ItraqConstants.h

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// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
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#pragma once

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/Map.h>
#include <OpenMS/KERNEL/Peak2D.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/DATASTRUCTURES/StringListUtils.h>
#include <OpenMS/DATASTRUCTURES/Matrix.h>

namespace OpenMS
{

  class OPENMS_DLLAPI ItraqConstants
  {

public:

    static const Int CHANNEL_COUNT[];
    enum ITRAQ_TYPES {FOURPLEX = 0, EIGHTPLEX, TMT_SIXPLEX, SIZE_OF_ITRAQ_TYPES};

    struct ChannelInfo
    {
      String description;       // description given by experimentalist (e.g. lung tissue)
      Int name;       // 114-117 or 113 to 121
      Int id;           // 0-4 or 0-8
      Peak2D::CoordinateType center;       // expected centroid of peak in MZ
      bool active;       // channel actually added to the experiment?
    };

    typedef Map<Int, ChannelInfo> ChannelMapType;

    typedef std::vector<Matrix<double> > IsotopeMatrices;

    static const Int CHANNELS_FOURPLEX[4][1];
    static const Int CHANNELS_EIGHTPLEX[8][1];
    static const Int CHANNELS_TMT_SIXPLEX[6][1];
    // channel names for 6plex TMT with ETD fragmentation( 114, 115, 116, 117, 118, 119)
    //static const Int CHANNELS_SIXPLEX_ETD[6][1];

    static const double ISOTOPECORRECTIONS_FOURPLEX[4][4];
    static const double ISOTOPECORRECTIONS_EIGHTPLEX[8][4];
    static const double ISOTOPECORRECTIONS_TMT_SIXPLEX[6][4];
    // default isotope correction matrix (6 plex TMT)
    //static const double ISOTOPECORRECTIONS_SIXPLEX_ETD[6][4];

    static StringList getIsotopeMatrixAsStringList(const int itraq_type, const IsotopeMatrices & isotope_corrections);

    static void updateIsotopeMatrixFromStringList(const int itraq_type, const StringList & channels, IsotopeMatrices & isotope_corrections);

    static void initChannelMap(const int itraq_type, ChannelMapType & map);

    static void updateChannelMap(const StringList & active_channels, ChannelMapType & map);

    static Matrix<double> translateIsotopeMatrix(const int & itraq_type, const IsotopeMatrices & isotope_corrections);

  };   // !class

} // !namespace