com.compomics.util.experiment.identification.spectrum_annotators

Class TagSpectrumAnnotator

java.lang.Object

com.compomics.util.experiment.identification.SpectrumAnnotator

com.compomics.util.experiment.identification.spectrum_annotators.TagSpectrumAnnotator

public class TagSpectrumAnnotator
extends SpectrumAnnotator

Annotates a spectrum with information from a tag.

Author:

Marc Vaudel

Field Summary

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

fragmentFactory, intensityLimit, isPpm, massShift, massShiftCTerm, massShiftNTerm, mzTolerance, pickMostAccuratePeak, precursorCharge, spectrumAnnotation, subtractIsotope, theoreticalFragmentIons, unmatchedIons

Constructor Summary

Constructors

Constructor and Description
TagSpectrumAnnotator()

Method Summary

Methods

Modifier and Type	Method and Description
ArrayList<IonMatch>	getCurrentAnnotation(MSnSpectrum spectrum, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, boolean pickMostAccuratePeak) Returns the currently matched ions with the given settings.
static NeutralLossesMap	getDefaultLosses(Tag tag, AminoAcidPattern.MatchingType matchingType, double mzTolerance) Returns the possible neutral losses expected by default for a given peptide.
ArrayList<IonMatch>	getSpectrumAnnotation(HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, MSnSpectrum spectrum, Tag tag, double intensityLimit, double mzTolerance, boolean isPpm, boolean pickMostAccuratePeak) Returns the spectrum annotations of a spectrum in a list of IonMatches.
Tag	getTag() Returns the tag to annotate.
void	setTag(Tag newTag, int precursorCharge) Sets a new peptide to match.

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

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

Methods inherited from class java.lang.Object

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

Constructor Detail

TagSpectrumAnnotator

public TagSpectrumAnnotator()

Method Detail

getTag

public Tag getTag()

Returns the tag to annotate.

Returns:

the tag to annotate

setTag

public void setTag(Tag newTag,
          int precursorCharge)

Sets a new peptide to match.

Parameters:

newTag - the new peptide

precursorCharge - the new precursor charge

getDefaultLosses

public static NeutralLossesMap getDefaultLosses(Tag tag,
                                AminoAcidPattern.MatchingType matchingType,
                                double mzTolerance)
                                         throws IOException,
                                                IllegalArgumentException,
                                                InterruptedException,
                                                FileNotFoundException,
                                                ClassNotFoundException

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:

tag - the tag 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:

IOException

IllegalArgumentException

InterruptedException

FileNotFoundException

ClassNotFoundException

getSpectrumAnnotation

public ArrayList<IonMatch> getSpectrumAnnotation(HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
                                        NeutralLossesMap neutralLosses,
                                        ArrayList<Integer> charges,
                                        int precursorCharge,
                                        MSnSpectrum spectrum,
                                        Tag tag,
                                        double intensityLimit,
                                        double mzTolerance,
                                        boolean isPpm,
                                        boolean pickMostAccuratePeak)

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:

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

spectrum - The spectrum to match

tag - The tag of interest

intensityLimit - The intensity limit to use

mzTolerance - The m/z tolerance to use

isPpm - a boolean indicating whether the mass tolerance is in ppm or in Da

pickMostAccuratePeak - 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 peak

Returns:

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

getCurrentAnnotation

public ArrayList<IonMatch> getCurrentAnnotation(MSnSpectrum spectrum,
                                       HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
                                       NeutralLossesMap neutralLosses,
                                       ArrayList<Integer> charges,
                                       boolean pickMostAccuratePeak)

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

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

pickMostAccuratePeak - 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 peak

Returns:

the currently matched ions with the given settings