PercolatorOutfile.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser $
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#ifndef OPENMS_FORMAT_PERCOLATOROUTFILE_H
#define OPENMS_FORMAT_PERCOLATOROUTFILE_H

#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

#endif // OPENMS_FORMAT_PERCOLATOROUTFILE_H