OpenMS
ItraqConstants.h
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1 // Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Chris Bielow $
6 // $Authors: Chris Bielow $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
11 #include <OpenMS/CONCEPT/Types.h>
12 #include <OpenMS/KERNEL/Peak2D.h>
16 
17 #include <map>
18 
19 namespace OpenMS
20 {
21 
27  class OPENMS_DLLAPI ItraqConstants
28  {
29 
30 public:
31 
32  static const Int CHANNEL_COUNT[];
33  enum ITRAQ_TYPES {FOURPLEX = 0, EIGHTPLEX, TMT_SIXPLEX, SIZE_OF_ITRAQ_TYPES};
34 
36  struct ChannelInfo
37  {
40  Int id;
42  bool active;
43  };
44 
46  typedef std::map<Int, ChannelInfo> ChannelMapType;
47 
49  typedef std::vector<Matrix<double>> IsotopeMatrices;
50 
52  static const Int CHANNELS_FOURPLEX[4][1];
54  static const Int CHANNELS_EIGHTPLEX[8][1];
56  static const Int CHANNELS_TMT_SIXPLEX[6][1];
57  // channel names for 6plex TMT with ETD fragmentation( 114, 115, 116, 117, 118, 119)
58  //static const Int CHANNELS_SIXPLEX_ETD[6][1];
59 
61  static const double ISOTOPECORRECTIONS_FOURPLEX[4][4];
63  static const double ISOTOPECORRECTIONS_EIGHTPLEX[8][4];
65  static const double ISOTOPECORRECTIONS_TMT_SIXPLEX[6][4];
66  // default isotope correction matrix (6 plex TMT)
67  //static const double ISOTOPECORRECTIONS_SIXPLEX_ETD[6][4];
68 
78  static StringList getIsotopeMatrixAsStringList(const int itraq_type, const IsotopeMatrices & isotope_corrections);
79 
92  static void updateIsotopeMatrixFromStringList(const int itraq_type, const StringList & channels, IsotopeMatrices & isotope_corrections);
93 
102  static void initChannelMap(const int itraq_type, ChannelMapType & map);
103 
113  static void updateChannelMap(const StringList & active_channels, ChannelMapType & map);
114 
124  static Matrix<double> translateIsotopeMatrix(const int & itraq_type, const IsotopeMatrices & isotope_corrections);
125 
126  }; // !class
127 
128 } // !namespace
129 
Some constants used throughout iTRAQ classes.
Definition: ItraqConstants.h:28
bool active
channel actually added to the experiment?
Definition: ItraqConstants.h:42
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
Int name
114-117 or 113 to 121
Definition: ItraqConstants.h:39
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:40
static void initChannelMap(const int itraq_type, ChannelMapType &map)
information about an iTRAQ channel
ITRAQ_TYPES
Definition: ItraqConstants.h:33
@ EIGHTPLEX
Definition: ItraqConstants.h:33
String description
description given by experimentalist (e.g. lung tissue)
Definition: ItraqConstants.h:38
Peak2D::CoordinateType center
expected centroid of peak in MZ
Definition: ItraqConstants.h:41
std::vector< Matrix< double > > IsotopeMatrices
(user defined?) isotope correction matrix in (-2, -1, +1, +2) row style
Definition: ItraqConstants.h:49
std::map< Int, ChannelInfo > ChannelMapType
maps iTRAQ channel (e.g. 117) to more information
Definition: ItraqConstants.h:46
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:37
double CoordinateType
Coordinate type (of the position)
Definition: Peak2D.h:38
A more convenient string class.
Definition: String.h:34
int Int
Signed integer type.
Definition: Types.h:72
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:44
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19