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IsobaricQuantitationMethod.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Stephan Aiche $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
38 #include <OpenMS/DATASTRUCTURES/String.h>
39
40 #include <OpenMS/KERNEL/Peak2D.h>
41
42 #include <vector>
43
44 namespace OpenMS
45 {
46
47 // Forward declarations
48 template <typename Value>
49 class Matrix;
50
54 class OPENMS_DLLAPI IsobaricQuantitationMethod :
55 public DefaultParamHandler
56 {
57 public:
58
62 struct IsobaricChannelInformation
63 {
65 String name;
67 Int id;
69 String description;
71 Peak2D::CoordinateType center;
72
74 IsobaricChannelInformation(const String local_name,
75 const Int local_id,
76 const String& local_description,
77 const Peak2D::CoordinateType& local_center,
78 const Int minus_2,
79 const Int minus_1,
80 const Int plus_1,
81 const Int plus_2) :
82 name(local_name),
83 id(local_id),
84 description(local_description),
85 center(local_center),
86 channel_id_minus_2(minus_2),
87 channel_id_minus_1(minus_1),
88 channel_id_plus_1(plus_1),
89 channel_id_plus_2(plus_2)
90 {
91 }
92
94 Int channel_id_minus_2;
96 Int channel_id_minus_1;
98 Int channel_id_plus_1;
99 // Id of the +2 isotopic channel (== -1 -> no channel)
100 Int channel_id_plus_2;
101 };
102
104 IsobaricQuantitationMethod();
105
107 ~IsobaricQuantitationMethod() override;
108
109 typedef std::vector<IsobaricChannelInformation> IsobaricChannelList;
110
116 virtual const String& getMethodName() const = 0;
117
123 virtual const IsobaricChannelList& getChannelInformation() const = 0;
124
130 virtual Size getNumberOfChannels() const = 0;
131
135 virtual Matrix<double> getIsotopeCorrectionMatrix() const = 0;
136
140 virtual Size getReferenceChannel() const = 0;
141
142 protected:
149 Matrix<double> stringListToIsotopCorrectionMatrix_(const StringList& stringlist) const;
150 };
151 } // namespace
152
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::IsobaricQuantitationMethod::IsobaricChannelInformation::name
String name
The name of the channel.
Definition: IsobaricQuantitationMethod.h:65
OpenMS::IsobaricQuantitationMethod::IsobaricChannelInformation::center
Peak2D::CoordinateType center
The expected centroid position of the channel peak in m/z.
Definition: IsobaricQuantitationMethod.h:71
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::IsobaricQuantitationMethod::IsobaricChannelInformation
Summary of an isobaric quantitation channel.
Definition: IsobaricQuantitationMethod.h:62
OpenMS::IsobaricQuantitationMethod
Abstract base class describing an isobaric quantitation method in terms of the used channels and an i...
Definition: IsobaricQuantitationMethod.h:54
OpenMS::IsobaricQuantitationMethod::IsobaricChannelInformation::channel_id_plus_2
Int channel_id_plus_2
Definition: IsobaricQuantitationMethod.h:100
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&#39;tor.
Definition: IsobaricQuantitationMethod.h:74
OpenMS::IsobaricQuantitationMethod::IsobaricChannelInformation::id
Int id
The id of the channel.
Definition: IsobaricQuantitationMethod.h:67
String.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Peak2D.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:96
DefaultParamHandler.h
OpenMS::IsobaricQuantitationMethod::IsobaricChannelList
std::vector< IsobaricChannelInformation > IsobaricChannelList
Definition: IsobaricQuantitationMethod.h:109
OpenMS::IsobaricQuantitationMethod::IsobaricChannelInformation::description
String description
Optional description of the channel.
Definition: IsobaricQuantitationMethod.h:69
double
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
int
OpenMS::IsobaricQuantitationMethod::IsobaricChannelInformation::channel_id_minus_2
Int channel_id_minus_2
Id of the -2 isotopic channel (== -1 -> no channel)
Definition: IsobaricQuantitationMethod.h:94
OpenMS::IsobaricQuantitationMethod::IsobaricChannelInformation::channel_id_plus_1
Int channel_id_plus_1
Id of the +1 isotopic channel (== -1 -> no channel)
Definition: IsobaricQuantitationMethod.h:98
OpenMS::Matrix
A two-dimensional matrix. Similar to std::vector, but uses a binary operator(,) for element access...
Definition: IsobaricQuantitationMethod.h:49
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127