IsobaricQuantitationMethod.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Stephan Aiche $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/DATASTRUCTURES/StringUtils.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h>
 
#include <OpenMS/KERNEL/Peak2D.h>
 
#include <array>
#include <memory>
#include <string_view>
#include <utility>
#include <vector>
 
namespace OpenMS
{
 
  // Forward declarations
  template <typename Value>
  class Matrix;
 
  class OPENMS_DLLAPI IsobaricQuantitationMethod :
    public DefaultParamHandler
  {
public:
 
    enum class MethodType
    {
      UNKNOWN = 0,
      TMT_6PLEX,
      TMT_10PLEX,
      TMT_11PLEX,
      TMT_16PLEX,
      TMT_18PLEX,
      TMT_32PLEX,
      TMT_35PLEX,
      ITRAQ_4PLEX,
      ITRAQ_8PLEX,
      SIZE_OF_METHODTYPE 
    };
 
    static std::string_view methodTypeName(MethodType mt);
 
    static std::string_view methodDisplayName(MethodType mt);
 
    static MethodType methodTypeFromName(std::string_view name);
 
    static std::unique_ptr<IsobaricQuantitationMethod> create(MethodType mt);
 
    struct IsobaricChannelInformation
    {
      std::string name;
      Int id;
      std::string description;
      Peak2D::CoordinateType center;
      std::vector<Int> affected_channels;
 
      IsobaricChannelInformation(std::string local_name,
                                 const Int local_id,
                                 std::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() = delete;
 
    ~IsobaricQuantitationMethod() override;
 
    typedef std::vector<IsobaricChannelInformation> IsobaricChannelList;
 
    const std::string& getMethodName() const;
 
    MethodType getMethodType() const { return iso_method_; }
 
    virtual const IsobaricChannelList& getChannelInformation() const = 0;
 
    virtual Size getNumberOfChannels() const = 0;
 
    virtual Matrix<double> getIsotopeCorrectionMatrix() const = 0;
 
    virtual Size getReferenceChannel() const = 0;
 
protected:
    explicit IsobaricQuantitationMethod(MethodType method_type);
 
    Matrix<double> stringListToIsotopeCorrectionMatrix_(const std::vector<std::string>& stringlist) const;
 
private:
    MethodType iso_method_;
  };
} // namespace