OpenMS
IsobaricQuantitationMethod.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: Timo Sachsenberg $
6 // $Authors: Stephan Aiche $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
14 
15 #include <OpenMS/KERNEL/Peak2D.h>
16 
17 #include <utility>
18 #include <vector>
19 
20 namespace OpenMS
21 {
22 
23  // Forward declarations
24  template <typename Value>
25  class Matrix;
26 
30  class OPENMS_DLLAPI IsobaricQuantitationMethod :
31  public DefaultParamHandler
32  {
33 public:
34 
39  {
49  std::vector<Int> affected_channels;
50 
53  const Int local_id,
54  String local_description,
55  const Peak2D::CoordinateType& local_center,
56  const std::vector<Int>& affected_channels) :
57  name(std::move(local_name)),
58  id(local_id),
59  description(std::move(local_description)),
60  center(local_center),
61  affected_channels(affected_channels)
62  {
63  }
64  };
65 
68 
71 
72  typedef std::vector<IsobaricChannelInformation> IsobaricChannelList;
73 
79  virtual const String& getMethodName() const = 0;
80 
86  virtual const IsobaricChannelList& getChannelInformation() const = 0;
87 
93  virtual Size getNumberOfChannels() const = 0;
94 
99 
103  virtual Size getReferenceChannel() const = 0;
104 
105 protected:
112  Matrix<double> stringListToIsotopeCorrectionMatrix_(const std::vector<String>& stringlist) const;
113  };
114 } // namespace
115 
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
Abstract base class describing an isobaric quantitation method in terms of the used channels and an i...
Definition: IsobaricQuantitationMethod.h:32
Matrix< double > stringListToIsotopeCorrectionMatrix_(const std::vector< String > &stringlist) const
Helper function to convert a string list containing an isotope correction matrix into a Matrix<double...
virtual Size getNumberOfChannels() const =0
Gives the number of channels available for this quantitation method.
virtual const IsobaricChannelList & getChannelInformation() const =0
Returns information on the different channels used by the quantitation method.
~IsobaricQuantitationMethod() override
d'tor
IsobaricQuantitationMethod()
c'tor setting the name for the underlying param handler
virtual const String & getMethodName() const =0
Returns a unique name for the quantitation method.
virtual Matrix< double > getIsotopeCorrectionMatrix() const =0
Returns an isotope correction matrix suitable for the given quantitation method.
virtual Size getReferenceChannel() const =0
Returns the index of the reference channel in the IsobaricChannelList (see IsobaricQuantitationMethod...
std::vector< IsobaricChannelInformation > IsobaricChannelList
Definition: IsobaricQuantitationMethod.h:72
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
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:97
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
Summary of an isobaric quantitation channel.
Definition: IsobaricQuantitationMethod.h:39
Int id
The id of the channel.
Definition: IsobaricQuantitationMethod.h:43
String description
Optional description of the channel.
Definition: IsobaricQuantitationMethod.h:45
IsobaricChannelInformation(String local_name, const Int local_id, String local_description, const Peak2D::CoordinateType &local_center, const std::vector< Int > &affected_channels)
C'tor.
Definition: IsobaricQuantitationMethod.h:52
String name
The name of the channel.
Definition: IsobaricQuantitationMethod.h:41
Peak2D::CoordinateType center
The expected centroid position of the channel peak in m/z.
Definition: IsobaricQuantitationMethod.h:47
std::vector< Int > affected_channels
Ids of the affected channels. Must contain 4 or 8 entries, depending on the number of columns in the ...
Definition: IsobaricQuantitationMethod.h:49