java.lang.Object
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.SimplePeptideAnnotator

public class SimplePeptideAnnotator
extends Object
A simple annotator for peptides.
Author:
Marc Vaudel
  • Constructor Details

    • SimplePeptideAnnotator

      public SimplePeptideAnnotator​(Peptide peptide, String[] fixedModifications, int charge, AnnotationParameters annotationSettings)
      Constructor. Fixed modifications must be indexed as provided by the peptide class.
      Parameters:
      peptide - the peptide to annotate
      fixedModifications - the fixed modifications of the peptide
      charge - the charge of the peptide
      annotationSettings - the annotation preferences
    • SimplePeptideAnnotator

      public SimplePeptideAnnotator()
      Empty default constructor
    • SimplePeptideAnnotator

      public SimplePeptideAnnotator​(Peptide peptide, String[] fixedModifications, int charge, boolean a, boolean b, boolean c, boolean x, boolean y, boolean z, boolean precursor, boolean immonium, boolean related, boolean reporter, boolean neutralLosses, boolean neutralLossesSequenceDependent, ReporterIon[] reporterIons)
      Constructor. Fixed modifications must be indexed as provided by the peptide class.
      Parameters:
      peptide - the peptide to annotate
      fixedModifications - the fixed modifications of the peptide
      charge - the charge of the peptide
      a - boolean indicating whether a ions should be annotated
      b - boolean indicating whether b ions should be annotated
      c - boolean indicating whether c ions should be annotated
      x - boolean indicating whether x ions should be annotated
      y - boolean indicating whether y ions should be annotated
      z - boolean indicating whether z ions should be annotated
      precursor - boolean indicating whether precursor ions should be annotated
      immonium - boolean indicating whether immonium ions should be annotated
      related - boolean indicating whether related ions should be annotated
      reporter - boolean indicating whether reporter ions should be annotated
      neutralLosses - boolean indicating whether fragment ions with neutral losses should be annotated
      neutralLossesSequenceDependent - boolean indicating whether the neutral losses should be selected depending on the sequence
      reporterIons - the reporter ions to annotate
  • Method Details

    • getIonMatches

      public ArrayList<IonMatch> getIonMatches​(SpectrumIndex spectrumIndex, int peptideCharge, int precursorIsotopeMax)
      Returns the ion matches for the given spectrum.
      Parameters:
      spectrumIndex - the spectrum index
      peptideCharge - the peptide charge
      precursorIsotopeMax - the number of isotopes to test for the precursor ion
      Returns:
      the ion matches in a list