fragment ions need to be initiated by the SpectrumAnnotator extending class.
      Parameters:
      specificAnnotationSettings - The specific annotation settings.
      peakMz - The m/z of the peak to match.
      peakIntensity - The intensity of the peak to match.
      Returns:
      A list of potential ion matches

    • getExpectedIons

      protected HashMap<Integer,ArrayList<Ion>> getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings)
      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. Note: fragment ions need to be initiated by the SpectrumAnnotator extending class.
      Parameters:
      specificAnnotationSettings - the specific annotation settings
      Returns:
      an ArrayList of IonMatch containing the ion matches with the given settings

    • matchReporterIon

      public static ArrayList<IonMatch> matchReporterIon(Ion theoreticIon, int charge, Spectrum spectrum, double massTolerance)
      Convenience method to match a reporter ion in a spectrum. The charge is assumed to be 1.
      Parameters:
      theoreticIon - the theoretic ion to look for
      charge - the charge of the ion
      spectrum - the spectrum
      massTolerance - the mass tolerance to use
      Returns:
      a list of all the ion matches