MQEvidenceExporter.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:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// $Maintainer: Chris Bielow$
// $Authors: Valentin Noske, Vincent Musch$
// --------------------------------------------------------------------------
 
#pragma once
 
#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/QC/MQExporterHelper.h>
 
#include <map>
 
class OPENMS_DLLAPI MQEvidence
{
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 MQEvidence(const OpenMS::String& path);
 
  ~MQEvidence();
 
  void exportFeatureMap(
    const OpenMS::FeatureMap& feature_map,
    const OpenMS::ConsensusMap& cmap,
    const OpenMS::MSExperiment& exp= {},
    const std::map<OpenMS::String,OpenMS::String>& prot_map = {});
};