com.compomics.util.experiment.identification

Class SpectrumAnnotator

java.lang.Object

com.compomics.util.experiment.identification.SpectrumAnnotator

Direct Known Subclasses:

PeptideSpectrumAnnotator, TagSpectrumAnnotator

public abstract class SpectrumAnnotator
extends java.lang.Object

The spectrum annotator annotates peaks in a spectrum.

Author:

Marc Vaudel

Field Summary

Fields

Modifier and Type	Field and Description
protected IonFactory	fragmentFactory The Fragment factory which will generate the fragment ions.
protected double	intensityLimit The intensity limit to use.
protected boolean	isPpm Boolean indicating whether the tolerance is in ppm (true) or in Dalton (false).
protected double	massShift m/z shift applied to all theoretic peaks.
protected double	massShiftCTerm C-terminal m/z shift applied to all reverse ions.
protected double	massShiftNTerm N-terminal m/z shift applied to all forward ions.
protected double	mzTolerance The m/z tolerance for peak matching.
protected int	precursorCharge The precursor charge as deduced by the search engine.
protected java.util.HashMap<java.lang.String,IonMatch>	spectrumAnnotation The spectrum annotation as a map: theoretic fragment key -> ionmatch.
protected static boolean	subtractIsotope Boolean indicating whether the isotopic number shall be removed from the theoretic mass when matching an ion.
protected java.util.ArrayList<Ion>	theoreticalFragmentIons The theoretic fragment ions.
protected java.util.ArrayList<java.lang.String>	unmatchedIons List of unmatched ions.

Constructor Summary

Constructors

Constructor and Description
SpectrumAnnotator()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	chargeValidated(Ion theoreticIon, int charge, int precursorCharge) Returns a boolean indicating whether the given charge can be found on the given fragment ion.
abstract java.util.ArrayList<IonMatch>	getCurrentAnnotation(MSnSpectrum spectrum, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, NeutralLossesMap neutralLosses, java.util.ArrayList<java.lang.Integer> charges) Returns the currently matched ions with the given settings.
java.lang.String	getCurrentlyLoadedSpectrumKey() Returns the spectrum currently inspected.
static NeutralLossesMap	getDefaultLosses(SpectrumIdentificationAssumption spectrumIdentificationAssumption, AminoAcidPattern.MatchingType matchingType, double mzTolerance) Returns the possible neutral losses expected by default for a given peptide.
protected java.util.HashMap<java.lang.Integer,java.util.ArrayList<Ion>>	getExpectedIons(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, NeutralLossesMap neutralLosses, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge) Returns the expected ions in a map indexed by the possible charges.
double	getMassShift() Returns the m/z shift applied to the fragment ions.
double	getMassShiftCTerm() Returns the C-terminal m/z shift applied to all reverse ions.
double	getMassShiftNTerm() Returns the N-terminal m/z shift applied to all forward ions.
static java.util.Vector<DefaultSpectrumAnnotation>	getSpectrumAnnotation(java.util.ArrayList<IonMatch> ionMatches) Translates the list of ion matches into a vector of annotations which can be read by the SpectrumPanel.
boolean	isAccounted(NeutralLossesMap neutralLosses, NeutralLoss neutralLoss, Ion ion) Returns a boolean indicating whether the neutral loss should be accounted for.
boolean	lossesValidated(NeutralLossesMap neutralLosses, Ion theoreticIon) Returns a boolean indicating whether the neutral losses of the given fragment ion are fit the requirement of the given neutral losses map.
protected void	matchInSpectrum(Ion theoreticIon, int inspectedCharge) Matches a theoretic ion in the spectrum.
protected java.util.ArrayList<IonMatch>	matchPeak(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge, NeutralLossesMap neutralLosses, Peak peak) This method matches the potential fragment ions of a given peptide with a given peak.
static java.util.ArrayList<IonMatch>	matchReporterIon(Ion theoreticIon, Spectrum spectrum, double massTolerance) Convenience method to match a reporter ion in a spectrum.
void	setMassShift(double aMassShift) Sets an m/z shift on all ions.
void	setMassShifts(double aMassShift, double aMassShiftNTerm, double aMassShiftCTerm) Sets the m/z shifts.
protected void	setMassTolerance(double mzTolerance, boolean isPpm) Sets a new m/z tolerance for peak matching.
protected void	setSpectrum(MSnSpectrum spectrum, double intensityLimit) Sets a new spectrum to annotate.
void	setTerminalMassShifts(double aMassShiftNTerm, double aMassShiftCTerm) Sets the terminal m/z shifts.

Methods inherited from class java.lang.Object

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

Field Detail

precursorCharge

protected int precursorCharge

The precursor charge as deduced by the search engine.

theoreticalFragmentIons

protected java.util.ArrayList<Ion> theoreticalFragmentIons

The theoretic fragment ions.

fragmentFactory

protected IonFactory fragmentFactory

The Fragment factory which will generate the fragment ions.

intensityLimit

protected double intensityLimit

The intensity limit to use.

spectrumAnnotation

protected java.util.HashMap<java.lang.String,IonMatch> spectrumAnnotation

The spectrum annotation as a map: theoretic fragment key -> ionmatch.

unmatchedIons

protected java.util.ArrayList<java.lang.String> unmatchedIons

List of unmatched ions.

