MRMFeatureQCFile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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//    may be used to endorse or promote products derived from this software
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// $Maintainer: Douglas McCloskey, Pasquale Domenico Colaianni $
// $Authors: Douglas McCloskey, Pasquale Domenico Colaianni $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/FORMAT/CsvFile.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/StringListUtils.h>
#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureQC.h>

namespace OpenMS
{
  class OPENMS_DLLAPI MRMFeatureQCFile :
    private CsvFile,
    public ProgressLogger
  {
public:
  MRMFeatureQCFile() = default;
  ~MRMFeatureQCFile() override = default;

  void load(const String& filename, MRMFeatureQC& mrmfqc, const bool is_component_group) const;

  /*
    @brief Stores an MRMFeatureQC file.

    @exception Exception::UnableToCreateFile is thrown if the file could not be created

    @param[in] filename The path to the input file
    @param[in] mrmfqc The output class which will contain the criteria
    @param[in] is_component_group true if the user intends to store ComponentGroupQCs data, false otherwise
  */
  void store(const String& filename, const MRMFeatureQC& mrmfqc, const bool is_component_group);
protected:
  void pushValuesFromLine_(
    const StringList& line,
    const std::map<String, Size>& headers,
    std::vector<MRMFeatureQC::ComponentQCs>& c_qcs
  ) const;

  void pushValuesFromLine_(
    const StringList& line,
    const std::map<String, Size>& headers,
    std::vector<MRMFeatureQC::ComponentGroupQCs>& cg_qcs
  ) const;

  void setPairValue_(
    const String& key,
    const String& value,
    const String& boundary,
    std::map<String, std::pair<double,double>>& meta_values_qc
  ) const;

  Int getCastValue_(
    const std::map<String, Size>& headers,
    const StringList& line,
    const String& header,
    const Int default_value
  ) const;

  double getCastValue_(
    const std::map<String, Size>& headers,
    const StringList& line,
    const String& header,
    const double default_value
  ) const;

  String getCastValue_(
    const std::map<String, Size>& headers,
    const StringList& line,
    const String& header,
    const String& default_value
  ) const;

  };

} // namespace OpenMS