ChromatogramSettings.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
//
// 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,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------

#ifndef OPENMS_METADATA_CHROMATOGRAMSETTINGS_H
#define OPENMS_METADATA_CHROMATOGRAMSETTINGS_H

#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/METADATA/InstrumentSettings.h>
#include <OpenMS/METADATA/AcquisitionInfo.h>
#include <OpenMS/METADATA/SourceFile.h>
#include <OpenMS/METADATA/Precursor.h>
#include <OpenMS/METADATA/Product.h>
#include <OpenMS/METADATA/DataProcessing.h>

#include <map>
#include <vector>

namespace OpenMS
{
  class OPENMS_DLLAPI ChromatogramSettings :
    public MetaInfoInterface
  {

public:

    enum ChromatogramType
    {
      MASS_CHROMATOGRAM = 0,
      TOTAL_ION_CURRENT_CHROMATOGRAM,
      SELECTED_ION_CURRENT_CHROMATOGRAM,
      BASEPEAK_CHROMATOGRAM,
      SELECTED_ION_MONITORING_CHROMATOGRAM,
      SELECTED_REACTION_MONITORING_CHROMATOGRAM,
      ELECTROMAGNETIC_RADIATION_CHROMATOGRAM,
      ABSORPTION_CHROMATOGRAM,
      EMISSION_CHROMATOGRAM,
      SIZE_OF_CHROMATOGRAM_TYPE // last entry!
    };

    static const char * const ChromatogramNames[SIZE_OF_CHROMATOGRAM_TYPE+1]; // avoid string[], since it gets copied onto heap on initialization

    ChromatogramSettings();
    ChromatogramSettings(const ChromatogramSettings & source);
    virtual ~ChromatogramSettings();

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

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


    const String & getNativeID() const;
    void setNativeID(const String & native_id);

    const String & getComment() const;
    void setComment(const String & comment);

    const InstrumentSettings & getInstrumentSettings() const;
    InstrumentSettings & getInstrumentSettings();
    void setInstrumentSettings(const InstrumentSettings & instrument_settings);

    const AcquisitionInfo & getAcquisitionInfo() const;
    AcquisitionInfo & getAcquisitionInfo();
    void setAcquisitionInfo(const AcquisitionInfo & acquisition_info);

    const SourceFile & getSourceFile() const;
    SourceFile & getSourceFile();
    void setSourceFile(const SourceFile & source_file);

    const Precursor & getPrecursor() const;
    Precursor & getPrecursor();
    void setPrecursor(const Precursor & precursor);

    const Product & getProduct() const;
    Product & getProduct();
    void setProduct(const Product & product);

    ChromatogramType getChromatogramType() const;

    void setChromatogramType(ChromatogramType type);

    void setDataProcessing(const std::vector< DataProcessingPtr > & data_processing);

    std::vector< DataProcessingPtr > & getDataProcessing();

    const std::vector< boost::shared_ptr<const DataProcessing > > getDataProcessing() const;

protected:

    String native_id_;
    String comment_;
    InstrumentSettings instrument_settings_;
    SourceFile source_file_;
    AcquisitionInfo acquisition_info_;
    Precursor precursor_;
    Product product_;
    std::vector< DataProcessingPtr > data_processing_;
    ChromatogramType type_;
  };

  OPENMS_DLLAPI std::ostream & operator<<(std::ostream & os, const ChromatogramSettings & spec);

} // namespace OpenMS

#endif // OPENMS_METADATA_CHROMATOGRAMSETTINGS_H