| OpenMS 2.5.0

ItraqConstants.h
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31 // $Maintainer: Chris Bielow $
32 // $Authors: Chris Bielow $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CONCEPT/Types.h>
38 #include <OpenMS/DATASTRUCTURES/Map.h>
39 #include <OpenMS/KERNEL/Peak2D.h>
40 #include <OpenMS/DATASTRUCTURES/String.h>
41 #include <OpenMS/DATASTRUCTURES/StringListUtils.h>
42 #include <OpenMS/DATASTRUCTURES/Matrix.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 {
63 String description;
64 Int name;
65 Int id;
66 Peak2D::CoordinateType center;
67 bool active;
68 };
69
71 typedef Map<Int, ChannelInfo> ChannelMapType;
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
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::ItraqConstants::ChannelInfo
stores information on an iTRAQ channel
Definition: ItraqConstants.h:61
OpenMS::ItraqConstants::ChannelMapType
Map< Int, ChannelInfo > ChannelMapType
maps iTRAQ channel (e.g. 117) to more information
Definition: ItraqConstants.h:71
OpenMS::ItraqConstants::ChannelInfo::description
String description
description given by experimentalist (e.g. lung tissue)
Definition: ItraqConstants.h:63
Types.h
OpenMS::ItraqConstants::ChannelInfo::active
bool active
channel actually added to the experiment?
Definition: ItraqConstants.h:67
OpenMS::ItraqConstants::ChannelInfo::center
Peak2D::CoordinateType center
expected centroid of peak in MZ
Definition: ItraqConstants.h:66
StringListUtils.h
OpenMS::ItraqConstants
Some constants used throughout iTRAQ classes.
Definition: ItraqConstants.h:52
OpenMS::ItraqConstants::ChannelInfo::name
Int name
114-117 or 113 to 121
Definition: ItraqConstants.h:64
OpenMS::ItraqConstants::IsotopeMatrices
std::vector< Matrix< double > > IsotopeMatrices
(user defined?) isotope correction matrix in (-2, -1, +1, +2) row style
Definition: ItraqConstants.h:74
String.h
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
Matrix.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Peak2D.h
Map.h
double
OpenMS::ItraqConstants::ChannelInfo::id
Int id
0-4 or 0-8
Definition: ItraqConstants.h:65
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
int
OpenMS::ItraqConstants::TMT_SIXPLEX
Definition: ItraqConstants.h:58
OpenMS::Matrix< double >
OpenMS::ItraqConstants::ITRAQ_TYPES
ITRAQ_TYPES
Definition: ItraqConstants.h:58