NuXLIonLikelihood.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/ID/FragmentIonLikelihoodModel.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h>
#include <OpenMS/KERNEL/MSExperiment.h>
 
#include <array>
#include <cstdint>
#include <vector>
 
namespace OpenMS
{
  class NuXLIonLikelihood
  {
  public:
    using Model = FragmentIonLikelihoodModel;
 
    enum Group : std::uint8_t { LINEAR = 0, XL_UNSHIFTED = 1, XL_SHIFTED = 2, XL_UNLOCALIZED = 3, GROUPS = 4 };
 
    struct Outcomes
    {
      std::vector<Model::Ion> ions;
      std::vector<std::uint8_t> groups; 
    };
 
    struct Evidence
    {
      Outcomes signal;
      Outcomes noise; 
    };
 
    struct Features
    {
      double llr = 0.0;                    
      double llr_shifted = 0.0;            
      double explained_presence = 0.0;     
      double top_predicted_observed = 0.0; 
    };
 
    NuXLIonLikelihood(double tolerance, bool ppm, int max_fragment_charge = 2);
 
    void setSpectra(const PeakMap& spectra);
 
    Evidence match(Size scan, const AASequence& peptide, int precursor_charge, const std::vector<double>& shifts, int site) const;
 
    void resetFold(Size fold);
 
    void addTraining(Size fold, const Evidence& evidence);
 
    void finalize();
 
    Features score(Size fold, const Outcomes& outcomes) const;
 
    static AASequence reversedSequence(const AASequence& peptide);
 
  private:
    Outcomes matchHypothesis_(Size scan, const AASequence& peptide, int precursor_charge, const std::vector<double>& shifts, int site) const;
 
    double tolerance_;
    bool ppm_;
    int max_fragment_charge_;
    Model::PeakLists peaks_;
    TheoreticalSpectrumGenerator tsg_;
    std::array<std::array<Model, GROUPS>, 2> models_;
  };
} // namespace OpenMS