MSPGenericFile.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.
//  * 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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// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// --------------------------------------------------------------------------
// $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/String.h>
#include <OpenMS/KERNEL/MSExperiment.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI MSPGenericFile :
    public DefaultParamHandler
  {
public:
    MSPGenericFile();
 
    MSPGenericFile(const String& filename, MSExperiment& library);
 
    ~MSPGenericFile() override = default;
 
    void getDefaultParameters(Param& params);
 
    friend class MSPGenericFile_friend;
 
    void load(const String& filename, MSExperiment& library);
 
    void store(const String& filename, const MSExperiment& library) const;
  
  private:
    void updateMembers_() override;
 
    void addSpectrumToLibrary(
      MSSpectrum& spectrum,
      MSExperiment& library
    );
 
    std::set<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<String> synonyms_;
 
    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_;
  };
}