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).

subtractIsotope

protected static final boolean subtractIsotope

Boolean indicating whether the isotopic number shall be removed from the theoretic mass when matching an ion. False by default for ms2 ions.

See Also:

Constant Field Values

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.

Constructor Detail

SpectrumAnnotator

public SpectrumAnnotator()

Method Detail

getSpectrumAnnotation

public static java.util.Vector<DefaultSpectrumAnnotation> getSpectrumAnnotation(java.util.ArrayList<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 void matchInSpectrum(Ion theoreticIon,
                   int inspectedCharge)

Matches a theoretic ion in the spectrum.

Parameters:

theoreticIon - the theoretic ion

inspectedCharge - the expected charge

setSpectrum

protected void setSpectrum(MSnSpectrum spectrum,
               double intensityLimit)

Sets a new spectrum to annotate.

Parameters:

spectrum - The spectrum to inspect

intensityLimit - the minimal intensity to account for

setMassTolerance

protected void setMassTolerance(double mzTolerance,
                    boolean isPpm)

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

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 are 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 abstract java.util.ArrayList<IonMatch> getCurrentAnnotation(MSnSpectrum spectrum,
                                                 java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
                                                 NeutralLossesMap neutralLosses,
                                                 java.util.ArrayList<java.lang.Integer> charges)

Returns the currently matched ions with the given settings.

Parameters:

spectrum - the spectrum of interest

iontypes - The expected fragment ions to look for

neutralLosses - 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 charges

Returns:

the currently matched ions with the given settings

getCurrentlyLoadedSpectrumKey

public java.lang.String getCurrentlyLoadedSpectrumKey()

Returns the spectrum currently inspected.

Returns:

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 aMassShift)

Sets an m/z shift on all ions. The previous mass main shift will be removed.

Parameters:

aMassShift - the m/z shift to apply

setMassShifts

public void setMassShifts(double aMassShift,
                 double aMassShiftNTerm,
                 double aMassShiftCTerm)

Sets the m/z shifts. The previous mass shifts will be removed.

Parameters:

aMassShift - the m/z shift to apply

aMassShiftNTerm - the n-terminal mass shift to apply to all forward ions

aMassShiftCTerm - the c-terminal mass shift to apply to all reverse ions

setTerminalMassShifts

public void setTerminalMassShifts(double aMassShiftNTerm,
                         double aMassShiftCTerm)

Sets the terminal m/z shifts.

Parameters:

aMassShiftNTerm - the n-terminal mass shift to apply to all forward ions

aMassShiftCTerm - the c-terminal mass shift to apply to all reverse ions

getDefaultLosses

public static NeutralLossesMap getDefaultLosses(SpectrumIdentificationAssumption spectrumIdentificationAssumption,
                                AminoAcidPattern.MatchingType matchingType,
                                double mzTolerance)
                                         throws java.io.IOException,
                                                java.lang.IllegalArgumentException,
                                                java.lang.InterruptedException,
                                                java.io.FileNotFoundException,
                                                java.lang.ClassNotFoundException,
                                                java.sql.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:

spectrumIdentificationAssumption - the spectrumIdentificationAssumption of interest

matchingType - the matching type to map ptms on the peptide sequence

mzTolerance - the ms2 m/z tolerance to use

Returns:

the expected possible neutral losses

Throws:

java.io.IOException

java.lang.IllegalArgumentException

java.lang.InterruptedException

java.io.FileNotFoundException

java.lang.ClassNotFoundException

java.sql.SQLException

matchPeak

protected java.util.ArrayList<IonMatch> matchPeak(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
                                      java.util.ArrayList<java.lang.Integer> charges,
                                      int precursorCharge,
                                      NeutralLossesMap neutralLosses,
                                      Peak peak)

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:

iontypes - The fragment ions selected

charges - The charges of the fragment to search for

precursorCharge - The precursor charge as deduced by the search engine

neutralLosses - 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 match

Returns:

A list of potential ion matches

getExpectedIons

protected java.util.HashMap<java.lang.Integer,java.util.ArrayList<Ion>> getExpectedIons(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
                                                                            NeutralLossesMap neutralLosses,
                                                                            java.util.ArrayList<java.lang.Integer> charges,
                                                                            int precursorCharge)

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:

iontypes - The expected ions to look for

neutralLosses - 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 charges

precursorCharge - The precursor charge

Returns:

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

matchReporterIon

public static java.util.ArrayList<IonMatch> matchReporterIon(Ion theoreticIon,
                                             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

spectrum - the spectrum

massTolerance - the mass tolerance to use

Returns:

a list of all the ion matches