IsobaricQuantitationMethod.h

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// $Maintainer: Timo Sachsenberg $
// $Authors: Stephan Aiche $
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#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;

  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();

    virtual ~IsobaricQuantitationMethod();

    typedef std::vector<IsobaricChannelInformation> IsobaricChannelList;

    virtual const String& getName() 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 StringList& stringlist) const;
  };
} // namespace

#endif // OPENMS_ANALYSIS_QUANTITATION_ISOBARICQUANTITATIONMETHOD_H