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

Class ImmoniumIonAnnotator

java.lang.Object

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

public class ImmoniumIonAnnotator
extends Object

Annotator for immonium and related ions.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor	Description
ImmoniumIonAnnotator()	Empty default constructor
ImmoniumIonAnnotator(char[] peptideSequence)	Constructor.
ImmoniumIonAnnotator(char[] peptideSequence, boolean immonium, boolean related)	Constructor.

Method Summary

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

Methods inherited from class java.lang.Object

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

Constructor Details

ImmoniumIonAnnotator

public ImmoniumIonAnnotator()

Empty default constructor

ImmoniumIonAnnotator

public ImmoniumIonAnnotator(char[] peptideSequence)

Constructor. Warning: there is no check for amino acid uniticy, if duplicates are present, they will be reported multiple times.

Parameters:

peptideSequence - the peptide sequence

ImmoniumIonAnnotator

public ImmoniumIonAnnotator(char[] peptideSequence,
 boolean immonium,
 boolean related)

Constructor. Warning: there is no check for amino acid uniticy, if duplicates are present, they will be reported multiple times.

Parameters:

peptideSequence - the peptide sequence

immonium - boolean indicating whether immonium ions should be annotated

related - boolean indicating whether related ions should be annotated

Method Details

getIonMatches

public ArrayList<IonMatch> getIonMatches(SpectrumIndex spectrumIndex)

Returns the ions matched in the given spectrum.

Parameters:

spectrumIndex - the index of the spectrum

Returns:

the ions matched in the given spectrum