OpenMS  2.8.0
ItraqConstants.h
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34 
35 #pragma once
36 
37 #include <OpenMS/CONCEPT/Types.h>
39 #include <OpenMS/KERNEL/Peak2D.h>
43 
44 namespace OpenMS
45 {
46 
52  class OPENMS_DLLAPI ItraqConstants
53  {
54 
55 public:
56 
57  static const Int CHANNEL_COUNT[];
58  enum ITRAQ_TYPES {FOURPLEX = 0, EIGHTPLEX, TMT_SIXPLEX, SIZE_OF_ITRAQ_TYPES};
59 
61  struct ChannelInfo
62  {
65  Int id;
67  bool active;
68  };
69 
72 
74  typedef std::vector<Matrix<double> > IsotopeMatrices;
75 
77  static const Int CHANNELS_FOURPLEX[4][1];
79  static const Int CHANNELS_EIGHTPLEX[8][1];
81  static const Int CHANNELS_TMT_SIXPLEX[6][1];
82  // channel names for 6plex TMT with ETD fragmentation( 114, 115, 116, 117, 118, 119)
83  //static const Int CHANNELS_SIXPLEX_ETD[6][1];
84 
86  static const double ISOTOPECORRECTIONS_FOURPLEX[4][4];
88  static const double ISOTOPECORRECTIONS_EIGHTPLEX[8][4];
90  static const double ISOTOPECORRECTIONS_TMT_SIXPLEX[6][4];
91  // default isotope correction matrix (6 plex TMT)
92  //static const double ISOTOPECORRECTIONS_SIXPLEX_ETD[6][4];
93 
103  static StringList getIsotopeMatrixAsStringList(const int itraq_type, const IsotopeMatrices & isotope_corrections);
104 
117  static void updateIsotopeMatrixFromStringList(const int itraq_type, const StringList & channels, IsotopeMatrices & isotope_corrections);
118 
127  static void initChannelMap(const int itraq_type, ChannelMapType & map);
128 
138  static void updateChannelMap(const StringList & active_channels, ChannelMapType & map);
139 
149  static Matrix<double> translateIsotopeMatrix(const int & itraq_type, const IsotopeMatrices & isotope_corrections);
150 
151  }; // !class
152 
153 } // !namespace
154 
Some constants used throughout iTRAQ classes.
Definition: ItraqConstants.h:53
bool active
channel actually added to the experiment?
Definition: ItraqConstants.h:67
static Matrix< double > translateIsotopeMatrix(const int &itraq_type, const IsotopeMatrices &isotope_corrections)
translate isotope correction matrix in -2,-1,+1,+2 form into 114,115,116,117 format
Map< Int, ChannelInfo > ChannelMapType
maps iTRAQ channel (e.g. 117) to more information
Definition: ItraqConstants.h:71
Int name
114-117 or 113 to 121
Definition: ItraqConstants.h:64
static void updateIsotopeMatrixFromStringList(const int itraq_type, const StringList &channels, IsotopeMatrices &isotope_corrections)
convert strings to isotope correction matrix rows
Int id
0-4 or 0-8
Definition: ItraqConstants.h:65
static void initChannelMap(const int itraq_type, ChannelMapType &map)
information about an iTRAQ channel
ITRAQ_TYPES
Definition: ItraqConstants.h:58
@ EIGHTPLEX
Definition: ItraqConstants.h:58
String description
description given by experimentalist (e.g. lung tissue)
Definition: ItraqConstants.h:63
Peak2D::CoordinateType center
expected centroid of peak in MZ
Definition: ItraqConstants.h:66
std::vector< Matrix< double > > IsotopeMatrices
(user defined?) isotope correction matrix in (-2, -1, +1, +2) row style
Definition: ItraqConstants.h:74
static StringList getIsotopeMatrixAsStringList(const int itraq_type, const IsotopeMatrices &isotope_corrections)
convert isotope correction matrix to stringlist
static void updateChannelMap(const StringList &active_channels, ChannelMapType &map)
activate & annotate channels
stores information on an iTRAQ channel
Definition: ItraqConstants.h:62
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:52
double CoordinateType
Coordinate type (of the position)
Definition: Peak2D.h:64
A more convenient string class.
Definition: String.h:60
int Int
Signed integer type.
Definition: Types.h:102
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47