PepNovoOutfile.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Timo Sachsenberg $
// $Authors: Sandro Andreotti, Chris Bielow $
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#pragma once

#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/METADATA/PeptideIdentification.h>

#include <vector>
#include <map>

namespace OpenMS
{
  class ProteinIdentification;

  class OPENMS_DLLAPI PepNovoOutfile
  {
public:
    
    typedef std::map<Size, std::pair<double, double> > IndexPosMappingType;
    
    PepNovoOutfile();

    PepNovoOutfile(const PepNovoOutfile & pepnovo_outfile);

    virtual ~PepNovoOutfile();

    PepNovoOutfile & operator=(const PepNovoOutfile & pepnovo_outfile);

    bool operator==(const PepNovoOutfile & pepnovo_outfile) const;

    void load(const std::string & result_filename, std::vector<PeptideIdentification> & peptide_identifications,
              ProteinIdentification & protein_identification,
              const double & score_threshold,
              const IndexPosMappingType & id_rt_mz,
              const std::map<String, String> & mod_id_map);

    void getSearchEngineAndVersion(const String & pepnovo_output_without_parameters_filename, ProteinIdentification & protein_identification);

  };

} //namespace OpenMS