OpenMS  3.0.0
IsotopeLabelingMDVs.h
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31 // $Maintainer: Ahmed Khalil $
32 // $Authors: Ahmed Khalil $
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34 
35 #pragma once
36 
40 #include <OpenMS/KERNEL/Feature.h>
41 
42 namespace OpenMS
43 {
48  class OPENMS_DLLAPI IsotopeLabelingMDVs :
49  public DefaultParamHandler
50  {
51  public:
55 
57  ~IsotopeLabelingMDVs() override;
59 
61  {
62  NOT_SELECTED,
63  TBDMS,
64  SIZE_OF_DERIVATIZATIONAGENT
65  };
66 
67  enum class MassIntensityType
68  {
69  NORM_MAX,
70  NORM_SUM,
71  SIZE_OF_MASSINTENSITYTYPE
72  };
73 
74  static const std::string NamesOfDerivatizationAgent[static_cast<int>(DerivatizationAgent::SIZE_OF_DERIVATIZATIONAGENT)];
75 
76  static const std::string NamesOfMassIntensityType[static_cast<int>(MassIntensityType::SIZE_OF_MASSINTENSITYTYPE)];
77 
92  void isotopicCorrection(
93  const Feature& normalized_feature, Feature& corrected_feature,
94  const Matrix<double>& correction_matrix, const DerivatizationAgent& correction_matrix_agent);
95 
110  void isotopicCorrections(
111  const FeatureMap& normalized_featureMap, FeatureMap& corrected_featureMap,
112  const Matrix<double>& correction_matrix, const DerivatizationAgent& correction_matrix_agent);
113 
125  void calculateIsotopicPurity(
126  Feature& normalized_feature,
127  const std::vector<double>& experiment_data, const std::string& isotopic_purity_name);
128 
140  void calculateIsotopicPurities(
141  FeatureMap& normalized_featureMap,
142  const std::vector<std::vector<double>>& experiment_data, const std::vector<std::string>& isotopic_purity_name);
143 
152  void calculateMDVAccuracy(
153  Feature& normalized_feature,
154  const std::string& feature_name, const std::string& fragment_isotopomer_theoretical_formula);
155 
164  void calculateMDVAccuracies(
165  FeatureMap& normalized_featureMap,
166  const std::string& feature_name,
167  const std::map<std::string, std::string>& fragment_isotopomer_theoretical_formulas);
168 
179  void calculateMDV(
180  const Feature& measured_feature, Feature& normalized_feature,
181  const MassIntensityType& mass_intensity_type, const std::string& feature_name);
182 
193  void calculateMDVs(
194  const FeatureMap& measured_featureMap, FeatureMap& normalized_featureMap,
195  const MassIntensityType& mass_intensity_type, const std::string& feature_name);
196 
197  protected:
199  void updateMembers_() override;
200  };
201 }
DefaultParamHandler.h
Feature.h
Matrix.h
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::Matrix< double >
FeatureMap.h
OpenMS::IsotopeLabelingMDVs::MassIntensityType
MassIntensityType
Definition: IsotopeLabelingMDVs.h:67
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::IsotopeLabelingMDVs
IsotopeLabelingMDVs is a class to support and analyze isotopic labeling experiments (i....
Definition: IsotopeLabelingMDVs.h:48
OpenMS::IsotopeLabelingMDVs::DerivatizationAgent
DerivatizationAgent
Definition: IsotopeLabelingMDVs.h:60