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 2002-2020.
//
// 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.
//  * Neither the name of any author or any participating institution
//    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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// --------------------------------------------------------------------------
// $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() = 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