OpenMS  3.0.0
ItraqConstants.h
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31 // $Maintainer: Chris Bielow $
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34 
35 #pragma once
36 
37 #include <OpenMS/CONCEPT/Types.h>
38 #include <OpenMS/KERNEL/Peak2D.h>
42 
43 #include <map>
44 
45 namespace OpenMS
46 {
47 
53  class OPENMS_DLLAPI ItraqConstants
54  {
55 
56 public:
57 
58  static const Int CHANNEL_COUNT[];
59  enum ITRAQ_TYPES {FOURPLEX = 0, EIGHTPLEX, TMT_SIXPLEX, SIZE_OF_ITRAQ_TYPES};
60 
62  struct ChannelInfo
63  {
66  Int id;
68  bool active;
69  };
70 
72  typedef std::map<Int, ChannelInfo> ChannelMapType;
73 
75  typedef std::vector<Matrix<double> > IsotopeMatrices;
76 
78  static const Int CHANNELS_FOURPLEX[4][1];
80  static const Int CHANNELS_EIGHTPLEX[8][1];
82  static const Int CHANNELS_TMT_SIXPLEX[6][1];
83  // channel names for 6plex TMT with ETD fragmentation( 114, 115, 116, 117, 118, 119)
84  //static const Int CHANNELS_SIXPLEX_ETD[6][1];
85 
87  static const double ISOTOPECORRECTIONS_FOURPLEX[4][4];
89  static const double ISOTOPECORRECTIONS_EIGHTPLEX[8][4];
91  static const double ISOTOPECORRECTIONS_TMT_SIXPLEX[6][4];
92  // default isotope correction matrix (6 plex TMT)
93  //static const double ISOTOPECORRECTIONS_SIXPLEX_ETD[6][4];
94 
104  static StringList getIsotopeMatrixAsStringList(const int itraq_type, const IsotopeMatrices & isotope_corrections);
105 
118  static void updateIsotopeMatrixFromStringList(const int itraq_type, const StringList & channels, IsotopeMatrices & isotope_corrections);
119 
128  static void initChannelMap(const int itraq_type, ChannelMapType & map);
129 
139  static void updateChannelMap(const StringList & active_channels, ChannelMapType & map);
140 
150  static Matrix<double> translateIsotopeMatrix(const int & itraq_type, const IsotopeMatrices & isotope_corrections);
151 
152  }; // !class
153 
154 } // !namespace
155 
double
Types.h
OpenMS::ItraqConstants::ChannelMapType
std::map< Int, ChannelInfo > ChannelMapType
maps iTRAQ channel (e.g. 117) to more information
Definition: ItraqConstants.h:72
OpenMS::ItraqConstants::ChannelInfo::active
bool active
channel actually added to the experiment?
Definition: ItraqConstants.h:68
OpenMS::String
A more convenient string class.
Definition: String.h:58
Matrix.h
OpenMS::ItraqConstants::TMT_SIXPLEX
Definition: ItraqConstants.h:59
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ItraqConstants::ChannelInfo
stores information on an iTRAQ channel
Definition: ItraqConstants.h:62
OpenMS::ItraqConstants::IsotopeMatrices
std::vector< Matrix< double > > IsotopeMatrices
(user defined?) isotope correction matrix in (-2, -1, +1, +2) row style
Definition: ItraqConstants.h:75
OpenMS::Matrix< double >
OpenMS::ItraqConstants
Some constants used throughout iTRAQ classes.
Definition: ItraqConstants.h:53
Peak2D.h
OpenMS::ItraqConstants::ChannelInfo::name
Int name
114-117 or 113 to 121
Definition: ItraqConstants.h:65
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
String.h
OpenMS::ItraqConstants::ChannelInfo::id
Int id
0-4 or 0-8
Definition: ItraqConstants.h:66
OpenMS::ItraqConstants::ITRAQ_TYPES
ITRAQ_TYPES
Definition: ItraqConstants.h:59
OpenMS::ItraqConstants::ChannelInfo::center
Peak2D::CoordinateType center
expected centroid of peak in MZ
Definition: ItraqConstants.h:67
OpenMS::ItraqConstants::ChannelInfo::description
String description
description given by experimentalist (e.g. lung tissue)
Definition: ItraqConstants.h:64
StringListUtils.h