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

Class PrecursorAnnotator

java.lang.Object

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

public class PrecursorAnnotator
extends Object

Annotator for the precursor peaks.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor	Description
PrecursorAnnotator()	Empty default constructor
PrecursorAnnotator(Peptide peptide, String[] fixedModifications)	Constructor.

Method Summary

Modifier and Type	Method	Description
ArrayList<IonMatch>	getIonMatches(SpectrumIndex spectrumIndex, int peptideCharge, int isotopeMax)	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

PrecursorAnnotator

public PrecursorAnnotator()

Empty default constructor

PrecursorAnnotator

public PrecursorAnnotator(Peptide peptide,
 String[] fixedModifications)

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

Parameters:

peptide - the peptide of interest.

fixedModifications - the fixed modifications

Method Details

getIonMatches

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

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

isotopeMax - the maximal isotopic value to annotate (inclusive)

Returns:

the ions matched in the given spectrum at the given charge