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MetaboliteFeatureDeconvolution.h
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Fabian Aicheler $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 // OpenMS
38 #include <OpenMS/KERNEL/FeatureMap.h>
39 #include <OpenMS/KERNEL/ConsensusMap.h>
40 #include <OpenMS/ANALYSIS/DECHARGING/ILPDCWrapper.h>
41 #include <OpenMS/DATASTRUCTURES/DPosition.h>
42 #include <OpenMS/DATASTRUCTURES/MassExplainer.h>
43
44 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
45
46 namespace OpenMS
47 {
48
49 class Compomer;
50
59 class OPENMS_DLLAPI MetaboliteFeatureDeconvolution :
60 public DefaultParamHandler
61 {
62 public:
63
64 enum CHARGEMODE {QFROMFEATURE = 1, QHEURISTIC, QALL};
65
66 typedef FeatureMap FeatureMapType;
67 typedef Feature FeatureType;
68 typedef DPosition<2> ClusterPointType;
69 typedef FeatureMapType::FeatureType::CoordinateType CoordinateType;
70 typedef ILPDCWrapper::PairsType PairsType;
71
75 MetaboliteFeatureDeconvolution();
77
79 MetaboliteFeatureDeconvolution(const MetaboliteFeatureDeconvolution& source);
80
82 MetaboliteFeatureDeconvolution& operator=(const MetaboliteFeatureDeconvolution& source);
83
85 ~MetaboliteFeatureDeconvolution() override;
87
98 void compute(const FeatureMapType& fm_in, FeatureMapType& fm_out, ConsensusMap& cons_map, ConsensusMap& cons_map_p);
99
100
101 protected:
102
103
104 void updateMembers_() override;
105
111 struct CmpInfo_;
112
113 /*
114 @brief test for obviously wrong parameter settings and warn
115
116 Currently supports the following scenarios:
117 * If the lower charge bound is too high, consensus features with gapped, even charges will occur (e.g. 30,32,34), instead of the true (15,16,17)
118 When more than 5% of the cf's look like this, we report it.
119
120 */
121 void checkSolution_(const ConsensusMap& cons_map) const;
122
127 void inferMoreEdges_(PairsType& edges, Map<Size, std::set<CmpInfo_> >& feature_adducts);
128
129 void candidateEdges_(FeatureMapType& fm_out, const Adduct& default_adduct, PairsType& feature_relation, Map<Size, std::set<CmpInfo_> >& feature_adducts);
130
131 void annotate_feature_(FeatureMapType& fm_out, Adduct& default_adduct, Compomer& c, const Size f_idx, const UInt side, const Int new_q, const Int old_q);
132
134 void printEdgesOfConnectedFeatures_(Size idx_1, Size idx_2, const PairsType& feature_relation);
135
142 inline bool intensityFilterPassed_(const Int q1, const Int q2, const Compomer& cmp, const FeatureType& f1, const FeatureType& f2);
143
150 bool chargeTestworthy_(const Int feature_charge, const Int putative_charge, const bool other_unchanged) const;
151
153 MassExplainer::AdductsType potential_adducts_;
155 Map<Size, String> map_label_;
157 Map<String, Size> map_label_inverse_;
159 bool enable_intensity_filter_;
161 bool negative_mode_;
163 CHARGEMODE q_try_;
165 Int verbose_level_;
166
167 };
168 } // namespace OpenMS
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::MassExplainer::AdductsType
Adduct::AdductsType AdductsType
Definition: MassExplainer.h:60
OpenMS::MetaboliteFeatureDeconvolution::map_label_
Map< Size, String > map_label_
labeling table
Definition: MetaboliteFeatureDeconvolution.h:155
OpenMS::ILPDCWrapper::PairsType
std::vector< ChargePair > PairsType
Definition: ILPDCWrapper.h:55
OpenMS::MetaboliteFeatureDeconvolution::map_label_inverse_
Map< String, Size > map_label_inverse_
labeling table inverse
Definition: MetaboliteFeatureDeconvolution.h:157
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::MetaboliteFeatureDeconvolution::PairsType
ILPDCWrapper::PairsType PairsType
Definition: MetaboliteFeatureDeconvolution.h:70
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenMS::MetaboliteFeatureDeconvolution::verbose_level_
Int verbose_level_
amount of debug information displayed
Definition: MetaboliteFeatureDeconvolution.h:165
OpenMS::MetaboliteFeatureDeconvolution::potential_adducts_
MassExplainer::AdductsType potential_adducts_
List of adducts used to explain mass differences.
Definition: MetaboliteFeatureDeconvolution.h:153
OpenMS::MetaboliteFeatureDeconvolution::negative_mode_
bool negative_mode_
status of ionization mode
Definition: MetaboliteFeatureDeconvolution.h:161
OpenMS::MetaboliteFeatureDeconvolution
An algorithm to decharge small molecule features (i.e. as found by FeatureFinder).
Definition: MetaboliteFeatureDeconvolution.h:59
OpenMS::MetaboliteFeatureDeconvolution::enable_intensity_filter_
bool enable_intensity_filter_
status of intensity filter for edges
Definition: MetaboliteFeatureDeconvolution.h:159
ConsensusMap.h
OpenMS::MetaboliteFeatureDeconvolution::FeatureType
Feature FeatureType
Definition: MetaboliteFeatureDeconvolution.h:67
ILPDCWrapper.h
FeatureMap.h
OpenMS::MetaboliteFeatureDeconvolution::q_try_
CHARGEMODE q_try_
status of charge discovery
Definition: MetaboliteFeatureDeconvolution.h:163
OpenMS::Adduct
Definition: Adduct.h:44
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
DPosition.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MetaboliteFeatureDeconvolution::QHEURISTIC
Definition: MetaboliteFeatureDeconvolution.h:64
DefaultParamHandler.h
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::DPosition< 2 >
MassExplainer.h
OpenMS::Constants::c
const double c
OpenMS::Compomer
Holds information on an edge connecting two features from a (putative) charge ladder.
Definition: Compomer.h:58
int
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
OpenMS::MetaboliteFeatureDeconvolution::CHARGEMODE
CHARGEMODE
Definition: MetaboliteFeatureDeconvolution.h:64
OpenMS::MetaboliteFeatureDeconvolution::CoordinateType
FeatureMapType::FeatureType::CoordinateType CoordinateType
Definition: MetaboliteFeatureDeconvolution.h:69
OpenMS::MetaboliteFeatureDeconvolution::ClusterPointType
DPosition< 2 > ClusterPointType
Definition: MetaboliteFeatureDeconvolution.h:68
OpenMS::MetaboliteFeatureDeconvolution::FeatureMapType
FeatureMap FeatureMapType
Definition: MetaboliteFeatureDeconvolution.h:66
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127