PepNovoOutfile.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: Timo Sachsenberg $
// $Authors: Sandro Andreotti, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/PeptideIdentificationList.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, PeptideIdentificationList & 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