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FeatureDeconvolution.h
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34 
35 #ifndef OPENMS_ANALYSIS_DECHARGING_FEATUREDECONVOLUTION_H
36 #define OPENMS_ANALYSIS_DECHARGING_FEATUREDECONVOLUTION_H
37 
38 // OpenMS
44 
45 namespace OpenMS
46 {
47 
48  class Compomer;
49 
58  class OPENMS_DLLAPI FeatureDeconvolution :
59  public DefaultParamHandler
60  {
61 public:
62 
63  enum CHARGEMODE {QFROMFEATURE = 1, QHEURISTIC, QALL};
64 
70 
76 
79 
81  FeatureDeconvolution & operator=(const FeatureDeconvolution & source);
82 
84  virtual ~FeatureDeconvolution();
86 
97  void compute(const FeatureMapType & fm_in, FeatureMapType & fm_out, ConsensusMap & cons_map, ConsensusMap & cons_map_p);
98 
99 protected:
100 
101  void updateMembers_();
102 
108  struct CmpInfo_;
109 
110  /*
111  @brief test for obviously wrong parameter settings and warn
112 
113  Currently supports the following scenarios:
114  * 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)
115  When more than 5% of the cf's look like this, we report it.
116 
117  */
118  void checkSolution_(const ConsensusMap & cons_map) const;
119 
124  void inferMoreEdges_(PairsType & edges, Map<Size, std::set<CmpInfo_> > & feature_adducts);
125 
127  void printEdgesOfConnectedFeatures_(Size idx_1, Size idx_2, const PairsType & feature_relation);
128 
136  inline bool intensityFilterPassed_(const Int q1, const Int q2, const Compomer & cmp, const FeatureType & f1, const FeatureType & f2);
137 
145  bool chargeTestworthy_(const Int feature_charge, const Int putative_charge, const bool other_unchanged) const;
146 
159 
160  };
161 } // namespace OpenMS
162 
163 #endif // OPENMS_ANALYSIS_DECHARGING_FEATUREDECONVOLUTION_H
Int verbose_level_
amount of debug information displayed
Definition: FeatureDeconvolution.h:158
Map< String, Size > map_label_inverse_
labeling table inverse
Definition: FeatureDeconvolution.h:152
FeatureMap FeatureMapType
Definition: FeatureDeconvolution.h:65
CHARGEMODE
Definition: FeatureDeconvolution.h:63
Holds information on an edge connecting two features from a (putative) charge ladder.
Definition: Compomer.h:58
A container for consensus elements.
Definition: ConsensusMap.h:60
DPosition< 2 > ClusterPointType
Definition: FeatureDeconvolution.h:67
CHARGEMODE q_try_
status of charge discovery
Definition: FeatureDeconvolution.h:156
Map< Size, String > map_label_
labeling table
Definition: FeatureDeconvolution.h:150
An LC-MS feature.
Definition: Feature.h:66
Definition: FeatureDeconvolution.h:63
An algorithm to decharge features (i.e. as found by FeatureFinder).
Definition: FeatureDeconvolution.h:58
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
ILPDCWrapper::PairsType PairsType
Definition: FeatureDeconvolution.h:69
MassExplainer::AdductsType potential_adducts_
List of adducts used to explain mass differences.
Definition: FeatureDeconvolution.h:148
FeatureMapType::FeatureType::CoordinateType CoordinateType
Definition: FeatureDeconvolution.h:68
Feature FeatureType
Definition: FeatureDeconvolution.h:66
Feature::CoordinateType CoordinateType
Definition: AdditiveSeries.C:52
Adduct::AdductsType AdductsType
Definition: MassExplainer.h:56
bool enable_intensity_filter_
status of intensity filter for edges
Definition: FeatureDeconvolution.h:154
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:90
std::vector< ChargePair > PairsType
Definition: ILPDCWrapper.h:51
int Int
Signed integer type.
Definition: Types.h:100
Map class based on the STL map (containing serveral convenience functions)
Definition: Map.h:50

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:13 using doxygen 1.8.5