IsobaricQuantitationMethod.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
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// $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 <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;
 
      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)
      {
      }
 
      Int channel_id_minus_2;
      Int channel_id_minus_1;
      Int channel_id_plus_1;
      // Id of the +2 isotopic channel (== -1 -> no channel)
      Int channel_id_plus_2;
    };
 
    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> stringListToIsotopCorrectionMatrix_(const std::vector<String>& stringlist) const;
  };
} // namespace