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

Class FragmentAnnotator

java.lang.Object

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

public class FragmentAnnotator
extends Object

Annotator for b and y ions without neutral losses.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor	Description
FragmentAnnotator()	Empty default constructor
FragmentAnnotator(Peptide peptide, String[] fixedModifications, SimplePeptideAnnotator.IonSeries ionSeries)	Constructor.
FragmentAnnotator(Peptide peptide, String[] fixedModifications, SimplePeptideAnnotator.IonSeries ionSeries, 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

FragmentAnnotator

public FragmentAnnotator()

Empty default constructor

FragmentAnnotator

public FragmentAnnotator(Peptide peptide,
 String[] fixedModifications,
 SimplePeptideAnnotator.IonSeries ionSeries)

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

Parameters:

peptide - the peptide

fixedModifications - the fixed modifications on the peptide

ionSeries - the ion series to annotate

FragmentAnnotator

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

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

Parameters:

peptide - the peptide

fixedModifications - the fixed modifications on the peptide

ionSeries - the ion series to annotate

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