NuXLRescoring.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/CONCEPT/Types.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
 
#include <algorithm>
#include <array>
#include <limits>
#include <string_view>
#include <vector>
 
namespace OpenMS
{
  struct NuXLRescoring
  {
    struct ScoreGap
    {
      float best = -std::numeric_limits<float>::infinity();
      float second = -std::numeric_limits<float>::infinity(); 
      std::string_view best_sequence;
 
      void add(float score, std::string_view sequence)
      {
        if (sequence == best_sequence) { best = std::max(best, score); return; }
        if (score > best)
        {
          second = best; // the old best has another sequence and is at least as good as every other hit seen so far
          best = score;
          best_sequence = sequence;
          return;
        }
        second = std::max(second, score);
      }
 
      float bestOtherThan(std::string_view sequence) const { return sequence == best_sequence ? second : best; }
    };
 
    static constexpr double TRAIN_FDR = 0.05;
 
    static std::array<std::vector<Size>, 2> confidentHitsPerHalf(const PeptideIdentificationList& peptide_ids, double fdr,
                                                                 std::array<std::array<Size, 2>, 2>& counts);
 
    static constexpr double DELTA_WEIGHT = 1.0;
    static constexpr double ION_LLR_WEIGHT = 0.3;
 
    static void rescoreHits(PeptideIdentificationList& peptide_ids);
  };
} // namespace OpenMS