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 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