OpenMS  3.0.0
OfflinePrecursorIonSelection.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Alexandra Zerck $
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34 
35 #pragma once
36 
37 
44 
45 namespace OpenMS
46 {
47  class PeptideIdentification;
48  class ProteinIdentification;
49  class String;
50 
51 
61  class OPENMS_DLLAPI OfflinePrecursorIonSelection :
62  public DefaultParamHandler
63  {
64 public:
66 
68  ~OfflinePrecursorIonSelection() override;
69 
79  void makePrecursorSelectionForKnownLCMSMap(const FeatureMap& features,
80  const PeakMap& experiment,
81  PeakMap& ms2,
82  std::set<Int>& charges_set,
83  bool feature_based);
84 
92  void getMassRanges(const FeatureMap& features,
93  const PeakMap& experiment,
94  std::vector<std::vector<std::pair<Size, Size> > >& indices);
95 
96  void createProteinSequenceBasedLPInclusionList(String include, String rt_model_file, String pt_model_file, FeatureMap& precursors);
97 
99  {
100  solver_ = solver;
101  std::cout << " LPSolver set to " << solver_ << std::endl;
102  }
103 
105  {
106  return solver_;
107  }
108 
109 private:
110 
111  template <typename PairType>
113  {
114  bool operator()(const PairType & left, const PairType & right) const
115  {
116  return left.second < right.second;
117  }
118 
119  };
120 
121  typedef std::map<std::pair<double, double>, int, PairComparatorSecondElement<std::pair<double, double> > > ExclusionListType_;
122 
126  void calculateXICs_(const FeatureMap& features,
127  const std::vector<std::vector<std::pair<Size, Size> > >& mass_ranges,
128  const PeakMap& experiment,
129  const std::set<Int>& charges_set,
130  std::vector<std::vector<std::pair<Size, double> > >& xics);
131 
135  void checkMassRanges_(std::vector<std::vector<std::pair<Size, Size> > >& mass_ranges,
136  const PeakMap& experiment);
137 
139  void updateExclusionList_(ExclusionListType_& exclusion_list) const;
140 
142  };
143 
144 }
145 
146 
OpenMS::OfflinePrecursorIonSelection::IndexTriple
PSLPFormulation::IndexTriple IndexTriple
Definition: OfflinePrecursorIonSelection.h:65
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
FeatureXMLFile.h
OpenMS::OfflinePrecursorIonSelection::getLPSolver
LPWrapper::SOLVER getLPSolver()
Definition: OfflinePrecursorIonSelection.h:104
OpenMS::PSLPFormulation::IndexTriple
Struct that holds the indices of the precursors in the feature map and the ilp formulation.
Definition: PSLPFormulation.h:70
ListUtils.h
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
PSLPFormulation.h
FeatureMap.h
IDMapper.h
MSExperiment.h
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::OfflinePrecursorIonSelection
Implements different algorithms for precursor ion selection.
Definition: OfflinePrecursorIonSelection.h:61
OpenMS::OfflinePrecursorIonSelection::PairComparatorSecondElement::operator()
bool operator()(const PairType &left, const PairType &right) const
Definition: OfflinePrecursorIonSelection.h:114
OpenMS::OfflinePrecursorIonSelection::PairComparatorSecondElement
Definition: OfflinePrecursorIonSelection.h:112
OpenMS::OfflinePrecursorIonSelection::ExclusionListType_
std::map< std::pair< double, double >, int, PairComparatorSecondElement< std::pair< double, double > > > ExclusionListType_
Definition: OfflinePrecursorIonSelection.h:121
OpenMS::LPWrapper::SOLVER
SOLVER
Definition: LPWrapper.h:130
OpenMS::OfflinePrecursorIonSelection::setLPSolver
void setLPSolver(LPWrapper::SOLVER solver)
Definition: OfflinePrecursorIonSelection.h:98
OpenMS::OfflinePrecursorIonSelection::solver_
LPWrapper::SOLVER solver_
Definition: OfflinePrecursorIonSelection.h:141