OSWFile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
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//    notice, this list of conditions and the following disclaimer.
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// $Maintainer: George Rosenberger $
// $Authors: George Rosenberger $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/KERNEL/StandardTypes.h>
 
#include <array>
#include <map>
 
namespace OpenMS
{
  class OPENMS_DLLAPI OSWFile
  {
public:
  
    enum class OSWLevel
    {
      MS1,
      MS2,
      TRANSITION,
      SIZE_OF_OSWLEVEL
    };
    static const std::array<std::string, (Size)OSWLevel::SIZE_OF_OSWLEVEL> names_of_oswlevel;
 
    struct PercolatorFeature
    {
      PercolatorFeature(double score, double qvalue, double pep)
       : score(score), qvalue(qvalue), posterior_error_prob(pep)
       {}
      PercolatorFeature(const PercolatorFeature& rhs) = default;
      
      double score;
      double qvalue;
      double posterior_error_prob;
    };
 
    static void readToPIN(const std::string& in_osw, const OSWFile::OSWLevel osw_level, std::ostream& pin_output,
                          const double ipf_max_peakgroup_pep, const double ipf_max_transition_isotope_overlap, const double ipf_min_transition_sn);
 
    static void writeFromPercolator(const std::string& in_osw, const OSWFile::OSWLevel osw_level, const std::map< std::string, PercolatorFeature >& features);
 
  };
 
} // namespace OpenMS