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

Class FragmentAnnotatorNL

java.lang.Object

com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.FragmentAnnotatorNL

public class FragmentAnnotatorNL
extends Object

A fragment annotator for peptide fragment ions with neutral losses.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor	Description
FragmentAnnotatorNL()	Empty default constructor
FragmentAnnotatorNL(Peptide peptide, String[] fixedModifications, SimplePeptideAnnotator.IonSeries ionSeries, boolean sequenceDependent)	Constructor.
FragmentAnnotatorNL(Peptide peptide, String[] fixedModifications, SimplePeptideAnnotator.IonSeries ionSeries, boolean sequenceDependent, boolean forward, boolean complementary)	Constructor.

Method Summary

Modifier and Type	Method	Description
ArrayList<IonMatch>	getIonMatches(SpectrumIndex spectrumIndex, int peptideCharge)	Returns the ions matched in the given spectrum at the given charge.

Methods inherited from class java.lang.Object

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

Constructor Details

FragmentAnnotatorNL

public FragmentAnnotatorNL()

Empty default constructor

FragmentAnnotatorNL

public FragmentAnnotatorNL(Peptide peptide,
 String[] fixedModifications,
 SimplePeptideAnnotator.IonSeries ionSeries,
 boolean sequenceDependent)

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

Parameters:

peptide - the peptide

fixedModifications - the fixed modifications of the peptide

ionSeries - the ion series to annotate

sequenceDependent - boolean indicating whether the H2O and NH3 losses should be adapted to the sequence

FragmentAnnotatorNL

public FragmentAnnotatorNL(Peptide peptide,
 String[] fixedModifications,
 SimplePeptideAnnotator.IonSeries ionSeries,
 boolean sequenceDependent,
 boolean forward,
 boolean complementary)

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

Parameters:

peptide - the peptide

fixedModifications - the fixed modifications

ionSeries - the ion series to annotate

sequenceDependent - boolean indicating whether the H2O and NH3 losses should be adapted to the sequence

forward - boolean indicating whether forward ions should be annotated

complementary - boolean indicating whether complementary ions should be annotated

Method Details

getIonMatches

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

Returns the ions matched in the given spectrum at the given charge.

Parameters:

spectrumIndex - the index of the spectrum

peptideCharge - the charge of the peptide

Returns:

the ions matched in the given spectrum at the given charge