java.lang.Object
com.compomics.util.experiment.identification.psm_scoring.PsmScoresEstimator

public class PsmScoresEstimator
extends Object
This class can be used to estimate PSM scores.
Author:
Marc Vaudel
  • Constructor Details

  • Method Details

    • getDecreasingScore

      public double getDecreasingScore​(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, int scoreIndex)
      Scores the match between the given peptide and spectrum using the given score. The score is forced to decrease with the quality of the match by taking the opposite value when relevant.
      Parameters:
      peptide - the peptide of interest
      peptideCharge - the charge of the peptide
      spectrumFile - the file of the spectrum
      spectrumTitle - the title of the spectrum
      spectrum - the spectrum of interest
      identificationParameters - the identification parameters
      specificAnnotationParameters - the annotation preferences specific to this PSM
      modificationParameters - the modification parameters
      sequenceProvider - a provider for the protein sequences
      modificationSequenceMatchingParameters - the sequence matching preferences for modification to peptide mapping
      peptideSpectrumAnnotator - the spectrum annotator to use
      scoreIndex - the index of the score to use
      Returns:
      the score of the match
    • getScore

      public double getScore​(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, int scoreIndex)
      Scores the match between the given peptide and spectrum using the given score.
      Parameters:
      peptide - the peptide of interest
      peptideCharge - the charge of the peptide
      spectrumFile - the file of the spectrum
      spectrumTitle - the title of the spectrum
      spectrum - the spectrum of interest
      identificationParameters - the identification parameters
      specificAnnotationParameters - the annotation preferences specific to this PSM
      modificationParameters - the modification parameters
      sequenceProvider - a provider for the protein sequences
      modificationSequenceMatchingParameters - the sequence matching preferences for modification to peptide mapping
      peptideSpectrumAnnotator - the spectrum annotator to use
      scoreIndex - the index of the score to use
      Returns:
      the score of the match
    • getScore

      public double getScore​(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, PsmScore psmScore)
      Scores the match between the given peptide and spectrum using the given score.
      Parameters:
      peptide - the peptide of interest
      peptideCharge - the charge of the peptide
      spectrum - the spectrum of interest
      spectrumFile - the file of the spectrum
      spectrumTitle - the title of the spectrum
      identificationParameters - the identification parameters
      specificAnnotationParameters - the annotation preferences specific to this psm
      modificationParameters - the modification parameters
      sequenceProvider - a provider for the protein sequences
      modificationSequenceMatchingParameters - the sequence matching preferences for modification to peptide mapping
      peptideSpectrumAnnotator - the spectrum annotator to use
      psmScore - the score to use
      Returns:
      the score of the match