PercolatorOutfile.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: Hendrik Weisser $
// $Authors: Hendrik Weisser $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/SpectrumMetaDataLookup.h>
 
#include <vector>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI PercolatorOutfile
  {
 
  public:
 
    enum class ScoreType { QVALUE, POSTERRPROB, SCORE, SIZE_OF_SCORETYPE };
 
    static const std::string score_type_names[static_cast<size_t>(ScoreType::SIZE_OF_SCORETYPE)];
 
    static ScoreType getScoreType(std::string score_type_name);
 
    PercolatorOutfile();
 
    void load(const std::string& filename, ProteinIdentification& proteins,
              PeptideIdentificationList& peptides,
              SpectrumMetaDataLookup& lookup,
              ScoreType output_score = ScoreType::QVALUE);
 
  private:
    void getPeptideSequence_(std::string peptide, AASequence& seq) const;
 
    void resolveMisassignedNTermMods_(std::string& peptide) const;
  };
 
} // namespace OpenMS