MQMsmsExporter.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
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//    may be used to endorse or promote products derived from this software
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// For a full list of authors, refer to the file AUTHORS.
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// $Maintainer: Chris Bielow$
// $Authors: Hendrik Beschorner, Lenny Kovac, Virginia Rossow$
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/QC/MQExporterHelper.h>
 
#include <fstream>
#include <OpenMS/KERNEL/ConsensusFeature.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/KERNEL/Feature.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/MATH/MISC/MathFunctions.h>
 
 
class OPENMS_DLLAPI MQMsms
 
{
private:
  std::fstream file_;                                 
  OpenMS::Size id_ = 0;                               
  OpenMS::String filename_;                           
 
  void exportHeader_();
 
  void exportRowFromFeature_(const OpenMS::Feature& f,
                             const OpenMS::ConsensusMap& cmap,
                             const OpenMS::Size c_feature_number,
                             const OpenMS::String& raw_file,
                             const std::multimap<OpenMS::String, std::pair<OpenMS::Size, OpenMS::Size>>& UIDs,
                             const OpenMS::ProteinIdentification::Mapping& mp_f,
                             const OpenMS::MSExperiment& exp = {},
                             const std::map<OpenMS::String,OpenMS::String>& prot_map = {});
 
public:
  explicit MQMsms(const OpenMS::String& path);
 
  ~MQMsms();
 
  void exportFeatureMap(const OpenMS::FeatureMap& feature_map, const OpenMS::ConsensusMap& cmap,
                        const OpenMS::MSExperiment& exp, const std::map<OpenMS::String,OpenMS::String>& prot_map = {});
 
};