| OpenMS 2.5.0

OfflinePrecursorIonSelection.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Alexandra Zerck $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37
38 #include <OpenMS/KERNEL/FeatureMap.h>
39 #include <OpenMS/KERNEL/MSExperiment.h>
40 #include <OpenMS/ANALYSIS/ID/IDMapper.h>
41 #include <OpenMS/FORMAT/FeatureXMLFile.h>
42 #include <OpenMS/ANALYSIS/TARGETED/PSLPFormulation.h>
43 #include <OpenMS/DATASTRUCTURES/ListUtils.h>
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:
65 typedef PSLPFormulation::IndexTriple IndexTriple;
66
67 OfflinePrecursorIonSelection();
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
98 void setLPSolver(LPWrapper::SOLVER solver)
99 {
100 solver_ = solver;
101 std::cout << " LPSolver set to " << solver_ << std::endl;
102 }
103
104 LPWrapper::SOLVER getLPSolver()
105 {
106 return solver_;
107 }
108
109 private:
110
111 typedef std::map<std::pair<double, double>, int, PairComparatorSecondElement<std::pair<double, double> > > ExclusionListType_;
112
116 void calculateXICs_(const FeatureMap& features,
117 const std::vector<std::vector<std::pair<Size, Size> > >& mass_ranges,
118 const PeakMap& experiment,
119 const std::set<Int>& charges_set,
120 std::vector<std::vector<std::pair<Size, double> > >& xics);
121
125 void checkMassRanges_(std::vector<std::vector<std::pair<Size, Size> > >& mass_ranges,
126 const PeakMap& experiment);
127
129 void updateExclusionList_(ExclusionListType_& exclusion_list) const;
130
131 LPWrapper::SOLVER solver_;
132 };
133
134 }
135
136
PSLPFormulation.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::OfflinePrecursorIonSelection::setLPSolver
void setLPSolver(LPWrapper::SOLVER solver)
Definition: OfflinePrecursorIonSelection.h:98
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::OfflinePrecursorIonSelection::solver_
LPWrapper::SOLVER solver_
Definition: OfflinePrecursorIonSelection.h:131
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenMS::OfflinePrecursorIonSelection::ExclusionListType_
std::map< std::pair< double, double >, int, PairComparatorSecondElement< std::pair< double, double > > > ExclusionListType_
Definition: OfflinePrecursorIonSelection.h:111
FeatureMap.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
OpenMS::OfflinePrecursorIonSelection::IndexTriple
PSLPFormulation::IndexTriple IndexTriple
Definition: OfflinePrecursorIonSelection.h:65
OpenMS::PairComparatorSecondElement
Class for comparison of std::pair using second ONLY e.g. for use with std::sort.
Definition: ComparatorUtils.h:339
FeatureXMLFile.h
int
OpenMS::OfflinePrecursorIonSelection::getLPSolver
LPWrapper::SOLVER getLPSolver()
Definition: OfflinePrecursorIonSelection.h:104
ListUtils.h
IDMapper.h
OpenMS::PSLPFormulation::IndexTriple
Struct that holds the indices of the precursors in the feature map and the ilp formulation.
Definition: PSLPFormulation.h:70
OpenMS::OfflinePrecursorIonSelection
Implements different algorithms for precursor ion selection.
Definition: OfflinePrecursorIonSelection.h:61
OpenMS::LPWrapper::SOLVER
SOLVER
Definition: LPWrapper.h:130