OpenMS  3.0.0
IsobaricQuantitationMethod.h
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32 // $Authors: Stephan Aiche $
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34 
35 #pragma once
36 
40 
41 #include <OpenMS/KERNEL/Peak2D.h>
42 
43 #include <vector>
44 
45 namespace OpenMS
46 {
47 
48  // Forward declarations
49  template <typename Value>
50  class Matrix;
51 
55  class OPENMS_DLLAPI IsobaricQuantitationMethod :
56  public DefaultParamHandler
57  {
58 public:
59 
64  {
73 
76  const Int local_id,
77  const String& local_description,
78  const Peak2D::CoordinateType& local_center,
79  const Int minus_2,
80  const Int minus_1,
81  const Int plus_1,
82  const Int plus_2) :
83  name(local_name),
84  id(local_id),
85  description(local_description),
86  center(local_center),
87  channel_id_minus_2(minus_2),
88  channel_id_minus_1(minus_1),
89  channel_id_plus_1(plus_1),
90  channel_id_plus_2(plus_2)
91  {
92  }
93 
100  // Id of the +2 isotopic channel (== -1 -> no channel)
102  };
103 
106 
108  ~IsobaricQuantitationMethod() override;
109 
110  typedef std::vector<IsobaricChannelInformation> IsobaricChannelList;
111 
117  virtual const String& getMethodName() const = 0;
118 
124  virtual const IsobaricChannelList& getChannelInformation() const = 0;
125 
131  virtual Size getNumberOfChannels() const = 0;
132 
136  virtual Matrix<double> getIsotopeCorrectionMatrix() const = 0;
137 
141  virtual Size getReferenceChannel() const = 0;
142 
143 protected:
150  Matrix<double> stringListToIsotopCorrectionMatrix_(const std::vector<String>& stringlist) const;
151  };
152 } // namespace
153 
DefaultParamHandler.h
double
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::IsobaricQuantitationMethod::IsobaricChannelInformation::channel_id_plus_2
Int channel_id_plus_2
Definition: IsobaricQuantitationMethod.h:101
OpenMS::IsobaricQuantitationMethod::IsobaricChannelInformation::id
Int id
The id of the channel.
Definition: IsobaricQuantitationMethod.h:68
OpenMS::IsobaricQuantitationMethod::IsobaricChannelInformation::channel_id_minus_2
Int channel_id_minus_2
Id of the -2 isotopic channel (== -1 -> no channel)
Definition: IsobaricQuantitationMethod.h:95
ListUtils.h
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::IsobaricQuantitationMethod::IsobaricChannelInformation
Summary of an isobaric quantitation channel.
Definition: IsobaricQuantitationMethod.h:63
OpenMS::Matrix
A two-dimensional matrix. Similar to std::vector, but uses a binary operator(,) for element access.
Definition: IsobaricQuantitationMethod.h:50
Peak2D.h
OpenMS::IsobaricQuantitationMethod::IsobaricChannelList
std::vector< IsobaricChannelInformation > IsobaricChannelList
Definition: IsobaricQuantitationMethod.h:110
OpenMS::IsobaricQuantitationMethod
Abstract base class describing an isobaric quantitation method in terms of the used channels and an i...
Definition: IsobaricQuantitationMethod.h:55
OpenMS::IsobaricQuantitationMethod::IsobaricChannelInformation::name
String name
The name of the channel.
Definition: IsobaricQuantitationMethod.h:66
OpenMS::IsobaricQuantitationMethod::IsobaricChannelInformation::IsobaricChannelInformation
IsobaricChannelInformation(const String local_name, const Int local_id, const String &local_description, const Peak2D::CoordinateType &local_center, const Int minus_2, const Int minus_1, const Int plus_1, const Int plus_2)
C'tor.
Definition: IsobaricQuantitationMethod.h:75
OpenMS::IsobaricQuantitationMethod::IsobaricChannelInformation::channel_id_plus_1
Int channel_id_plus_1
Id of the +1 isotopic channel (== -1 -> no channel)
Definition: IsobaricQuantitationMethod.h:99
String.h
OpenMS::IsobaricQuantitationMethod::IsobaricChannelInformation::channel_id_minus_1
Int channel_id_minus_1
Id of the -1 isotopic channel (== -1 -> no channel)
Definition: IsobaricQuantitationMethod.h:97
OpenMS::IsobaricQuantitationMethod::IsobaricChannelInformation::description
String description
Optional description of the channel.
Definition: IsobaricQuantitationMethod.h:70
OpenMS::IsobaricQuantitationMethod::IsobaricChannelInformation::center
Peak2D::CoordinateType center
The expected centroid position of the channel peak in m/z.
Definition: IsobaricQuantitationMethod.h:72