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 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