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

Class TagSpectrumAnnotator

java.lang.Object

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

com.compomics.util.experiment.identification.spectrum_annotation.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.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
TagSpectrumAnnotator()

Method Summary

Modifier and Type	Method and Description
ArrayList<IonMatch>	getCurrentAnnotation(MSnSpectrum spectrum, AnnotationSettings annotationSettings, SpecificAnnotationSettings specificAnnotationSettings) Returns the currently matched ions with the given settings.
static NeutralLossesMap	getDefaultLosses(Tag tag, SequenceMatchingPreferences ptmSequenceMatchingSettings) Returns the possible neutral losses expected by default for a given tag.
ArrayList<IonMatch>	getSpectrumAnnotation(AnnotationSettings annotationSettings, SpecificAnnotationSettings specificAnnotationSettings, MSnSpectrum spectrum, Tag tag) 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 tag 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

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 tag to match.

Parameters:

newTag - the new tag

precursorCharge - the new precursor charge

getDefaultLosses

public static NeutralLossesMap getDefaultLosses(Tag tag,
                                                SequenceMatchingPreferences ptmSequenceMatchingSettings)
                                         throws IOException,
                                                InterruptedException,
                                                ClassNotFoundException

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

Parameters:

tag - the tag of interest

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

getSpectrumAnnotation

public ArrayList<IonMatch> getSpectrumAnnotation(AnnotationSettings annotationSettings,
                                                 SpecificAnnotationSettings specificAnnotationSettings,
                                                 MSnSpectrum spectrum,
                                                 Tag tag)

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

tag - the tag of interest

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