MSPGenericFile.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: Douglas McCloskey, Pasquale Domenico Colaianni $
// $Authors: Douglas McCloskey, Pasquale Domenico Colaianni $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/config.h> // OPENMS_DLLAPI
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/DATASTRUCTURES/StringUtils.h>
#include <OpenMS/KERNEL/MSExperiment.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI MSPGenericFile :
    public DefaultParamHandler
  {
public:
    MSPGenericFile();
 
    MSPGenericFile(const std::string& filename, MSExperiment& library);
 
    ~MSPGenericFile() override = default;
 
    void getDefaultParameters(Param& params);
 
    friend class MSPGenericFile_friend;
 
    void load(const std::string& filename, MSExperiment& library);
 
    void store(const std::string& filename, const MSExperiment& library) const;
  
  private:
    void updateMembers_() override;
 
    void addSpectrumToLibrary(
      MSSpectrum& spectrum,
      MSExperiment& library
    );
 
    std::set<std::string> loaded_spectra_names_;
 
    /*
      The synonyms of a spectrum are collected into this variable and,
      when `addSpectrumtoLibrary()` is called, the elements are concatenated
      and the result is saved as a "Synon" metaValue.
      The synonyms are separated by `synonyms_separator_`.
    */
    std::vector<std::string> synonyms_;
 
    std::string synonyms_separator_;
  };
 
  class MSPGenericFile_friend
  {
public:
    MSPGenericFile_friend() = default;
    ~MSPGenericFile_friend() = default;
 
    void addSpectrumToLibrary(
      MSSpectrum& spectrum,
      MSExperiment& library
    )
    {
      return msp_.addSpectrumToLibrary(spectrum, library);
    }
 
    MSPGenericFile msp_;
  };
}