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

Class SimplePeptideAnnotator

java.lang.Object

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

public class SimplePeptideAnnotator
extends Object

A simple annotator for peptides.

Author:

Marc Vaudel

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	SimplePeptideAnnotator.IonSeries	The type of ion series to annotate.

Constructor Summary

Constructors

Constructor	Description
SimplePeptideAnnotator()	Empty default constructor
SimplePeptideAnnotator(Peptide peptide, String[] fixedModifications, int charge, boolean a, boolean b, boolean c, boolean x, boolean y, boolean z, boolean precursor, boolean immonium, boolean related, boolean reporter, boolean neutralLosses, boolean neutralLossesSequenceDependent, ReporterIon[] reporterIons)	Constructor.
SimplePeptideAnnotator(Peptide peptide, String[] fixedModifications, int charge, AnnotationParameters annotationSettings)	Constructor.

Method Summary

Modifier and Type	Method	Description
ArrayList<IonMatch>	getIonMatches(SpectrumIndex spectrumIndex, int peptideCharge, int precursorIsotopeMax)	Returns the ion matches for the given spectrum.

Methods inherited from class java.lang.Object

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

Constructor Details

SimplePeptideAnnotator

public SimplePeptideAnnotator(Peptide peptide,
 String[] fixedModifications,
 int charge,
 AnnotationParameters annotationSettings)

Constructor. Fixed modifications must be indexed as provided by the peptide class.

Parameters:

peptide - the peptide to annotate

fixedModifications - the fixed modifications of the peptide

charge - the charge of the peptide

annotationSettings - the annotation preferences

SimplePeptideAnnotator

public SimplePeptideAnnotator()

Empty default constructor

SimplePeptideAnnotator

public SimplePeptideAnnotator(Peptide peptide,
 String[] fixedModifications,
 int charge,
 boolean a,
 boolean b,
 boolean c,
 boolean x,
 boolean y,
 boolean z,
 boolean precursor,
 boolean immonium,
 boolean related,
 boolean reporter,
 boolean neutralLosses,
 boolean neutralLossesSequenceDependent,
 ReporterIon[] reporterIons)

Constructor. Fixed modifications must be indexed as provided by the peptide class.

Parameters:

peptide - the peptide to annotate

fixedModifications - the fixed modifications of the peptide

charge - the charge of the peptide

a - boolean indicating whether a ions should be annotated

b - boolean indicating whether b ions should be annotated

c - boolean indicating whether c ions should be annotated

x - boolean indicating whether x ions should be annotated

y - boolean indicating whether y ions should be annotated

z - boolean indicating whether z ions should be annotated

precursor - boolean indicating whether precursor ions should be annotated

immonium - boolean indicating whether immonium ions should be annotated

related - boolean indicating whether related ions should be annotated

reporter - boolean indicating whether reporter ions should be annotated

neutralLosses - boolean indicating whether fragment ions with neutral losses should be annotated

neutralLossesSequenceDependent - boolean indicating whether the neutral losses should be selected depending on the sequence

reporterIons - the reporter ions to annotate

Method Details

getIonMatches

public ArrayList<IonMatch> getIonMatches(SpectrumIndex spectrumIndex,
 int peptideCharge,
 int precursorIsotopeMax)

Returns the ion matches for the given spectrum.

Parameters:

spectrumIndex - the spectrum index

peptideCharge - the peptide charge

precursorIsotopeMax - the number of isotopes to test for the precursor ion

Returns:

the ion matches in a list