PercolatorTypes.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/DATASTRUCTURES/TypeAliases.h>
#include <OpenMS/DATASTRUCTURES/StringUtils.h>
 
#include <string>
#include <vector>
 
namespace OpenMS
{
  struct OPENMS_DLLAPI RescoreInput
  {
    std::vector<std::vector<double>> features;
    std::vector<bool> is_decoy;
    std::vector<int> cv_group_keys;
    StringList feature_names;
 
    std::vector<int>    scan_numbers;
    std::vector<int>    spec_file_numbers;
    std::vector<double> exp_masses;
    std::vector<double> calc_masses;
 
    std::vector<double> feature_matrix;
 
    std::vector<std::string> peptide_keys;
 
    size_t rowCount() const
    {
      return features.empty() && !feature_matrix.empty() ? is_decoy.size() : features.size();
    }
 
    size_t featureCount() const
    {
      if (!features.empty()) return features.front().size();
      return feature_matrix.empty() ? 0 : feature_names.size();
    }
 
    const double* row(size_t i) const
    {
      return !features.empty() ? features[i].data() : feature_matrix.data() + i * feature_names.size();
    }
  };
 
  struct OPENMS_DLLAPI RescoreOutput
  {
    std::vector<double> scores;     
    std::vector<double> q_values;   
    std::vector<double> peps;       
    std::vector<double> peptide_q_values;
    std::vector<double> peptide_peps;
  };
 
  struct OPENMS_DLLAPI PercolatorModel
  {
    int format_version = 1;
    StringList feature_names;
    std::vector<double> weights;
    std::string normalizer_type;
    int seed = 0;
  };
}