// --------------------------------------------------------------------------
//                   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: Stephan Aiche $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_QUANTITATION_ISOBARICQUANTITATIONMETHOD_H
#define OPENMS_ANALYSIS_QUANTITATION_ISOBARICQUANTITATIONMETHOD_H

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/DATASTRUCTURES/String.h>

#include <OpenMS/KERNEL/Peak2D.h>

#include <vector>

namespace OpenMS
{

  // Forward declarations
  template <typename Value>
  class Matrix;

  /**
    @brief Abstract base class describing an isobaric quantitation method in terms of the used channels and an isotope correction matrix.
  */
  class OPENMS_DLLAPI IsobaricQuantitationMethod :
    public DefaultParamHandler
  {
public:

    /**
      @brief Summary of an isobaric quantitation channel.
    */
    struct IsobaricChannelInformation
    {
      /// The name of the channel.
      String name;
      /// The id of the channel.
      Int id;
      /// Optional description of the channel.
      String description;
      /// The expected centroid position of the channel peak in m/z.
      Peak2D::CoordinateType center;

      /// C'tor
      IsobaricChannelInformation(const String local_name,
                                 const Int local_id,
                                 const String& local_description,
                                 const Peak2D::CoordinateType& local_center,
                                 const Int minus_2,
                                 const Int minus_1,
                                 const Int plus_1,
                                 const Int plus_2) :
        name(local_name),
        id(local_id),
        description(local_description),
        center(local_center),
        channel_id_minus_2(minus_2),
        channel_id_minus_1(minus_1),
        channel_id_plus_1(plus_1),
        channel_id_plus_2(plus_2)
      {
      }

      /// Id of the -2 isotopic channel (== -1 -> no channel)
      Int channel_id_minus_2;
      /// Id of the -1 isotopic channel (== -1 -> no channel)
      Int channel_id_minus_1;
      /// Id of the +1 isotopic channel (== -1 -> no channel)
      Int channel_id_plus_1;
      // Id of the +2 isotopic channel (== -1 -> no channel)
      Int channel_id_plus_2;
    };

    /// @brief c'tor setting the name for the underlying param handler
    IsobaricQuantitationMethod();

    /// @brief d'tor
    virtual ~IsobaricQuantitationMethod();

    typedef std::vector<IsobaricChannelInformation> IsobaricChannelList;

    /**
      @brief Returns a unique name for the quantitation method.

      @return The unique name or identifier of the quantitation method.
    */
    virtual const String& getName() const = 0;

    /**
      @brief Returns information on the different channels used by the quantitation method.

      @return A st::vector containing the channel information for this quantitation method.
    */
    virtual const IsobaricChannelList& getChannelInformation() const = 0;

    /**
      @brief Gives the number of channels available for this quantitation method.

      @return The number of channels available for this quantitation method.
    */
    virtual Size getNumberOfChannels() const = 0;

    /**
      @brief Returns an isotope correction matrix suitable for the given quantitation method.
    */
    virtual Matrix<double> getIsotopeCorrectionMatrix() const = 0;

    /**
      @brief Returns the index of the reference channel in the IsobaricChannelList (see IsobaricQuantitationMethod::getChannelInformation()).
    */
    virtual Size getReferenceChannel() const = 0;

protected:
    /**
      @brief Helper function to convert a string list containing an isotope correction matrix into a Matrix<double>.

      @param stringlist The StringList to convert.
      @return An isotope correction matrix as Matrix<double>.
    */
    Matrix<double> stringListToIsotopCorrectionMatrix_(const StringList& stringlist) const;
  };
} // namespace

#endif // OPENMS_ANALYSIS_QUANTITATION_ISOBARICQUANTITATIONMETHOD_H
