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MetaboliteFeatureDeconvolution.h
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34 
35 #ifndef OPENMS_ANALYSIS_DECHARGING_METABOLITEFEATUREDECONVOLUTION_H
36 #define OPENMS_ANALYSIS_DECHARGING_METABOLITEFEATUREDECONVOLUTION_H
37 
38 // OpenMS
44 
46 
47 namespace OpenMS
48 {
49 
50  class Compomer;
51 
60  class OPENMS_DLLAPI MetaboliteFeatureDeconvolution :
61  public DefaultParamHandler
62  {
63 public:
64 
65  enum CHARGEMODE {QFROMFEATURE = 1, QHEURISTIC, QALL};
66 
72 
78 
81 
84 
88 
99  void compute(const FeatureMapType& fm_in, FeatureMapType& fm_out, ConsensusMap& cons_map, ConsensusMap& cons_map_p);
100 
101 
102 protected:
103 
104  void updateMembers_();
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 
130  void printEdgesOfConnectedFeatures_(Size idx_1, Size idx_2, const PairsType& feature_relation);
131 
138  inline bool intensityFilterPassed_(const Int q1, const Int q2, const Compomer& cmp, const FeatureType& f1, const FeatureType& f2);
139 
146  bool chargeTestworthy_(const Int feature_charge, const Int putative_charge, const bool other_unchanged) const;
147 
162 
163  };
164 } // namespace OpenMS
165 
166 #endif // OPENMS_ANALYSIS_DECHARGING_METABOLITEFEATUREDECONVOLUTION_H
bool negative_mode_
status of ionization mode
Definition: MetaboliteFeatureDeconvolution.h:157
ILPDCWrapper::PairsType PairsType
Definition: MetaboliteFeatureDeconvolution.h:71
A container for features.
Definition: FeatureMap.h:94
Holds information on an edge connecting two features from a (putative) charge ladder.
Definition: Compomer.h:59
A container for consensus elements.
Definition: ConsensusMap.h:72
Feature FeatureType
Definition: MetaboliteFeatureDeconvolution.h:68
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
An algorithm to decharge small molecule features (i.e. as found by FeatureFinder).
Definition: MetaboliteFeatureDeconvolution.h:60
Map< String, Size > map_label_inverse_
labeling table inverse
Definition: MetaboliteFeatureDeconvolution.h:153
Int verbose_level_
amount of debug information displayed
Definition: MetaboliteFeatureDeconvolution.h:161
Feature::CoordinateType CoordinateType
Definition: AdditiveSeries.cpp:51
FeatureMapType::FeatureType::CoordinateType CoordinateType
Definition: MetaboliteFeatureDeconvolution.h:70
Map< Size, String > map_label_
labeling table
Definition: MetaboliteFeatureDeconvolution.h:151
An LC-MS feature.
Definition: Feature.h:70
FeatureMap FeatureMapType
Definition: MetaboliteFeatureDeconvolution.h:67
CHARGEMODE
Definition: MetaboliteFeatureDeconvolution.h:65
CHARGEMODE q_try_
status of charge discovery
Definition: MetaboliteFeatureDeconvolution.h:159
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
bool enable_intensity_filter_
status of intensity filter for edges
Definition: MetaboliteFeatureDeconvolution.h:155
MassExplainer::AdductsType potential_adducts_
List of adducts used to explain mass differences.
Definition: MetaboliteFeatureDeconvolution.h:149
Adduct::AdductsType AdductsType
Definition: MassExplainer.h:59
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
std::vector< ChargePair > PairsType
Definition: ILPDCWrapper.h:54
int Int
Signed integer type.
Definition: Types.h:103
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51
Definition: MetaboliteFeatureDeconvolution.h:65
DPosition< 2 > ClusterPointType
Definition: MetaboliteFeatureDeconvolution.h:69

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:02 using doxygen 1.8.13