java.lang.Object
com.compomics.util.experiment.identification.psm_scoring.psm_scores.SnrScore

public class SnrScore
extends Object
This score uses the intensity distribution of the peaks to evaluate an SNR score.
Author:
Marc Vaudel
  • Constructor Details

    • SnrScore

      public SnrScore()
      Constructor.
  • Method Details

    • getScore

      public double getScore​(Peptide peptide, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, PeptideSpectrumAnnotator peptideSpectrumAnnotator, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
      Returns the score.
      Parameters:
      peptide - the peptide of interest
      spectrumFile - the file of the spectrum
      spectrumTitle - the title of the spectrum
      spectrum - the spectrum of interest
      annotationSettings - the general spectrum annotation settings
      specificAnnotationSettings - the annotation settings specific to this PSM
      peptideSpectrumAnnotator - the spectrum annotator to use
      modificationParameters - the modification parameters
      sequenceProvider - a provider for the protein sequences
      modificationSequenceMatchingParameters - the sequence matching preferences for modification to peptide mapping
      Returns:
      the score of the match
    • getScore

      public double getScore​(Peptide peptide, Spectrum spectrum, ArrayList<IonMatch> ionMatchesList)
      Returns the score.
      Parameters:
      peptide - the peptide of interest
      spectrum - the spectrum of interest
      ionMatchesList - the ion matches obtained from spectrum annotation
      Returns:
      the score of the match
    • getScore

      public double getScore​(Peptide peptide, Spectrum spectrum, HashMap<Double,​ArrayList<IonMatch>> ionMatches)
      Returns the score.
      Parameters:
      peptide - the peptide of interest
      spectrum - the spectrum of interest
      ionMatches - the ion matches obtained from spectrum annotation indexed by mz
      Returns:
      the score of the match