IsobaricQuantitationMethod.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 2002-2022.
//
// 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.
// --------------------------------------------------------------------------
// 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 $
// --------------------------------------------------------------------------

#pragma once

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

#include <OpenMS/KERNEL/Peak2D.h>

#include <utility>
#include <vector>

namespace OpenMS
{

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

  class OPENMS_DLLAPI IsobaricQuantitationMethod :
    public DefaultParamHandler
  {
public:

    struct IsobaricChannelInformation
    {
      String name;
      Int id;
      String description;
      Peak2D::CoordinateType center;
      std::vector<Int> affected_channels;

      IsobaricChannelInformation(String local_name,
                                 const Int local_id,
                                 String  local_description,
                                 const Peak2D::CoordinateType& local_center,
                                 const std::vector<Int>& affected_channels) :
          name(std::move(local_name)),
          id(local_id),
          description(std::move(local_description)),
          center(local_center),
          affected_channels(affected_channels)
      {
      }
    };

    IsobaricQuantitationMethod();

    ~IsobaricQuantitationMethod() override;

    typedef std::vector<IsobaricChannelInformation> IsobaricChannelList;

    virtual const String& getMethodName() const = 0;

    virtual const IsobaricChannelList& getChannelInformation() const = 0;

    virtual Size getNumberOfChannels() const = 0;

    virtual Matrix<double> getIsotopeCorrectionMatrix() const = 0;

    virtual Size getReferenceChannel() const = 0;

protected:
    Matrix<double> stringListToIsotopeCorrectionMatrix_(const std::vector<String>& stringlist) const;
  };
} // namespace