// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2016.
//
// 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.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------

#ifndef OPENMS_METADATA_DATAPROCESSING_H
#define OPENMS_METADATA_DATAPROCESSING_H

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

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

namespace OpenMS
{
  /**
      @brief Description of the applied preprocessing steps

      @ingroup Metadata
  */
  class OPENMS_DLLAPI DataProcessing :
    public MetaInfoInterface
  {

public:

    //The different processing types
    enum ProcessingAction
    {
      DATA_PROCESSING,                ///< General data processing (if no other term applies)
      CHARGE_DECONVOLUTION,               ///< Charge deconvolution
      DEISOTOPING,                                ///< Deisotoping
      SMOOTHING,                                  ///< Smoothing of the signal to reduce noise
      CHARGE_CALCULATION,             ///< Determination of the peak charge
      PRECURSOR_RECALCULATION,          ///< Recalculation of precursor m/z
      BASELINE_REDUCTION,                 ///< Baseline reduction
      PEAK_PICKING,                           ///< Peak picking (conversion from raw to peak data)
      ALIGNMENT,                                  ///< Retention time alignment of different maps
      CALIBRATION,                                  ///< Calibration of m/z positions
      NORMALIZATION,                            ///< Normalization of intensity values
      FILTERING,                                  ///< Data filtering or extraction
      QUANTITATION,                             ///< Quantitation
      FEATURE_GROUPING,                     ///< %Feature grouping
      IDENTIFICATION_MAPPING,           ///< %Identification mapping
      FORMAT_CONVERSION,              ///< General file format conversion (if no other term applies)
      CONVERSION_MZDATA,                  ///< Conversion to mzData format
      CONVERSION_MZML,                        ///< Conversion to mzML format
      CONVERSION_MZXML,                       ///< Conversion to mzXML format
      CONVERSION_DTA,                 ///< Conversion to DTA format
      SIZE_OF_PROCESSINGACTION
    };
    /// Names of inlet types
    static const std::string NamesOfProcessingAction[SIZE_OF_PROCESSINGACTION];

    /// Constructor
    DataProcessing();
    /// Copy constructor
    DataProcessing(const DataProcessing & source);
    /// Destructor
    ~DataProcessing();

    /// Assignment operator
    DataProcessing & operator=(const DataProcessing & source);

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

    /// returns a const reference to the software used for processing
    const Software & getSoftware() const;
    /// returns a mutable reference to the software used for processing
    Software & getSoftware();
    /// sets the software used for processing
    void setSoftware(const Software & software);

    /// returns a const reference to the applied processing actions
    const std::set<ProcessingAction> & getProcessingActions() const;
    /// returns a mutable reference to the description of the applied processing
    std::set<ProcessingAction> & getProcessingActions();
    /// sets the description of the applied processing
    void setProcessingActions(const std::set<ProcessingAction> & actions);

    /// returns the time of completion of the processing
    const DateTime & getCompletionTime() const;
    /// sets the time of completion taking a DateTime object
    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

#endif // OPENMS_METADATA_DATAPROCESSING_H
