PercolatorOutfile.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.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/SpectrumMetaDataLookup.h>
 
#include <vector>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI PercolatorOutfile
  {
 
  public:
 
    enum ScoreType { QVALUE, POSTERRPROB, SCORE, SIZE_OF_SCORETYPE };
 
    static const std::string score_type_names[SIZE_OF_SCORETYPE];
 
    static enum ScoreType getScoreType(String score_type_name);
 
    PercolatorOutfile();
 
    void load(const String& filename, ProteinIdentification& proteins,
              std::vector<PeptideIdentification>& peptides,
              SpectrumMetaDataLookup& lookup,
              enum ScoreType output_score = QVALUE);
 
  private:
    void getPeptideSequence_(String peptide, AASequence& seq) const;
 
    void resolveMisassignedNTermMods_(String& peptide) const;
  };
 
} // namespace OpenMS