libopenms-dev 1.11.1-5 / usr / include / OpenMS / METADATA / DataProcessing.h

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
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// $Maintainer: Andreas Bertsch $
// $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>

namespace OpenMS
{
  /**
      @brief Descripton 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,                  ///< Convertion 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 construcor
    DataProcessing(const DataProcessing & source);
    /// Destructor
    ~DataProcessing();

    /// Assignement 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 completition of the processing
    const DateTime & getCompletionTime() const;
    /// sets the time of completition taking a DateTime object
    void setCompletionTime(const DateTime & completion_time);

protected:

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

#endif // OPENMS_METADATA_DATAPROCESSING_H