DataProcessing.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:
//  * 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"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/METADATA/MetaInfoInterface.h>
#include <OpenMS/METADATA/Software.h>
#include <OpenMS/DATASTRUCTURES/DateTime.h>

#include <set>
#include <boost/shared_ptr.hpp>

namespace OpenMS
{
  class OPENMS_DLLAPI DataProcessing :
    public MetaInfoInterface
  {

public:

    //The different processing types
    enum ProcessingAction
    {
      DATA_PROCESSING,                
      CHARGE_DECONVOLUTION,               
      DEISOTOPING,                                
      SMOOTHING,                                  
      CHARGE_CALCULATION,             
      PRECURSOR_RECALCULATION,          
      BASELINE_REDUCTION,                 
      PEAK_PICKING,                           
      ALIGNMENT,                                  
      CALIBRATION,                                  
      NORMALIZATION,                            
      FILTERING,                                  
      QUANTITATION,                             
      FEATURE_GROUPING,                     
      IDENTIFICATION_MAPPING,           
      FORMAT_CONVERSION,              
      CONVERSION_MZDATA,                  
      CONVERSION_MZML,                        
      CONVERSION_MZXML,                       
      CONVERSION_DTA,                 
      IDENTIFICATION,                 
      SIZE_OF_PROCESSINGACTION
    };
    static const std::string NamesOfProcessingAction[SIZE_OF_PROCESSINGACTION];

    DataProcessing() = default;
    DataProcessing(const DataProcessing&) = default;

    // note: we implement the move constructor ourselves due to a bug in MSVS
    // 2015/2017 which cannot produce a default move constructor for classes
    // that contain STL containers (other than vector).

    DataProcessing(DataProcessing&&) noexcept;
    ~DataProcessing();

    DataProcessing& operator=(const DataProcessing&) = default;
    DataProcessing& operator=(DataProcessing&&)& = default;

    bool operator==(const DataProcessing& rhs) const;
    bool operator!=(const DataProcessing& rhs) const;

    const Software& getSoftware() const;
    Software& getSoftware();
    void setSoftware(const Software& software);

    const std::set<ProcessingAction>& getProcessingActions() const;
    std::set<ProcessingAction>& getProcessingActions();
    void setProcessingActions(const std::set<ProcessingAction>& actions);

    const DateTime& getCompletionTime() const;
    void setCompletionTime(const DateTime& completion_time);

protected:

    Software software_;
    std::set<ProcessingAction> processing_actions_;
    DateTime completion_time_;
  };

  typedef boost::shared_ptr<DataProcessing> DataProcessingPtr;
  typedef boost::shared_ptr<const DataProcessing> ConstDataProcessingPtr;

} // namespace OpenMS